@article{RN160, author = {Brodel, Andreas K. and Jaramillo, Alfonso and Isalan, Mark}, title = {Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication}, journal = {Nat. Protocols}, volume = {12}, number = {9}, pages = {1830-1843}, ISSN = {1754-2189}, DOI = {10.1038/nprot.2017.084 http://www.nature.com/nprot/journal/v12/n9/abs/nprot.2017.084.html#supplementary-information}, url = {http://dx.doi.org/10.1038/nprot.2017.084}, year = {2017}, type = {Journal Article} } @incollection{Pachaly.2008, author = {Pachaly, B. and Weis, J.}, title = {The Direct Process to Methylchlorosilanes: Reflections on Chemistry and Process Technology}, pages = {478--483}, publisher = {Wiley-VCH}, isbn = {9783527620777}, editor = {Auner, Norbert and Weis, Johann}, booktitle = {Organosilicon chemistry}, year = {2008}, address = {Weinheim}, doi = {10.1002/9783527620777.ch79b} } @article{Cui.2009, abstract = {We introduce a novel design of carbon-silicon core-shell nanowires for high power and long life lithium battery electrodes. Amorphous silicon was coated onto carbon nanofibers to form a core-shell structure and the resulted core-shell nanowires showed great performance as anode material. Since carbon has a much smaller capacity compared to silicon, the carbon core experiences less structural stress or damage during lithium cycling and can function as a mechanical support and an efficient electron conducting pathway. These nanowires have a high charge storage capacity of approximately 2000 mAh/g and good cycling life. They also have a high Coulmbic efficiency of 90{\%} for the first cycle and 98-99.6{\%} for the following cycles. A full cell composed of LiCoO(2) cathode and carbon-silicon core-shell nanowire anode is also demonstrated. Significantly, using these core-shell nanowires we have obtained high mass loading and an area capacity of approximately 4 mAh/cm(2), which is comparable to commercial battery values.}, author = {Cui, Li-Feng and Yang, Yuan and Hsu, Ching-Mei and Cui, Yi}, year = {2009}, title = {Carbon-silicon core-shell nanowires as high capacity electrode for lithium ion batteries}, keywords = {Carbon/chemistry;Electric Power Supplies;Electrodes;Ions/chemistry;Lithium/chemistry;Materials Testing;Nanotechnology;Nanowires/chemistry;Particle Size;Silicon/chemistry;Surface Properties}, pages = {3370--3374}, volume = {9}, number = {9}, issn = {1530-6992}, journal = {Nano letters}, doi = {10.1021/nl901670t} } @article{badran2015development, title={Development of potent in vivo mutagenesis plasmids with broad mutational spectra}, author={Badran, Ahmed H and Liu, David R}, journal={Nature communications}, volume={6}, pages={8425}, year={2015}, publisher={Nature Publishing Group} } @book{mathmodelsib, author = {Edelstein-Keshet, L.}, title = {Mathematical Models in Biology}, publisher = {Society for Industrial and Applied Mathematics}, year = {2005}, doi = {10.1137/1.9780898719147}, address = {}, edition = {}, URL = {http://epubs.siam.org/doi/abs/10.1137/1.9780898719147}, eprint = {http://epubs.siam.org/doi/pdf/10.1137/1.9780898719147} } @article{CG01, author = {Bennett, M. R. and Pang, W. L. and Ostroff, N. A. and Baumgartner, B. L. and Nayak, S. and Tsimring, L. S. and Hasty, J.}, title = {Metabolic gene regulation in a dynamically changing environment}, journal = {Nature}, volume = {454}, number = {7208}, pages = {1119-22}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, DOI = {10.1038/nature07211}, url = {https://www.ncbi.nlm.nih.gov/pubmed/18668041}, year = {2008}, type = {Journal Article} } @article{CG02, author = {Xie, J. and Nair, A. and Hermiston, T. W.}, title = {A comparative study examining the cytotoxicity of inducible gene expression system ligands in different cell types}, journal = {Toxicol In Vitro}, volume = {22}, number = {1}, pages = {261-6}, ISSN = {0887-2333 (Print) 0887-2333 (Linking)}, DOI = {10.1016/j.tiv.2007.08.019}, url = {https://www.ncbi.nlm.nih.gov/pubmed/17928190}, year = {2008}, type = {Journal Article} } @article{CG03, author = {Zoltowski, B. D. and Motta-Mena, L. B. and Gardner, K. H.}, title = {Blue light-induced dimerization of a bacterial LOV-HTH DNA-binding protein}, journal = {Biochemistry}, volume = {52}, number = {38}, pages = {6653-61}, ISSN = {1520-4995 (Electronic) 0006-2960 (Linking)}, DOI = {10.1021/bi401040m}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23992349}, year = {2013}, type = {Journal Article} } @article{CG04, author = {Jayaraman, P. and Devarajan, K. and Chua, T. K. and Zhang, H. and Gunawan, E. and Poh, C. L.}, title = {Blue light-mediated transcriptional activation and repression of gene expression in bacteria}, journal = {Nucleic Acids Res}, volume = {44}, number = {14}, pages = {6994-7005}, ISSN = {1362-4962 (Electronic) 0305-1048 (Linking)}, DOI = {10.1093/nar/gkw548}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27353329}, year = {2016}, type = {Journal Article} } @article{CG05', author = {Takakado, A. and Nakasone, Y. and Terazima, M.}, title = {Photoinduced dimerization of a photosensory DNA-binding protein EL222 and its LOV domain}, journal = {Phys Chem Chem Phys}, volume = {19}, number = {36}, pages = {24855-24865}, ISSN = {1463-9084 (Electronic) 1463-9076 (Linking)}, DOI = {10.1039/c7cp03686h}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28868541}, year = {2017}, type = {Journal Article} } @article {CG06, author = {Jovanovic, Goran and Model, Peter}, title = {PspF and IHF bind co-operatively in the psp promoter-regulatory region of Escherichia coli}, journal = {Molecular Microbiology}, volume = {25}, number = {3}, publisher = {Blackwell Science Ltd}, issn = {1365-2958}, url = {http://dx.doi.org/10.1046/j.1365-2958.1997.4791844.x}, doi = {10.1046/j.1365-2958.1997.4791844.x}, pages = {473--481}, year = {1997}, } MK BibTex @article{alkorta1998industrial, title={Industrial applications of pectic enzymes: a review}, author={Alkorta, Itziar and Garbisu, Carlos and Llama, Mar{\'\i}a J and Serra, Juan L}, journal={Process Biochemistry}, volume={33}, number={1}, pages={21--28}, year={1998}, publisher={Elsevier} } @article{bajpai1999application, title={Application of enzymes in the pulp and paper industry}, author={Bajpai, Pratima}, journal={Biotechnology progress}, volume={15}, number={2}, pages={147--157}, year={1999}, publisher={Wiley Online Library} } @article{kirk2002industrial, title={Industrial enzyme applications}, author={Kirk, Ole and Borchert, Torben Vedel and Fuglsang, Claus Crone}, journal={Current opinion in biotechnology}, volume={13}, number={4}, pages={345--351}, year={2002}, publisher={Elsevier} } @article{packer2015methods, title={Methods for the directed evolution of proteins}, author={Packer, Michael S and Liu, David R}, journal={Nature Reviews Genetics}, volume={16}, number={7}, pages={379--394}, year={2015}, publisher={Nature Research} } @article{ahn2004high, title={High-level expression of human cytochrome P450 1A2 by co-expression with human molecular chaperone HDJ-1 (Hsp40)}, author={Ahn, Taeho and Yang, Siyoung and Yun, Chul-Ho}, journal={Protein expression and purification}, volume={36}, number={1}, pages={48--52}, year={2004}, publisher={Elsevier} } @article{perera2010caffeine, title={Caffeine and paraxanthine HPLC assay for CYP1A2 phenotype assessment using saliva and plasma}, author={Perera, Vidya and Gross, Annette S and McLachlan, Andrew J}, journal={Biomedical Chromatography}, volume={24}, number={10}, pages={1136--1144}, year={2010}, publisher={Wiley Online Library} } @article{Carlson.2014, abstract = {Phage-assisted continuous evolution (PACE) uses a modified filamentous bacteriophage life cycle to substantially accelerate laboratory evolution experiments. In this work, we expand the scope and capabilities of the PACE method with two key advances that enable the evolution of biomolecules with radically altered or highly specific new activities. First, we implemented small molecule-controlled modulation of selection stringency that enables otherwise inaccessible activities to be evolved directly from inactive starting libraries through a period of evolutionary drift. Second, we developed a general negative selection that enables continuous counterselection against undesired activities. We integrated these developments to continuously evolve mutant T7 RNA polymerase enzymes with $\sim$10,000-fold altered, rather than merely broadened, substrate specificities during a single three-day PACE experiment. The evolved enzymes exhibit specificity for their target substrate that exceeds that of wild-type RNA polymerases for their cognate substrates while maintaining wild type-like levels of activity.}, author = {Carlson, Jacob C. and Badran, Ahmed H. and Guggiana-Nilo, Drago A. and Liu, David R.}, year = {2014}, title = {Negative selection and stringency modulation in phage-assisted continuous evolution}, keywords = {Bacteriophages/genetics/metabolism;Biological Evolution;DNA-Directed RNA Polymerases/genetics/metabolism;Evolution, Molecular;Genetic Variation;Mutation;Promoter Regions, Genetic;Substrate Specificity;Viral Proteins/genetics/metabolism}, pages = {216--222}, volume = {10}, number = {3}, issn = {1552-4450}, journal = {Nature chemical biology}, doi = {10.1038/nchembio.1453} } @article{Frampton.2009, author = {Frampton, Mark B. and Zelisko, Paul Martin}, year = {2009}, title = {Organosilicon Biotechnology}, pages = {147--163}, volume = {1}, number = {3}, issn = {1876-990X}, journal = {Silicon}, doi = {10.1007/s12633-009-9021-3} } @article{Franz.2013, abstract = {The incorporation of silicon and synthesis of organosilicon small molecules provide unique opportunities for medicinal applications. The biological investigation of organosilicon small molecules is particularly interesting because of differences in their chemical properties that can contribute to enhanced potency and improved pharmacological attributes. Applications such as inhibitor design, imaging, drug release technology, and mapping inhibitor binding are discussed.}, author = {Franz, Annaliese K. and Wilson, Sean O.}, year = {2013}, title = {Organosilicon molecules with medicinal applications}, keywords = {Amino Acids/chemistry;Drug Stability;Hydrogen Bonding;Organosilicon Compounds/administration {\&} dosage/pharmacology}, pages = {388--405}, volume = {56}, number = {2}, issn = {1520-4804}, journal = {Journal of medicinal chemistry}, doi = {10.1021/jm3010114} } @article{Henkin.2008, abstract = {Riboswitches are RNA elements that undergo a shift in structure in response to binding of a regulatory molecule. These elements are encoded within the transcript they regulate, and act in cis to control expression of the coding sequence(s) within that transcript; their function is therefore distinct from that of small regulatory RNAs (sRNAs) that act in trans to regulate the activity of other RNA transcripts. Riboswitch RNAs control a broad range of genes in bacterial species, including those involved in metabolism or uptake of amino acids, cofactors, nucleotides, and metal ions. Regulation occurs as a consequence of direct binding of an effector molecule, or through sensing of a physical parameter such as temperature. Here we review the global role of riboswitch RNAs in bacterial cell metabolism.}, author = {Henkin, Tina M.}, year = {2008}, title = {Riboswitch RNAs: using RNA to sense cellular metabolism}, keywords = {Bacteria/metabolism;Gene Expression Regulation, Bacterial;RNA, Bacterial/chemistry/metabolism}, pages = {3383--3390}, volume = {22}, number = {24}, issn = {0890-9369}, journal = {Genes {\&} development}, doi = {10.1101/gad.1747308} } @article{Kan.2016, abstract = {Enzymes that catalyze carbon-silicon bond formation are unknown in nature, despite the natural abundance of both elements. Such enzymes would expand the catalytic repertoire of biology, enabling living systems to access chemical space previously only open to synthetic chemistry. We have discovered that heme proteins catalyze the formation of organosilicon compounds under physiological conditions via carbene insertion into silicon-hydrogen bonds. The reaction proceeds both in vitro and in vivo, accommodating a broad range of substrates with high chemo- and enantioselectivity. Using directed evolution, we enhanced the catalytic function of cytochrome c from Rhodothermus marinus to achieve more than 15-fold higher turnover than state-of-the-art synthetic catalysts. This carbon-silicon bond-forming biocatalyst offers an environmentally friendly and highly efficient route to producing enantiopure organosilicon molecules.}, author = {Kan, S. B. Jennifer and Lewis, Russell D. and Chen, Kai and Arnold, Frances H.}, year = {2016}, title = {Directed evolution of cytochrome c for carbon-silicon bond formation: Bringing silicon to life}, pages = {1048--1051}, volume = {354}, number = {6315}, issn = {0036-8075}, journal = {Science (New York, N.Y.)}, doi = {10.1126/science.aah6219} } @book{Schwarz.2016, abstract = {The Future of Boron in Medicinal Chemistry: Therapeutic and Diagnostic Applications -- Drug Design Based on the Carbon/Silicon Switch Strategy -- Silicon Mimics of Unstable Carbon -- Selenium-Functionalized Molecules (SeFMs) as Potential Drugs and Nutritional Supplements -- Selenium-Based Drug Design Medicinal chemistry is both science and art. The science of medicinal chemistry offers mankind one of its best hopes for improving the quality of life. The art of medicinal chemistry continues to challenge its practitioners with the need for both intuition and experience to discover new drugs. Hence sharing the experience of drug research is uniquely beneficial to the field of medicinal chemistry. Drug research requires interdisciplinary team-work at the interface between chemistry, biology and medicine. Therefore, the topic-related series Topics in Medicinal Chemistry covers all relevant aspects of drug research, e.g. pathobiochemistry of diseases, identification and validation of (emerging) drug targets, structural biology, drugability of targets, drug design approaches, chemogenomics, synthetic chemistry including combinatorial methods, bioorganic chemistry, natural compounds, high-throughput screening, pharmacological in vitro and in vivo investigations, drug-receptor interactions on the molecular level, structure-activity relationships, drug absorption, distribution, metabolism, elimination, toxicology and pharmacogenomics. In general, special volumes are edited by well known guest editors}, year = {2016}, title = {Atypical Elements in Drug Design}, keywords = {Chemistry;Inorganic chemistry;Medicinal chemistry;Medizin / Gesundheit {\#} Sonstiges;Pharmaceutical technology;Technik / Wissen {\#} Chemie}, address = {Cham and s.l.}, edition = {1st ed. 2016}, volume = {17}, publisher = {{Springer International Publishing}}, isbn = {978-3-319-27740-0}, series = {Topics in Medicinal Chemistry}, editor = {Schwarz, Jacob}, doi = {10.1007/978-3-319-27742-4} } @incollection{Tacke.2016, author = {Tacke, Reinhold and D{\"o}rrich, Steffen}, title = {Drug Design Based on the Carbon/Silicon Switch Strategy}, pages = {29--59}, volume = {17}, publisher = {{Springer International Publishing}}, isbn = {978-3-319-27740-0}, series = {Topics in Medicinal Chemistry}, editor = {Schwarz, Jacob}, booktitle = {Atypical Elements in Drug Design}, year = {2016}, address = {Cham and s.l.}, doi = {10.1007/7355{\textunderscore }2014{\textunderscore }55} } @article{bains2003silicon, title={Silicon chemistry as a novel source of chemical diversity in drug design.}, author={Bains, W and Tacke, R}, journal={Current opinion in drug discovery \& development}, volume={6}, number={4}, pages={526--543}, year={2003} } @misc{brandt2013silicon, title={Silicon-chemistry carbon balance—an assessment of greenhouse gas emissions and reductions}, author={Brandt, Bernd and Kletzer, Evelin and Pilz, Harald and Hadzhiyska, Dariya and Seizov, Peter}, year={2013} } @article{kan2016directed, title={Directed evolution of cytochrome c for carbon--silicon bond formation: Bringing silicon to life}, author={Kan, SB Jennifer and Lewis, Russell D and Chen, Kai and Arnold, Frances H}, journal={Science}, volume={354}, number={6315}, pages={1048--1051}, year={2016}, publisher={American Association for the Advancement of Science} } @article{ziello2007hypoxia, title={Hypoxia-Inducible Factor (HIF)-1 regulatory pathway and its potential for therapeutic intervention in malignancy and ischemia}, author={Ziello, Jennifer E and Jovin, Ion S and Huang, Yan}, journal={The Yale journal of biology and medicine}, volume={80}, number={2}, pages={51}, year={2007}, publisher={Yale Journal of Biology and Medicine} } @article{yasui1988expression, title={Expression of epidermal growth factor receptor in human gastric and colonic carcinomas}, author={Yasui, Wataru and Sumiyoshi, Hiromichi and Hata, Jotaro and Kameda, Takashi and Ochiai, Atsushi and Ito, Hisao and Tahara, Eiichi}, journal={Cancer research}, volume={48}, number={1}, pages={137--141}, year={1988}, publisher={AACR} } @article{kazumori1981electron', title={Electron microscopic studies of bacteriophage $\varphi$ X174 intact and ‘eclipsing’particles, and the genome by the staining and shadowing method}, author={Kazumori, Yazaki}, journal={Journal of virological methods}, volume={2}, number={3}, pages={159--167}, year={1981}, publisher={Elsevier} } @misc{astmstandard', title={Standard test method for resistance of materials used in protective clothing to penetration by blood-borne pathogens using Phi-X 174 bacteriophage penetration as a test system 1671}, author={ASTM, F}, publisher={1997} } @article{lee2012virus', title={Virus-based piezoelectric energy generation}, author={Lee, Byung Yang and Zhang, Jinxing and Zueger, Chris and Chung, Woo-Jae and Yoo, So Young and Wang, Eddie and Meyer, Joel and Ramesh, Ramamoorthy and Lee, Seung-Wuk}, journal={Nature nanotechnology}, volume={7}, number={6}, pages={351--356}, year={2012}, publisher={Nature Research} } @article{lin1972role, title={Role of bacteriophage M13 gene 2 in viral DNA replication}, author={Lin, Norm S-C and Pratt, David}, journal={Journal of molecular biology}, volume={72}, number={1}, pages={37--49}, year={1972}, publisher={Elsevier} } @article{RN10, type = {Journal Article} } @misc{RN67', url = {https://vimeo.com/168851338}, type = {Generic} } @misc{RN49', type = {Generic} } @misc{RN64', type = {Generic} } @misc{RN63', url = {http://www.nasa.gov/mission_pages/station/research/news/biomolecule_sequencer}, type = {Generic} } @misc{RN93', type = {Generic} } @misc{RN60', url = {http://www.bio-itworld.com/2015/12/9/citizen-sequencers-taking-oxford-nanopores-minion-classroom-beyond.html}, type = {Generic} } @misc{RN51', type = {Generic} } @misc{RN74', url = {https://github.com/minoTour/minoTour}, type = {Generic} } @misc{RN103, type = {Generic} } @misc{RN115', type = {Generic} } @misc{RN62, url = {http://www.technologyreview.com/s/601669/now-theyre-sequencing-dna-in-outer-space/}, type = {Generic} } @misc{RN116', type = {Generic} } @misc{RN109', type = {Generic} } @misc{RN58', url = {http://apps.who.int/ebola/current-situation/ebola-situation-report-11-november-2015}, type = {Generic} } @article{RN30, author = {Akbari, O. S. and Bellen, H. J. and Bier, E. and Bullock, S. L. and Burt, A. and Church, G. M. and Cook, K. R. and Duchek, P. and Edwards, O. R. and Esvelt, K. M. and Gantz, V. M. and Golic, K. G. and Gratz, S. J. and Harrison, M. M. and Hayes, K. R. and James, A. A. and Kaufman, T. C. and Knoblich, J. and Malik, H. S. and Matthews, K. A. and O'Connor-Giles, K. M. and Parks, A. L. and Perrimon, N. and Port, F. and Russell, S. and Ueda, R. and Wildonger, J.}, title = {BIOSAFETY. Safeguarding gene drive experiments in the laboratory}, journal = {Science}, volume = {349}, number = {6251}, pages = {927-9}, ISSN = {1095-9203 (Electronic) 0036-8075 (Linking)}, DOI = {10.1126/science.aac7932}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26229113}, year = {2015}, type = {Journal Article} } @article{JM_1, doi = {10.1093/hmg/ddu125}, url = {https://doi.org/10.1093/hmg/ddu125}, year = {2014}, month = {mar}, publisher = {Oxford University Press ({OUP})}, volume = {23}, number = {R1}, pages = {R40--R46}, author = {F. Zhang and Y. Wen and X. Guo}, title = {{CRISPR}/Cas9 for genome editing: progress, implications and challenges}, journal = {Human Molecular Genetics} } @article{JM_2, doi = {10.1038/srep16277}, url = {https://doi.org/10.1038/srep16277}, year = {2015}, month = {nov}, publisher = {Springer Nature}, volume = {5}, number = {1}, author = {Yonggang Zhang and Chaoran Yin and Ting Zhang and Fang Li and Wensheng Yang and Rafal Kaminski and Philip Regis Fagan and Raj Putatunda and Won-Bin Young and Kamel Khalili and Wenhui Hu}, title = {{CRISPR}/{gRNA}-directed synergistic activation mediator ({SAM}) induces specific, persistent and robust reactivation of the {HIV}-1 latent reservoirs}, journal = {Scientific Reports} } @article{JM_3, doi = {10.1126/science.aaf5573}, url = {https://doi.org/10.1126/science.aaf5573}, year = {2016}, month = {jun}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {353}, number = {6299}, pages = {aaf5573}, author = {Omar O. Abudayyeh and Jonathan S. Gootenberg and Silvana Konermann and Julia Joung and Ian M. Slaymaker and David B. T. Cox and Sergey Shmakov and Kira S. Makarova and Ekaterina Semenova and Leonid Minakhin and Konstantin Severinov and Aviv Regev and Eric S. Lander and Eugene V. Koonin and Feng Zhang}, title = {C2c2 is a single-component programmable {RNA}-guided {RNA}-targeting {CRISPR} effector}, journal = {Science} } @article{RN141', author = {Qi, L. S. and Larson, M. H. and Gilbert, L. A. and Doudna, J. A. and Weissman, J. S. and Arkin, A. P. and Lim, W. A.}, title = {Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression}, journal = {Cell}, volume = {152}, number = {5}, pages = {1173-83}, ISSN = {1097-4172 (Electronic) 0092-8674 (Linking)}, DOI = {10.1016/j.cell.2013.02.022}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23452860}, year = {2013}, type = {Journal Article} } @article{Jinek2012, doi = {10.1126/science.1225829}, url = {https://doi.org/10.1126/science.1225829}, year = {2012}, month = {jun}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {337}, number = {6096}, pages = {816--821}, author = {M. Jinek and K. Chylinski and I. Fonfara and M. Hauer and J. A. Doudna and E. Charpentier}, title = {A Programmable Dual-{RNA}-Guided {DNA} Endonuclease in Adaptive Bacterial Immunity}, journal = {Science} } @article{JM_5, doi = {10.1038/nature14592}, url = {https://doi.org/10.1038/nature14592}, year = {2015}, month = {jun}, publisher = {Springer Nature}, volume = {523}, number = {7561}, pages = {481--485}, author = {Benjamin P. Kleinstiver and Michelle S. Prew and Shengdar Q. Tsai and Ved V. Topkar and Nhu T. Nguyen and Zongli Zheng and Andrew P. W. Gonzales and Zhuyun Li and Randall T. Peterson and Jing-Ruey Joanna Yeh and Martin J. Aryee and J. Keith Joung}, title = {Engineered {CRISPR}-Cas9 nucleases with altered {PAM} specificities}, journal = {Nature} } @article{Gao2017, doi = {10.1038/nbt.3900}, url = {https://doi.org/10.1038/nbt.3900}, year = {2017}, month = {jun}, publisher = {Springer Nature}, volume = {35}, number = {8}, pages = {789--792}, author = {Linyi Gao and David B T Cox and Winston X Yan and John C Manteiga and Martin W Schneider and Takashi Yamano and Hiroshi Nishimasu and Osamu Nureki and Nicola Crosetto and Feng Zhang}, title = {Engineered Cpf1 variants with altered {PAM} specificities}, journal = {Nature Biotechnology} } @article{Mali2013x, doi = {10.1038/nbt.2675}, url = {https://doi.org/10.1038/nbt.2675}, year = {2013}, month = {aug}, publisher = {Springer Nature}, volume = {31}, number = {9}, pages = {833--838}, author = {Prashant Mali and John Aach and P Benjamin Stranges and Kevin M Esvelt and Mark Moosburner and Sriram Kosuri and Luhan Yang and George M Church}, title = {{CAS}9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering}, journal = {Nature Biotechnology} } @book{RN47', author = {Alberts, Bruce}, title = {Molecular biology of the cell}, publisher = {Garland Science, Taylor and Francis Group}, address = {New York, NY}, edition = {Sixth edition.}, pages = {1 volume (various pagings)}, ISBN = {9780815344322 (hardcover) 0815344325 (hardcover) 9780815344643 (paperback) 0815344643 (paperback) 9780815345244 (looseleaf) 0815345240 (looseleaf)}, year = {2015}, type = {Book} } @article{RN81', author = {Ashton, P. M. and Nair, S. and Dallman, T. and Rubino, S. and Rabsch, W. and Mwaigwisya, S.}, title = {MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island}, journal = {Nat Biotechnol}, volume = {33}, DOI = {10.1038/nbt.3103}, url = {http://dx.doi.org/10.1038/nbt.3103}, year = {2015}, type = {Journal Article} } @article{RN79', author = {Ayub, M. and Bayley, H.}, title = {Individual RNA base recognition in immobilized oligonucleotides using a protein nanopore}, journal = {Nano Lett}, volume = {12}, DOI = {10.1021/nl3027873}, url = {http://dx.doi.org/10.1021/nl3027873}, year = {2012}, type = {Journal Article} } @article{RN16, author = {Badran, A. H. and Guzov, V. M. and Huai, Q. and Kemp, M. M. and Vishwanath, P. and Kain, W. and Nance, A. M. and Evdokimov, A. and Moshiri, F. and Turner, K. H. and Wang, P. and Malvar, T. and Liu, D. R.}, title = {Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance}, journal = {Nature}, volume = {533}, number = {7601}, pages = {58-63}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, DOI = {10.1038/nature17938}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27120167}, year = {2016}, type = {Journal Article} } @article{RN120', author = {Badran, A. H. and Guzov, V. M. and Huai, Q. and Kemp, M. M. and Vishwanath, P. and Kain, W. and Nance, A. M. and Evdokimov, A. and Moshiri, F. and Turner, K. H. and Wang, P. and Malvar, T. and Liu, D. 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B. and Esvelt, K. M. and Moosburner, M. and Kosuri, S. and Yang, L. and Church, G. M.}, title = {CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering}, journal = {Nat Biotechnol}, volume = {31}, number = {9}, pages = {833-8}, ISSN = {1546-1696 (Electronic) 1087-0156 (Linking)}, DOI = {10.1038/nbt.2675}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23907171}, year = {2013}, type = {Journal Article} } @article{RN36', author = {Mali, P. and Esvelt, K. M. and Church, G. M.}, title = {Cas9 as a versatile tool for engineering biology}, journal = {Nat Methods}, volume = {10}, number = {10}, pages = {957-63}, ISSN = {1548-7105 (Electronic) 1548-7091 (Linking)}, DOI = {10.1038/nmeth.2649}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24076990}, year = {2013}, type = {Journal Article} } @article{RN41', author = {Mali, P. and Yang, L. and Esvelt, K. M. and Aach, J. and Guell, M. and DiCarlo, J. E. and Norville, J. E. and Church, G. 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Y.}, title = {A first look at the Oxford Nanopore MinION sequencer}, journal = {Mol Ecol Resour}, volume = {14}, DOI = {10.1111/1755-0998.12324}, url = {http://dx.doi.org/10.1111/1755-0998.12324}, year = {2014}, type = {Journal Article} } @article{RN99', author = {Miles, G. and Hoisington-Lopez, J. and Duncavage, E.}, title = {Nanopore sequencing of a DNA library prepared from formalin-fixed paraffin-embedded tissue}, journal = {Lab Invest}, volume = {95}, year = {2015}, type = {Journal Article} } @article{RN100', author = {Miller, R. R. and Montoya, V. and Gardy, J. L. and Patrick, D. M. and Tang, P.}, title = {Metagenomics for pathogen detection in public health}, journal = {Genome Med}, volume = {5}, DOI = {10.1186/gm485}, url = {http://dx.doi.org/10.1186/gm485}, year = {2013}, type = {Journal Article} } @article{RN2, author = {Mrazek, Jan and Toso, Daniel and Ryazantsev, Sergey and Zhang, Xing and Zhou, Z. Hong and Fernandez, Beatriz Campo and Kickhoefer, Valerie A. and Rome, Leonard H.}, title = {Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles}, journal = {ACS Nano}, volume = {8}, number = {11}, pages = {11552-11559}, ISSN = {1936-0851 1936-086X}, DOI = {10.1021/nn504778h}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245718/}, year = {2014}, type = {Journal Article} } @article{RN69', author = {Nivala, J. and Marks, D. B. and Akeson, M.}, title = {Unfoldase-mediated protein translocation through an α-hemolysin nanopore}, journal = {Nat Biotechnol}, volume = {31}, DOI = {10.1038/nbt.2503}, url = {http://dx.doi.org/10.1038/nbt.2503}, year = {2013}, type = {Journal Article} } @article{RN118', author = {Norris, A. L. and Workman, R. E. and Fan, Y. and Eshleman, J. R. and Timp, W.}, title = {Nanopore sequencing detects structural variants in cancer}, journal = {Cancer Biol Ther}, volume = {17}, DOI = {10.1080/15384047.2016.1139236}, url = {http://dx.doi.org/10.1080/15384047.2016.1139236}, year = {2016}, type = {Journal Article} } @article{RN73', author = {Ondov, B. D. and Treangen, T. J. and Melsted, P. and Mallonee, A. B. and Bergman, N. H. and Koren, S.}, title = {Mash: fast genome and metagenome distance estimation using MinHash}, journal = {Genome Biol}, volume = {17}, DOI = {10.1186/s13059-016-0997-x}, url = {http://dx.doi.org/10.1186/s13059-016-0997-x}, year = {2016}, type = {Journal Article} } @article{RN34', author = {Oye, K. A. and Esvelt, K. and Appleton, E. and Catteruccia, F. and Church, G. and Kuiken, T. and Lightfoot, S. B. and McNamara, J. and Smidler, A. and Collins, J. P.}, title = {Biotechnology. Regulating gene drives}, journal = {Science}, volume = {345}, number = {6197}, pages = {626-8}, ISSN = {1095-9203 (Electronic) 0036-8075 (Linking)}, DOI = {10.1126/science.1254287}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25035410}, year = {2014}, type = {Journal Article} } @article{RN32', author = {Oye, K. A. and Esvelt, K. M.}, title = {Gene drives raise dual-use concerns--response}, journal = {Science}, volume = {345}, number = {6200}, pages = {1010-1}, ISSN = {1095-9203 (Electronic) 0036-8075 (Linking)}, DOI = {10.1126/science.345.6200.1010-c}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25170143}, year = {2014}, type = {Journal Article} } @article{RN101', author = {Pallen, M. J.}, title = {Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections}, journal = {Parasitology}, volume = {141}, DOI = {10.1017/s0031182014000134}, url = {http://dx.doi.org/10.1017/S0031182014000134}, year = {2014}, type = {Journal Article} } @article{RN8, author = {Park, K. and Jung, J. and Son, J. and Kim, S. H. and Chung, B. H.}, title = {Anchoring foreign substances on live cell surfaces using Sortase A specific binding peptide}, journal = {Chem Commun (Camb)}, volume = {49}, number = {83}, pages = {9585-7}, ISSN = {1364-548X (Electronic) 1359-7345 (Linking)}, DOI = {10.1039/c3cc44753g}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24018381}, year = {2013}, type = {Journal Article} } @article{RN102', author = {Quick, J. and Ashton, P. and Calus, S. and Chatt, C. and Gossain, S. and Hawker, J.}, title = {Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella}, journal = {Genome Biol}, volume = {16}, DOI = {10.1186/s13059-015-0677-2}, url = {http://dx.doi.org/10.1186/s13059-015-0677-2}, year = {2015}, type = {Journal Article} } @article{RN104', author = {Quick, J. and Loman, N. J. and Duraffour, S. and Simpson, J. T. and Severi, E. and Cowley, L.}, title = {Real-time, portable genome sequencing for ebola surveillance}, journal = {Nature}, volume = {530}, DOI = {10.1038/nature16996}, url = {http://dx.doi.org/10.1038/nature16996}, year = {2016}, type = {Journal Article} } @article{RN84', author = {Quick, J. and Quinlan, A. and Loman, N.}, title = {A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer}, journal = {GigaScience}, volume = {3}, DOI = {10.1186/2047-217x-3-22}, url = {http://dx.doi.org/10.1186/2047-217X-3-22}, year = {2014}, type = {Journal Article} } @article{RN105', author = {Quick, J. and Quinlan, A. R. and Loman, N. J.}, title = {A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer}, journal = {Gigascience}, volume = {3}, DOI = {10.1186/2047-217x-3-22}, url = {http://dx.doi.org/10.1186/2047-217X-3-22}, year = {2014}, type = {Journal Article} } @article{RN106', author = {Ramgren, A. C. and Newhall, H. S. and James, K. E.}, title = {DNA barcoding and metabarcoding with the Oxford Nanopore MinION}, journal = {Genome}, volume = {58}, year = {2015}, type = {Journal Article} } @article{RN20', author = {Rashid, A. and Baldwin, T. and Gines, M. and Bregitzer, P. and Esvelt Klos, K.}, title = {A High-Throughput RNA Extraction for Sprouted Single-Seed Barley (Hordeum vulgare L.) Rich in Polysaccharides}, journal = {Plants (Basel)}, volume = {6}, number = {1}, ISSN = {2223-7747 (Linking)}, DOI = {10.3390/plants6010001}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28025509}, year = {2016}, type = {Journal Article} } @article{RN107', author = {Risse, J. and Thomson, M. and Patrick, S. and Blakely, G. and Koutsovoulos, G. and Blaxter, M.}, title = {A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data}, journal = {Gigascience}, volume = {4}, DOI = {10.1186/s13742-015-0101-6}, url = {http://dx.doi.org/10.1186/s13742-015-0101-6}, year = {2015}, type = {Journal Article} } @article{RN113', author = {Schreiber, J. and Wescoe, Z. L. and Abu-Shumays, R. and Vivian, J. T. and Baatar, B. and Karplus, K.}, title = {Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands}, journal = {Proc Natl Acad Sci U S A}, volume = {110}, DOI = {10.1073/pnas.1310615110}, url = {http://dx.doi.org/10.1073/pnas.1310615110}, year = {2013}, type = {Journal Article} } @article{RN65', author = {Smith, A. M. and Abu-Shumays, R. and Akeson, M. and Bernick, D. L.}, title = {Capture, unfolding, and detection of individual tRNA molecules using a nanopore device}, journal = {Front Bioeng Biotechnol}, volume = {3}, DOI = {10.3389/fbioe.2015.00091}, url = {http://dx.doi.org/10.3389/fbioe.2015.00091}, year = {2015}, type = {Journal Article} } @article{RN86', author = {Sović, I. and Šikić, M. and Wilm, A. and Fenlon, S. N. and Chen, S. and Nagarajan, N.}, title = {Fast and sensitive mapping of nanopore sequencing reads with GraphMap}, journal = {Nat Commun}, volume = {7}, DOI = {10.1038/ncomms11307}, url = {http://dx.doi.org/10.1038/ncomms11307}, year = {2016}, type = {Journal Article} } @article{RN55', author = {Szalay, T. and Golovchenko, J. A.}, title = {De novo sequencing and variant calling with nanopores using PoreSeq}, journal = {Nat Biotechnol}, volume = {33}, DOI = {10.1038/nbt.3360}, url = {http://dx.doi.org/10.1038/nbt.3360}, year = {2015}, type = {Journal Article} } @article{RN42', author = {Toth-Fejel, S. and Muller, P. and Ham, B. and Esvelt, K. and Dumas, N. and Calhoun, K. and Pommier, R.}, title = {DNA fingerprints provide a patient-specific breast cancer marker}, journal = {Ann Surg Oncol}, volume = {11}, number = {6}, pages = {560-7}, ISSN = {1068-9265 (Print) 1068-9265 (Linking)}, DOI = {10.1245/ASO.2004.03.049}, url = {https://www.ncbi.nlm.nih.gov/pubmed/15150063}, year = {2004}, type = {Journal Article} } @article{RN1, author = {Votteler, J. and Ogohara, C. and Yi, S. and Hsia, Y. and Nattermann, U. and Belnap, D. M. and King, N. P. and Sundquist, W. I.}, title = {Designed proteins induce the formation of nanocage-containing extracellular vesicles}, journal = {Nature}, volume = {540}, number = {7632}, pages = {292-295}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, DOI = {10.1038/nature20607}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27919066}, year = {2016}, type = {Journal Article} } @article{RN108', author = {Wang, J. and Moore, N. E. and Deng, Y. -. M. and Eccles, D. A. and Hall, R. J.}, title = {MinION nanopore sequencing of an influenza genome}, journal = {Front Microbiol}, volume = {6}, year = {2015}, type = {Journal Article} } @article{RN110', author = {Ward, A. C. and Kim, W.}, title = {MinIONTM: new, long read, portable nucleic acid sequencing device}, journal = {J Bacteriol Virol}, volume = {45}, DOI = {10.4167/jbv.2015.45.4.285}, url = {http://dx.doi.org/10.4167/jbv.2015.45.4.285}, year = {2015}, type = {Journal Article} } @article{RN111', author = {Watson, M. and Thomson, M. and Risse, J. and Talbot, R. and Santoyo-Lopez, J. and Gharbi, K.}, title = {poRe: an R package for the visualization and analysis of nanopore sequencing data}, journal = {Bioinformatics}, volume = {31}, DOI = {10.1093/bioinformatics/btu590}, url = {http://dx.doi.org/10.1093/bioinformatics/btu590}, year = {2015}, type = {Journal Article} } @article{RN112', author = {Wei, S. and Williams, Z.}, title = {Rapid short-read sequencing and aneuploidy detection using MinION nanopore technology}, journal = {Genetics}, volume = {202}, DOI = {10.1534/genetics.115.182311}, url = {http://dx.doi.org/10.1534/genetics.115.182311}, year = {2016}, type = {Journal Article} } @article{RN114', author = {Wescoe, Z. L. and Schreiber, J. and Akeson, M.}, title = {Nanopores discriminate among five C5-cytosine variants in DNA}, journal = {J Am Chem Soc}, volume = {136}, DOI = {10.1021/ja508527b}, url = {http://dx.doi.org/10.1021/ja508527b}, year = {2014}, type = {Journal Article} } @article{RN6, author = {Wheeler, L. C. and Lim, S. A. and Marqusee, S. and Harms, M. J.}, title = {The thermostability and specificity of ancient proteins}, journal = {Curr Opin Struct Biol}, volume = {38}, pages = {37-43}, ISSN = {1879-033X (Electronic) 0959-440X (Linking)}, DOI = {10.1016/j.sbi.2016.05.015}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27288744}, year = {2016}, type = {Journal Article} } @article{RN11, author = {Whitfield, J. H. and Zhang, W. H. and Herde, M. K. and Clifton, B. E. and Radziejewski, J. and Janovjak, H. and Henneberger, C. and Jackson, C. J.}, title = {Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction}, journal = {Protein Sci}, volume = {24}, number = {9}, pages = {1412-22}, ISSN = {1469-896X (Electronic) 0961-8368 (Linking)}, DOI = {10.1002/pro.2721}, url = {https://www.ncbi.nlm.nih.gov/pubmed/26061224}, year = {2015}, type = {Journal Article} } @article{RN13, author = {Willbanks, A. and Leary, M. and Greenshields, M. and Tyminski, C. and Heerboth, S. and Lapinska, K. and Haskins, K. and Sarkar, S.}, title = {The Evolution of Epigenetics: From Prokaryotes to Humans and Its Biological Consequences}, journal = {Genet Epigenet}, volume = {8}, pages = {25-36}, ISSN = {1179-237X (Linking)}, DOI = {10.4137/GEG.S31863}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27512339}, year = {2016}, type = {Journal Article} } @article{RN22', author = {Winkler, L. R. and Michael Bonman, J. and Chao, S. and Admassu Yimer, B. and Bockelman, H. and Esvelt Klos, K.}, title = {Population Structure and Genotype-Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars}, journal = {Front Plant Sci}, volume = {7}, pages = {1077}, ISSN = {1664-462X (Linking)}, DOI = {10.3389/fpls.2016.01077}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27524988}, year = {2016}, type = {Journal Article} } @article{RN35', author = {Yaung, S. J. and Esvelt, K. M. and Church, G. M.}, title = {CRISPR/Cas9-mediated phage resistance is not impeded by the DNA modifications of phage T4}, journal = {PLoS One}, volume = {9}, number = {6}, pages = {e98811}, ISSN = {1932-6203 (Electronic) 1932-6203 (Linking)}, DOI = {10.1371/journal.pone.0098811}, url = {https://www.ncbi.nlm.nih.gov/pubmed/24886988}, year = {2014}, type = {Journal Article} } @article{RN31', author = {Yaung, S. J. and Esvelt, K. M. and Church, G. M.}, title = {Complete Genome Sequences of T4-Like Bacteriophages RB3, RB5, RB6, RB7, RB9, RB10, RB27, RB33, RB55, RB59, and RB68}, journal = {Genome Announc}, volume = {3}, number = {1}, DOI = {10.1128/genomeA.01122-14}, url = {https://www.ncbi.nlm.nih.gov/pubmed/25555735}, year = {2015}, type = {Journal Article} } @article{RN59', author = {Zaaijer, S.}, title = {Columbia University Ubiquitous Genomics 2015 Class, Erlich Y}, journal = {Elife}, volume = {5}, DOI = {10.7554/eLife.14258}, url = {http://dx.doi.org/10.7554/eLife.14258}, year = {2016}, type = {Journal Article} } @article{RN140, title = {Translation initiation in Escherichia coli}, type = {Journal Article}, journal = {Molecular Microbiology}, year = {1992}, } % This file was created with Citavi 5.3.1.0 @article{., title = {816 816..821} } @article{.b, title = {PII: 0092-8674(95)90135-3} } @article{.c, title = {1341 1348..1353} } @article{BHATTACHARYYAETAL..2000, abstract = {Mutations in breast cancer tumor susceptibility genes, BRCA1 and BRCA2, predispose women to early onset breast cancer and other malignancies. The Brca genes are involved in multiple cellular processes in response to DNA damage including checkpoint activation, gene transcription, and DNA repair. Biochemical interaction with the recombinational repair protein Rad51 (Scully, R., Chen, J., Ochs, R. L., Keegan, K., Hoekstra, M., Feunteun, J., and Livingston, D. M. (1997) Cell 90, 425-435), as well as genetic evidence (Moynahan, M. E., Chiu, J. W., Koller, B. H., and Jasin, M. (1999) Mol. Cell 4, 511-518 and Snouwaert, J. N., Gowen, L. C., Latour, A. M., Mohn, A. R., Xiao, A., DiBiase, L., and Koller, B. H. (1999) Oncogene 18, 7900-7907), demonstrates that Brca1 is involved in recombinational repair of DNA double strand breaks. Using isogenic Brca1(+/+) and brca1(-/-) mouse embryonic stem (ES) cell lines, we investigated the role of Brca1 in the cellular response to two different categories of DNA damage: x-ray induced damage and cross-linking damage caused by the chemotherapeutic agent, cisplatinum. Immunoflourescence studies with normal and brca1(-/-) mutant mouse ES cell lines indicate that Brca1 promotes assembly of subnuclear Rad51 foci following both types of DNA damage. These foci are likely to be oligomeric complexes of Rad51 engaged in repair of DNA lesions or in processes that allow cells to tolerate such lesions during DNA replication. Clonogenic assays show that brca1(-/-) mutants are 5-fold more sensitive to cisplatinum compared with wild-type cells. Our studies suggest that Brca1 contributes to damage repair and/or tolerance by promoting assembly of Rad51. This function appears to be shared with Brca2.}, author = {Bhattacharyya, A. and Ear, U. S. and Koller, B. H. and Weichselbaum, R. R. and Bishop, D. K.}, year = {2000}, title = {The breast cancer susceptibility gene BRCA1 is required for subnuclear assembly of Rad51 and survival following treatment with the DNA cross-linking agent cisplatin}, keywords = {0 (BRCA2 Protein);0 (Cross-Linking Reagents);0 (DNA-Binding Proteins);0 (Neoplasm Proteins);0 (Transcription Factors);Animals;BRCA2 Protein;Cell Nucleus/metabolism;Cell Survival;Cisplatin/pharmacology;Cross-Linking Reagents;DNA Damage;DNA Repair;DNA-Binding Proteins/metabolism;Dose-Response Relationship, Drug;Dose-Response Relationship, Radiation;EC 2.7.7.- (Rad51 protein, mouse);EC 2.7.7.- (Rad51 Recombinase);Female;Genes, BRCA1;Genetic Predisposition to Disease;Mammary Neoplasms, Animal/genetics;Mice;Neoplasm Proteins/genetics;Q20Q21Q62J (Cisplatin);Rad51 Recombinase;Transcription Factors/genetics;X-Rays/adverse effects}, pages = {23899--23903}, volume = {275}, number = {31}, issn = {0021-9258}, journal = {The Journal of biological chemistry}, doi = {10.1074/jbc.C000276200} } @article{BIKARDETAL..2013, abstract = {The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease that participates in the CRISPR-Cas immune defense against prokaryotic viruses. We describe the use of a Cas9 nuclease mutant that retains DNA-binding activity and can be engineered as a programmable transcription repressor by preventing the binding of the RNA polymerase (RNAP) to promoter sequences or as a transcription terminator by blocking the running RNAP. In addition, a fusion between the omega subunit of the RNAP and a Cas9 nuclease mutant directed to bind upstream promoter regions can achieve programmable transcription activation. The simple and efficient modulation of gene expression achieved by this technology is a useful asset for the study of gene networks and for the development of synthetic biology and biotechnological applications.}, author = {Bikard, David and Jiang, Wenyan and Samai, Poulami and Hochschild, Ann and Zhang, Feng and Marraffini, Luciano A.}, year = {2013}, title = {Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system}, keywords = {Bacterial Proteins/genetics/metabolism;Endoribonucleases/genetics/metabolism;Escherichia coli/genetics/metabolism;Gene Expression Regulation, Bacterial;Gene Regulatory Networks;Genes, Bacterial;Genes, Synthetic;Genetic Loci;Inverted Repeat Sequences;Promoter Regions, Genetic;Protein Binding;Repressor Proteins/genetics/metabolism;RNA, Bacterial/genetics/metabolism;Streptococcus pneumoniae/genetics/metabolism;Streptococcus pyogenes/enzymology/genetics;Transcriptional Activation}, pages = {7429--7437}, volume = {41}, number = {15}, issn = {0305-1048}, journal = {Nucleic acids research}, doi = {10.1093/nar/gkt520} } @article{BRODELETAL..2016, abstract = {Nature Communications 7, (2016). doi:10.1038/ncomms13858}, author = {Br{\"o}del, Andreas K. and Jaramillo, Alfonso and Isalan, Mark}, year = {2016}, title = {Engineering orthogonal dual transcription factors for multi-input synthetic promoters}, pages = {13858}, volume = {7}, issn = {2041-1723}, journal = {Nature communications}, doi = {10.1038/ncomms13858} } @article{BUISSONETAL..2010, abstract = {Inherited mutations in human PALB2 are associated with a predisposition to breast and pancreatic cancers. PALB2's tumor-suppressing effect is thought to be based on its ability to facilitate BRCA2's function in homologous recombination. However, the biochemical properties of PALB2 are unknown. Here we show that human PALB2 binds DNA, preferentially D-loop structures, and directly interacts with the RAD51 recombinase to stimulate strand invasion, a vital step of homologous recombination. This stimulation occurs through reinforcing biochemical mechanisms, as PALB2 alleviates inhibition by RPA and stabilizes the RAD51 filament. Moreover, PALB2 can function synergistically with a BRCA2 chimera (termed piccolo, or piBRCA2) to further promote strand invasion. Finally, we show that PALB2-deficient cells are sensitive to PARP inhibitors. Our studies provide the first biochemical insights into PALB2's function with piBRCA2 as a mediator of homologous recombination in DNA double-strand break repair.}, author = {Buisson, Remi and Dion-Cote, Anne-Marie and Coulombe, Yan and Launay, Helene and Cai, Hong and Stasiak, Alicja Z. and Stasiak, Andrzej and Xia, Bing and Masson, Jean-Yves}, year = {2010}, title = {Cooperation of breast cancer proteins PALB2 and piccolo BRCA2 in stimulating homologous recombination}, keywords = {0 (Apoptosis Regulatory Proteins);0 (BLID protein, human);0 (BRCA2 Protein);0 (BRCA2 protein, human);0 (DNA, Neoplasm);0 (Neoplasm Proteins);0 (Nuclear Proteins);0 (PALB2 protein, human);0 (Peptide Fragments);0 (Poly(ADP-ribose) Polymerase Inhibitors);0 (Tumor Suppressor Proteins);Apoptosis Regulatory Proteins;Base Sequence;BRCA2 Protein/chemistry/physiology;Breast Neoplasms/metabolism;DNA Breaks, Double-Stranded;DNA Repair/physiology;DNA, Neoplasm/metabolism;EC 2.4.2.30 (PARP1 protein, human);EC 2.4.2.30 (Poly (ADP-Ribose) Polymerase-1);EC 2.7.7.- (RAD51 protein, human);EC 2.7.7.- (Rad51 Recombinase);Female;Humans;Models, Biological;Molecular Sequence Data;Neoplasm Proteins/chemistry/physiology;Nuclear Proteins/chemistry/genetics/physiology;Nucleic Acid Conformation;Peptide Fragments/chemistry/metabolism;Poly (ADP-Ribose) Polymerase-1;Poly(ADP-ribose) Polymerase Inhibitors;Protein Interaction Domains and Motifs;Protein Interaction Mapping;Rad51 Recombinase/chemistry/physiology;Recombination, Genetic/physiology;Structure-Activity Relationship;Tumor Suppressor Proteins/chemistry/genetics/physiology}, pages = {1247--1254}, volume = {17}, number = {10}, issn = {1545-9985}, journal = {Nature structural {\&} molecular biology}, doi = {10.1038/nsmb.1915} } @article{CARREIRAETAL..2009, abstract = {The breast cancer susceptibility protein, BRCA2, is essential for recombinational DNA repair. BRCA2 delivers RAD51 to double-stranded DNA (dsDNA) breaks through interaction with eight conserved, approximately 35 amino acid motifs, the BRC repeats. Here we show that the solitary BRC4 promotes assembly of RAD51 onto single-stranded DNA (ssDNA), but not dsDNA, to stimulate DNA strand exchange. BRC4 acts by blocking ATP hydrolysis and thereby maintaining the active ATP-bound form of the RAD51-ssDNA filament. Single-molecule visualization shows that BRC4 does not disassemble RAD51-dsDNA filaments but rather blocks nucleation of RAD51 onto dsDNA. Furthermore, this behavior is manifested by a domain of BRCA2 comprising all eight BRC repeats. These results establish that the BRC repeats modulate RAD51-DNA interaction in two opposing but functionally reinforcing ways: targeting active RAD51 to ssDNA and prohibiting RAD51 nucleation onto dsDNA. Thus, BRCA2 recruits RAD51 to DNA breaks and, we propose, the BRC repeats regulate DNA-binding selectivity.}, author = {Carreira, Aura and Hilario, Jovencio and Amitani, Ichiro and Baskin, Ronald J. and Shivji, Mahmud K. K. and Venkitaraman, Ashok R. and Kowalczykowski, Stephen C.}, year = {2009}, title = {The BRC repeats of BRCA2 modulate the DNA-binding selectivity of RAD51}, keywords = {0 (BRCA2 Protein);0 (DNA, Single-Stranded);8L70Q75FXE (Adenosine Triphosphate);Adenosine Triphosphate/metabolism;Amino Acid Motifs;BRCA2 Protein/chemistry/metabolism;DNA;DNA, Single-Stranded/metabolism;EC 2.7.7.- (Rad51 Recombinase);Humans;Models, Biological;Rad51 Recombinase/metabolism;Recombination, Genetic}, pages = {1032--1043}, volume = {136}, number = {6}, issn = {0092-8674}, journal = {Cell}, doi = {10.1016/j.cell.2009.02.019} } @article{CHAPMANETAL..2012, abstract = {MOLCEL, 47 (2012) 497-510. doi:10.1016/j.molcel.2012.07.029}, author = {Chapman, J. Ross and Taylor, Martin R. G. and Boulton, Simon J.}, year = {2012}, title = {Playing the end game: DNA double-strand break repair pathway choice}, keywords = {Animals;Cell Cycle/genetics;DNA Breaks, Double-Stranded;DNA Repair;Genomic Instability;Humans;Recombination, Genetic}, pages = {497--510}, volume = {47}, number = {4}, issn = {1097-2765}, journal = {Molecular cell}, doi = {10.1016/j.molcel.2012.07.029} } @article{CHENETAL..2000, abstract = {The DNA-dependent protein kinase (DNA-PK), consisting of Ku and the DNA-PK catalytic subunit (DNA-PKcs), and the DNA ligase IV-XRCC4 complex function together in the repair of DNA double-strand breaks by non-homologous end joining. These protein complexes are also required for the completion of V(D)J recombination events in immune cells. Here we demonstrate that the DNA ligase IV-XRCC4 complex binds specifically to the ends of duplex DNA molecules and can act as a bridging factor, linking together duplex DNA molecules with complementary but non-ligatable ends. Although the DNA end-binding protein Ku inhibited DNA joining by DNA ligase IV-XRCC4, it did not prevent this complex from binding to DNA. Instead, DNA ligase IV-XRCC4 and Ku bound simultaneously to the ends of duplex DNA molecules. DNA ligase IV-XRCC4 and DNA-PKcs also formed complexes at the ends of DNA molecules, but DNA-PKcs did not inhibit ligation. Interestingly, DNA-PKcs stimulated intermolecular ligation by DNA ligase IV-XRCC4. In the presence of DNA-PK, the majority of the joining events catalyzed by DNA ligase IV-XRCC4 were intermolecular because Ku inhibited intramolecular ligation, but DNA-PKcs still stimulated intramolecular ligation. We suggest that DNA-PKcs-containing complexes formed at DNA ends enhance the association of DNA ends via protein-protein interactions, thereby stimulating intermolecular ligation.}, author = {Chen, L. and Trujillo, K. and Sung, P. and Tomkinson, A. E.}, year = {2000}, title = {Interactions of the DNA ligase IV-XRCC4 complex with DNA ends and the DNA-dependent protein kinase}, keywords = {0 (DNA-Binding Proteins);0 (LIG4 protein, human);0 (Macromolecular Substances);0 (Nuclear Proteins);0 (XRCC4 protein, human);9007-49-2 (DNA);Animals;Catalysis;Cell Line;DNA Ligase ATP;DNA Ligases/metabolism;DNA Repair;DNA/metabolism;DNA-Activated Protein Kinase;DNA-Binding Proteins/metabolism;EC 2.7.11.1 (DNA-Activated Protein Kinase);EC 2.7.11.1 (PRKDC protein, human);EC 2.7.11.1 (Protein-Serine-Threonine Kinases);EC 6.5.1.- (DNA Ligases);EC 6.5.1.1 (DNA Ligase ATP);Humans;Macromolecular Substances;Nuclear Proteins;Protein Binding;Protein-Serine-Threonine Kinases/metabolism;Spodoptera}, pages = {26196--26205}, volume = {275}, number = {34}, issn = {0021-9258}, journal = {The Journal of biological chemistry}, doi = {10.1074/jbc.M000491200} } @article{CRITCHLOWETAL..1997, author = {Critchlow, Susan E. and Bowater, Richard P. and Jackson, Stephen P.}, year = {1997}, title = {Mammalian DNA double-strand break repair protein XRCC4 interacts with DNA ligase IV}, pages = {588--598}, volume = {7}, number = {8}, issn = {09609822}, journal = {Current Biology}, doi = {10.1016/S0960-9822(06)00258-2} } @article{DELTCHEVAETAL..2011, abstract = {Nature 471, 602 (2011). doi:10.1038/nature09886}, author = {Deltcheva, Elitza and Chylinski, Krzysztof and Sharma, Cynthia M. and Gonzales, Karine and Chao, Yanjie and Pirzada, Zaid A. and Eckert, Maria R. and Vogel, Jorg and Charpentier, Emmanuelle}, year = {2011}, title = {CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III}, keywords = {0 (Bacterial Proteins);0 (DNA, Viral);0 (RNA Precursors);0 (RNA, Bacterial);0 (RNA, Guide);Bacterial Proteins/chemistry/genetics/immunology/metabolism;Conserved Sequence;DNA, Viral/genetics/metabolism;EC 3.1.26.3 (Ribonuclease III);Escherichia coli;Models, Biological;Prophages/genetics;Ribonuclease III/metabolism;RNA Precursors/genetics/metabolism;RNA Processing, Post-Transcriptional;RNA, Bacterial/biosynthesis/genetics/immunology/metabolism;RNA, Guide/genetics;Streptococcus pyogenes/genetics/immunology/metabolism/virology}, pages = {602--607}, volume = {471}, number = {7340}, issn = {0028-0836}, journal = {Nature}, doi = {10.1038/nature09886} } @article{DOUDNAETAL..2014, abstract = {The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics.}, author = {Doudna, Jennifer A. and Charpentier, Emmanuelle}, year = {2014}, title = {Genome editing. The new frontier of genome engineering with CRISPR-Cas9}, keywords = {0 (RNA, Guide);Animals;Clustered Regularly Interspaced Short Palindromic Repeats;DNA Cleavage;Gene Targeting;Genetic Engineering/methods;Genome, Human/genetics;Humans;RNA, Guide}, pages = {1258096}, volume = {346}, number = {6213}, issn = {0036-8075}, journal = {Science (New York, N.Y.)}, doi = {10.1126/science.1258096} } @article{ESCRIBANODIAZETAL..2013, abstract = {Molecular Cell, 49 (2013) 872-883. doi:10.1016/j.molcel.2013.01.001}, author = {Escribano-Diaz, Cristina and Orthwein, Alexandre and Fradet-Turcotte, Amelie and Xing, Mengtan and Young, Jordan T. F. and Tkac, Jan and Cook, Michael A. and Rosebrock, Adam P. and Munro, Meagan and Canny, Marella D. and Xu, Dongyi and Durocher, Daniel}, year = {2013}, title = {A cell cycle-dependent regulatory circuit composed of 53BP1-RIF1 and BRCA1-CtIP controls DNA repair pathway choice}, keywords = {0 (BRCA1 Protein);0 (BRCA1 protein, human);0 (Carrier Proteins);0 (Intracellular Signaling Peptides and Proteins);0 (Nuclear Proteins);0 (RBBP8 protein, human);0 (Rif1 protein, human);0 (Telomere-Binding Proteins);0 (TP53BP1 protein, human);0 (Tumor Suppressor p53-Binding Protein 1);Binding Sites;BRCA1 Protein/genetics/metabolism;Carrier Proteins/genetics/metabolism;Cell Cycle/genetics;DNA End-Joining Repair/genetics;DNA Repair;HEK293 Cells;HeLa Cells;Humans;Intracellular Signaling Peptides and Proteins/genetics/metabolism;Nuclear Proteins/genetics/metabolism;S Phase;Telomere-Binding Proteins/genetics/metabolism;Tumor Suppressor p53-Binding Protein 1}, pages = {872--883}, volume = {49}, number = {5}, issn = {1097-2765}, journal = {Molecular cell}, doi = {10.1016/j.molcel.2013.01.001} } @article{FALCKETAL..2005, abstract = {Ataxia-telangiectasia mutated (ATM), ataxia-telangiectasia and Rad3-related (ATR) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) are members of the phosphoinositide-3-kinase-related protein kinase (PIKK) family, and are rapidly activated in response to DNA damage. ATM and DNA-PKcs respond mainly to DNA double-strand breaks, whereas ATR is activated by single-stranded DNA and stalled DNA replication forks. In all cases, activation involves their recruitment to the sites of damage. Here we identify related, conserved carboxy-terminal motifs in human Nbs1, ATRIP and Ku80 proteins that are required for their interaction with ATM, ATR and DNA-PKcs, respectively. These motifs are essential not only for efficient recruitment of ATM, ATR and DNA-PKcs to sites of damage, but are also critical for ATM-, ATR- and DNA-PKcs-mediated signalling events that trigger cell cycle checkpoints and DNA repair. Our findings reveal that recruitment of these PIKKs to DNA lesions occurs by common mechanisms through an evolutionarily conserved motif, and provide direct evidence that PIKK recruitment is required for PIKK-dependent DNA-damage signalling.}, author = {Falck, Jacob and Coates, Julia and Jackson, Stephen P.}, year = {2005}, title = {Conserved modes of recruitment of ATM, ATR and DNA-PKcs to sites of DNA damage}, keywords = {0 (Antigens, Nuclear);0 (Cell Cycle Proteins);0 (DNA-Binding Proteins);0 (NBN protein, human);0 (Nuclear Proteins);0 (Tumor Suppressor Proteins);9007-49-2 (DNA);Amino Acid Motifs;Amino Acid Sequence;Animals;Antigens, Nuclear/chemistry/metabolism;Ataxia Telangiectasia Mutated Proteins;Binding Sites;Cell Cycle Proteins/chemistry/genetics/metabolism;Conserved Sequence;Cricetinae;DNA Damage;DNA/genetics/metabolism;DNA-Activated Protein Kinase;DNA-Binding Proteins/chemistry/genetics/metabolism;EC 2.7.1.- (Phosphatidylinositol 3-Kinases);EC 2.7.11.1 (Ataxia Telangiectasia Mutated Proteins);EC 2.7.11.1 (ATM protein, human);EC 2.7.11.1 (ATR protein, human);EC 2.7.11.1 (DNA-Activated Protein Kinase);EC 2.7.11.1 (PRKDC protein, human);EC 2.7.11.1 (Protein-Serine-Threonine Kinases);EC 3.6.4.12 (Xrcc6 protein, human);EC 4.2.99.- (Ku Autoantigen);Humans;Ku Autoantigen;Molecular Sequence Data;Nuclear Proteins/chemistry/genetics/metabolism;Phosphatidylinositol 3-Kinases/chemistry;Phosphorylation;Protein Binding;Protein Transport;Protein-Serine-Threonine Kinases/chemistry/genetics/metabolism;Signal Transduction;Tumor Suppressor Proteins/chemistry/genetics/metabolism}, pages = {605--611}, volume = {434}, number = {7033}, issn = {0028-0836}, journal = {Nature}, doi = {10.1038/nature03442} } @article{FRYEETAL..2016, abstract = {Nature Reviews Genetics 17, 365 (2016). doi:10.1038/nrg.2016.47}, author = {Frye, Michaela and Jaffrey, Samie R. and Pan, Tao and Rechavi, Gideon and Suzuki, Tsutomu}, year = {2016}, title = {RNA modifications: what have we learned and where are we headed?}, pages = {365--372}, volume = {17}, number = {6}, issn = {1471-0056}, journal = {Nature reviews. Genetics}, doi = {10.1038/nrg.2016.47} } @article{GAOETAL..2016, abstract = {Nature Biotechnology, (2016). doi:10.1038/nbt.3547}, author = {Gao, Feng and Shen, Xiao Z. and Jiang, Feng and Wu, Yongqiang and Han, Chunyu}, year = {2016}, title = {DNA-guided genome editing using the Natronobacterium gregoryi Argonaute}, pages = {768--773}, volume = {34}, number = {7}, issn = {1087-0156}, journal = {Nature biotechnology}, doi = {10.1038/nbt.3547} } @article{HUERTASETAL..2009, abstract = {In G(0) and G(1), DNA double strand breaks are repaired by nonhomologous end joining, whereas in S and G(2), they are also repaired by homologous recombination. The human CtIP protein controls double strand break (DSB) resection, an event that occurs effectively only in S/G(2) and that promotes homologous recombination but not non-homologous end joining. Here, we mutate a highly conserved cyclin-dependent kinase (CDK) target motif in CtIP and reveal that mutating Thr-847 to Ala impairs resection, whereas mutating it to Glu to mimic constitutive phosphorylation does not. Moreover, we show that unlike cells expressing wild-type CtIP, cells expressing the Thr-to-Glu mutant resect DSBs even after CDK inhibition. Finally, we establish that Thr-847 mutations to either Ala or Glu affect DSB repair efficiency, cause hypersensitivity toward DSB-generating agents, and affect the frequency and nature of radiation-induced chromosomal rearrangements. These results suggest that CDK-mediated control of resection in human cells operates by mechanisms similar to those recently established in yeast.}, author = {Huertas, Pablo and Jackson, Stephen P.}, year = {2009}, title = {Human CtIP mediates cell cycle control of DNA end resection and double strand break repair}, keywords = {0 (Carrier Proteins);0 (Nuclear Proteins);0 (Protein Kinase Inhibitors);0 (RBBP8 protein, human);9007-49-2 (DNA);Amino Acid Sequence;Animals;Carrier Proteins/chemistry/genetics/metabolism;Cell Cycle/drug effects;Cell Line, Tumor;Conserved Sequence;Cyclin-Dependent Kinases/antagonists {\&} inhibitors/metabolism;DNA Damage/genetics;DNA Repair/genetics;DNA/genetics/metabolism;EC 2.7.11.22 (Cyclin-Dependent Kinases);Genomic Instability;Humans;Molecular Sequence Data;Mutation/genetics;Nuclear Proteins/chemistry/genetics/metabolism;Protein Kinase Inhibitors/pharmacology;Sequence Alignment}, pages = {9558--9565}, volume = {284}, number = {14}, issn = {0021-9258}, journal = {The Journal of biological chemistry}, doi = {10.1074/jbc.M808906200} } @article{HUERTASETAL..2009b, abstract = {In G(0) and G(1), DNA double strand breaks are repaired by nonhomologous end joining, whereas in S and G(2), they are also repaired by homologous recombination. The human CtIP protein controls double strand break (DSB) resection, an event that occurs effectively only in S/G(2) and that promotes homologous recombination but not non-homologous end joining. Here, we mutate a highly conserved cyclin-dependent kinase (CDK) target motif in CtIP and reveal that mutating Thr-847 to Ala impairs resection, whereas mutating it to Glu to mimic constitutive phosphorylation does not. Moreover, we show that unlike cells expressing wild-type CtIP, cells expressing the Thr-to-Glu mutant resect DSBs even after CDK inhibition. Finally, we establish that Thr-847 mutations to either Ala or Glu affect DSB repair efficiency, cause hypersensitivity toward DSB-generating agents, and affect the frequency and nature of radiation-induced chromosomal rearrangements. These results suggest that CDK-mediated control of resection in human cells operates by mechanisms similar to those recently established in yeast.}, author = {Huertas, Pablo and Jackson, Stephen P.}, year = {2009}, title = {Human CtIP mediates cell cycle control of DNA end resection and double strand break repair}, keywords = {0 (Carrier Proteins);0 (Nuclear Proteins);0 (Protein Kinase Inhibitors);0 (RBBP8 protein, human);9007-49-2 (DNA);Amino Acid Sequence;Animals;Carrier Proteins/chemistry/genetics/metabolism;Cell Cycle/drug effects;Cell Line, Tumor;Conserved Sequence;Cyclin-Dependent Kinases/antagonists {\&} inhibitors/metabolism;DNA Damage/genetics;DNA Repair/genetics;DNA/genetics/metabolism;EC 2.7.11.22 (Cyclin-Dependent Kinases);Genomic Instability;Humans;Molecular Sequence Data;Mutation/genetics;Nuclear Proteins/chemistry/genetics/metabolism;Protein Kinase Inhibitors/pharmacology;Sequence Alignment}, pages = {9558--9565}, volume = {284}, number = {14}, issn = {0021-9258}, journal = {The Journal of biological chemistry}, doi = {10.1074/jbc.M808906200} } @article{HUETAL..2016, abstract = {Cell Chemical Biology, 23 (2016) 57-73. doi:10.1016/j.chembiol.2015.12.009}, author = {Hu, Johnny H. and Davis, Kevin M. and Liu, David R.}, year = {2016}, title = {Chemical Biology Approaches to Genome Editing: Understanding, Controlling, and Delivering Programmable Nucleases}, keywords = {9007-49-2 (DNA);Animals;Base Sequence;Clustered Regularly Interspaced Short Palindromic Repeats;CRISPR-Cas Systems;Deoxyribonucleases/genetics/metabolism;DNA/genetics/metabolism;EC 3.1.- (Deoxyribonucleases);Genetic Engineering/methods;Genome;Humans}, pages = {57--73}, volume = {23}, number = {1}, issn = {2451-9456}, journal = {Cell chemical biology}, doi = {10.1016/j.chembiol.2015.12.009} } @article{ISMAILETAL..2015, abstract = {Nature Cell Biology 17, 11 (2015). doi:10.1038/ncb3259}, author = {Ismail, Ismail Hassan and Gagne, Jean-Philippe and Genois, Marie-Michelle and Strickfaden, Hilmar and McDonald, Darin and Xu, Zhizhong and Poirier, Guy G. and Masson, Jean-Yves and Hendzel, Michael J.}, year = {2015}, title = {The RNF138 E3 ligase displaces Ku to promote DNA end resection and regulate DNA repair pathway choice}, keywords = {0 (DNA, Neoplasm);0 (DNA, Single-Stranded);0 (Luminescent Proteins);Ataxia Telangiectasia Mutated Proteins/metabolism;Cell Line, Tumor;DNA Breaks, Double-Stranded;DNA End-Joining Repair;DNA Helicases/genetics/metabolism;DNA Repair;DNA, Neoplasm/genetics/metabolism;DNA, Single-Stranded/genetics/metabolism;EC 2.3.2.27 (RNF138 protein, human);EC 2.3.2.27 (Ubiquitin-Protein Ligases);EC 2.7.11.1 (Ataxia Telangiectasia Mutated Proteins);EC 2.7.11.1 (ATR protein, human);EC 3.6.4.- (DNA Helicases);EC 3.6.4.12 (XRCC5 protein, human);EC 4.2.99.- (Ku Autoantigen);HEK293 Cells;HeLa Cells;Humans;Immunoblotting;Ku Autoantigen;Luminescent Proteins/genetics/metabolism;MCF-7 Cells;Microscopy, Confocal;Mutation;Protein Binding;Recombinational DNA Repair;RNA Interference;Ubiquitination;Ubiquitin-Protein Ligases/genetics/metabolism}, pages = {1446--1457}, volume = {17}, number = {11}, issn = {1465-7392}, journal = {Nature cell biology}, doi = {10.1038/ncb3259} } @article{ISMAILETAL..2015b, abstract = {Nature Cell Biology 17, 11 (2015). doi:10.1038/ncb3259}, author = {Ismail, Ismail Hassan and Gagne, Jean-Philippe and Genois, Marie-Michelle and Strickfaden, Hilmar and McDonald, Darin and Xu, Zhizhong and Poirier, Guy G. and Masson, Jean-Yves and Hendzel, Michael J.}, year = {2015}, title = {The RNF138 E3 ligase displaces Ku to promote DNA end resection and regulate DNA repair pathway choice}, keywords = {0 (DNA, Neoplasm);0 (DNA, Single-Stranded);0 (Luminescent Proteins);Ataxia Telangiectasia Mutated Proteins/metabolism;Cell Line, Tumor;DNA Breaks, Double-Stranded;DNA End-Joining Repair;DNA Helicases/genetics/metabolism;DNA Repair;DNA, Neoplasm/genetics/metabolism;DNA, Single-Stranded/genetics/metabolism;EC 2.3.2.27 (RNF138 protein, human);EC 2.3.2.27 (Ubiquitin-Protein Ligases);EC 2.7.11.1 (Ataxia Telangiectasia Mutated Proteins);EC 2.7.11.1 (ATR protein, human);EC 3.6.4.- (DNA Helicases);EC 3.6.4.12 (XRCC5 protein, human);EC 4.2.99.- (Ku Autoantigen);HEK293 Cells;HeLa Cells;Humans;Immunoblotting;Ku Autoantigen;Luminescent Proteins/genetics/metabolism;MCF-7 Cells;Microscopy, Confocal;Mutation;Protein Binding;Recombinational DNA Repair;RNA Interference;Ubiquitination;Ubiquitin-Protein Ligases/genetics/metabolism}, pages = {1446--1457}, volume = {17}, number = {11}, issn = {1465-7392}, journal = {Nature cell biology}, doi = {10.1038/ncb3259} } @article{JASINETAL..2013, abstract = {In this review, we discuss the repair of DNA double-strand breaks (DSBs) using a homologous DNA sequence (i.e., homologous recombination [HR]), focusing mainly on yeast and mammals. We provide a historical context for the current view of HR and describe how DSBs are processed during HR as well as interactions with other DSB repair pathways. We discuss the enzymology of the process, followed by studies on DSB repair in living cells. Whenever possible, we cite both original articles and reviews to aid the reader for further studies.}, author = {Jasin, Maria and Rothstein, Rodney}, year = {2013}, title = {Repair of strand breaks by homologous recombination}, keywords = {0 (DNA-Binding Proteins);Animals;DNA Breaks, Double-Stranded;DNA Repair;DNA-Binding Proteins/metabolism;EC 2.7.7.- (Rad51 Recombinase);Genetic Engineering/methods;Homologous Recombination;Humans;Meiosis;Plasmids/genetics;Rad51 Recombinase/metabolism;Recombination, Genetic;Saccharomyces cerevisiae/genetics}, pages = {a012740}, volume = {5}, number = {11}, issn = {1943-0264}, journal = {Cold Spring Harbor perspectives in biology}, doi = {10.1101/cshperspect.a012740} } @article{JUERSETAL..2003, abstract = {The open-closed conformational switch in the active site of Escherichia coli beta-galactosidase was studied by X-ray crystallography and enzyme kinetics. Replacement of Gly794 by alanine causes the apoenzyme to adopt the closed rather than the open conformation. Binding of the competitive inhibitor isopropyl thio-beta-D-galactoside (IPTG) requires the mutant enzyme to adopt its less favored open conformation, weakening affinity relative to wild type. In contrast, transition-state inhibitors bind to the enzyme in the closed conformation, which is favored for the mutant, and display increased affinity relative to wild type. Changes in affinity suggest that the free energy difference between the closed and open forms is 1-2 kcal/mol. By favoring the closed conformation, the substitution moves the resting state of the enzyme along the reaction coordinate relative to the native enzyme and destabilizes the ground state relative to the first transition state. The result is that the rate constant for galactosylation is increased but degalactosylation is slower. The covalent intermediate may be better stabilized than the second transition state. The substitution also results in better binding of glucose to both the free and the galactosylated enzyme. However, transgalactosylation with glucose to produce allolactose (the inducer of the lac operon) is slower with the mutant than with the native enzyme. This suggests either that the glucose is misaligned for the reaction or that the galactosylated enzyme with glucose bound is stabilized relative to the transition state for transgalactosylation.}, author = {Juers, Douglas H. and Hakda, Shamina and Matthews, Brian W. and Huber, Reuben E.}, year = {2003}, title = {Structural basis for the altered activity of Gly794 variants of Escherichia coli beta-galactosidase}, pages = {13505--13511}, volume = {42}, number = {46}, issn = {0006-2960}, journal = {Biochemistry}, doi = {10.1021/bi035506j} } @article{JUNOPETAL..2000, abstract = {XRCC4 is essential for carrying out non-homologous DNA end joining (NHEJ) in all eukaryotes and, in particular, V(D)J recombination in vertebrates. Xrcc4 protein forms a complex with DNA ligase IV that rejoins two DNA ends in the last step of V(D)J recombination and NHEJ to repair double strand breaks. XRCC4-defective cells are extremely sensitive to ionizing radiation, and disruption of the XRCC4 gene results in embryonic lethality in mice. Here we report the crystal structure of a functional fragment of Xrcc4 at 2.7 A resolution. Xrcc4 protein forms a strikingly elongated dumb-bell-like tetramer. Each of the N-terminal globular head domains consists of a beta-sandwich and a potentially DNA-binding helix- turn-helix motif. The C-terminal stalk comprising a single alpha-helix {\textgreater}120 A in length is partly incorporated into a four-helix bundle in the Xrcc4 tetramer and partly involved in interacting with ligase IV. The Xrcc4 structure suggests a possible mode of coupling ligase IV association with DNA binding for effective ligation of DNA ends.}, author = {Junop, M. S. and Modesti, M. and Guarne, A. and Ghirlando, R. and Gellert, M. and Yang, W.}, year = {2000}, title = {Crystal structure of the Xrcc4 DNA repair protein and implications for end joining}, keywords = {0 (Bacterial Proteins);0 (Cell Cycle Proteins);0 (DNA-Binding Proteins);0 (DNL4 protein, S cerevisiae);0 (LIG4 protein, human);0 (Macromolecular Substances);0 (SMC protein, Bacteria);0 (XRCC4 protein, human);9007-49-2 (DNA);Amino Acid Sequence;Animals;Bacterial Proteins/chemistry;Binding Sites;Cell Cycle Proteins/chemistry;Crystallization;Crystallography, X-Ray;Dimerization;DNA Ligase ATP;DNA Ligases/chemistry/metabolism;DNA Repair;DNA/chemistry/metabolism;DNA-Binding Proteins/chemistry/genetics/metabolism;EC 6.5.1.- (DNA Ligases);EC 6.5.1.1 (DNA Ligase ATP);Humans;Macromolecular Substances;Mice;Models, Molecular;Molecular Sequence Data;Protein Structure, Quaternary;Saccharomyces cerevisiae/genetics;Sequence Homology, Amino Acid}, pages = {5962--5970}, volume = {19}, number = {22}, issn = {0261-4189}, journal = {The EMBO journal}, doi = {10.1093/emboj/19.22.5962} } @article{KIMETAL..2014, abstract = {Nature Reviews Genetics 15, 321 (2014). doi:10.1038/nrg3686}, author = {Kim, Hyongbum and Kim, Jin-Soo}, year = {2014}, title = {A guide to genome engineering with programmable nucleases}, keywords = {Animals;DNA Breaks, Double-Stranded;DNA Repair;EC 3.1.- (Endonucleases);Endonucleases/chemistry/metabolism;Genetic Engineering/methods;Genome;Humans;Mutagenesis, Site-Directed/methods;Translocation, Genetic/genetics;Zinc Fingers}, pages = {321--334}, volume = {15}, number = {5}, issn = {1471-0056}, journal = {Nature reviews. Genetics}, doi = {10.1038/nrg3686} } @article{KULKARNIETAL..2014, abstract = {Human cytomegalovirus (HCMV) is a ubiquitous pathogen capable of causing life threatening consequences in neonates and immune-compromised individuals. HCMV inflicts site-specific double strand breaks (DSBs) in the cellular genome. DNA damage infliction raises the corollary question of virus modulation of DNA repair. We recently reported HDR was stimulated in wt human foreskin fibroblasts (HFFs) during fully permissive infection or expression of the HCMV protein IE1-72 (IE72). These studies have been extended into semi-permissive T98G glioblastoma cells. T98Gs encode a mutant p53, which may contribute to their high baseline rate of HDR. We fully expected HCMV infection to increase HDR in T98Gs, similar to its effects in HFFs. Surprisingly in T98Gs HCMV infection, or sole expression of IE72, decreased HDR by two-fold. Transient expression of wt p53 in T98Gs also reduced HDR by two-fold. Dual transient expression of wt p53 and IE72 restored high baseline HDR levels. GST pulldown experiments revealed that both IE72 and wt p53 bound the important HDR protein, Rad51. We conclude that the expression of certain HCMV proteins can modulate HDR in an infected cell, dependent upon p53 status. We propose a model of the protein interactions explaining this behavior.}, author = {Kulkarni, Amit S. and Fortunato, Elizabeth A.}, year = {2014}, title = {Modulation of homology-directed repair in T98G glioblastoma cells due to interactions between wildtype p53, Rad51 and HCMV IE1-72}, keywords = {0 (IE1 protein, cytomegalovirus);0 (Immediate-Early Proteins);0 (Tumor Suppressor Protein p53);Cell Line, Tumor;Cytomegalovirus/growth {\&} development;DNA Repair;EC 2.7.7.- (RAD51 protein, human);EC 2.7.7.- (Rad51 Recombinase);homology directed repair;Host-Pathogen Interactions;human cytomegalovirus;Humans;IE72;Immediate-Early Proteins/metabolism;p53;Protein Binding;Rad51;Rad51 Recombinase/metabolism;Tumor Suppressor Protein p53/metabolism}, pages = {968--985}, volume = {6}, number = {3}, issn = {1999-4915}, journal = {Viruses}, doi = {10.3390/v6030968} } @article{LIETAL..2008, abstract = {Homologous recombination (HR) comprises a series of interrelated pathways that function in the repair of DNA double-stranded breaks (DSBs) and interstrand crosslinks (ICLs). In addition, recombination provides critical support for DNA replication in the recovery of stalled or broken replication forks, contributing to tolerance of DNA damage. A central core of proteins, most critically the RecA homolog Rad51, catalyzes the key reactions that typify HR: homology search and DNA strand invasion. The diverse functions of recombination are reflected in the need for context-specific factors that perform supplemental functions in conjunction with the core proteins. The inability to properly repair complex DNA damage and resolve DNA replication stress leads to genomic instability and contributes to cancer etiology. Mutations in the BRCA2 recombination gene cause predisposition to breast and ovarian cancer as well as Fanconi anemia, a cancer predisposition syndrome characterized by a defect in the repair of DNA interstrand crosslinks. The cellular functions of recombination are also germane to DNA-based treatment modalities of cancer, which target replicating cells by the direct or indirect induction of DNA lesions that are substrates for recombination pathways. This review focuses on mechanistic aspects of HR relating to DSB and ICL repair as well as replication fork support.}, author = {Li, Xuan and Heyer, Wolf-Dietrich}, year = {2008}, title = {Homologous recombination in DNA repair and DNA damage tolerance}, keywords = {9007-49-2 (DNA);Animals;Crossing Over, Genetic/physiology;DNA Breaks, Double-Stranded;DNA Damage/physiology;DNA Repair/genetics/physiology;DNA Replication/physiology;DNA/metabolism;EC 2.7.7.- (Rad51 Recombinase);Humans;Models, Biological;Mutagenesis/physiology;Protein Binding;Rad51 Recombinase/metabolism;Recombination, Genetic/physiology;Sequence Homology}, pages = {99--113}, volume = {18}, number = {1}, issn = {1001-0602}, journal = {Cell research}, doi = {10.1038/cr.2008.1} } @article{MAETAL..2012, abstract = {PALB2/FANCN is mutated in breast and pancreatic cancers and Fanconi anemia (FA). It controls the intranuclear localization, stability, and DNA repair function of BRCA2 and links BRCA1 and BRCA2 in DNA homologous recombination repair and breast cancer suppression. Here, we show that PALB2 directly interacts with KEAP1, an oxidative stress sensor that binds and represses the master antioxidant transcription factor NRF2. PALB2 shares with NRF2 a highly conserved ETGE-type KEAP1 binding motif and can effectively compete with NRF2 for KEAP1 binding. PALB2 promotes NRF2 accumulation and function in the nucleus and lowers the cellular reactive oxygen species (ROS) level. In addition, PALB2 also regulates the rate of NRF2 export from the nucleus following induction. Our findings identify PALB2 as a regulator of cellular redox homeostasis and provide a new link between oxidative stress and the development of cancer and FA.}, author = {Ma, Jianglin and Cai, Hong and Wu, Tongde and Sobhian, Bijan and Huo, Yanying and Alcivar, Allen and Mehta, Monal and Cheung, Ka Lung and Ganesan, Shridar and Kong, Ah-Ng Tony and Zhang, Donna D. and Xia, Bing}, year = {2012}, title = {PALB2 interacts with KEAP1 to promote NRF2 nuclear accumulation and function}, keywords = {0 (Intracellular Signaling Peptides and Proteins);0 (KEAP1 protein, human);0 (Kelch-Like ECH-Associated Protein 1);0 (NFE2L2 protein, human);0 (NF-E2-Related Factor 2);0 (Nuclear Proteins);0 (PALB2 protein, human);0 (Reactive Oxygen Species);0 (Tumor Suppressor Proteins);Cell Line, Tumor;Cell Nucleus/metabolism;Cell Transformation, Neoplastic;DNA Repair;Humans;Intracellular Signaling Peptides and Proteins/metabolism;Kelch-Like ECH-Associated Protein 1;Neoplasms/metabolism/pathology;NF-E2-Related Factor 2/metabolism;Nuclear Proteins/metabolism;Oxidation-Reduction;Oxidative Stress;Protein Binding;Reactive Oxygen Species/metabolism;Tumor Suppressor Proteins/metabolism}, pages = {1506--1517}, volume = {32}, number = {8}, issn = {0270-7306}, journal = {Molecular and cellular biology}, doi = {10.1128/MCB.06271-11} } @article{MENCHONETAL..2016, abstract = {srep , (2016). doi:10.1038/srep22878}, author = {Menchon, Gregory and Bombarde, Oriane and Trivedi, Mansi and Negrel, Aurelie and Inard, Cyril and Giudetti, Brigitte and Baltas, Michel and Milon, Alain and Modesti, Mauro and Czaplicki, Georges and Calsou, Patrick}, year = {2016}, title = {Structure-Based Virtual Ligand Screening on the XRCC4/DNA Ligase IV Interface}, keywords = {0 (DNA-Binding Proteins);0 (Ligands);0 (XRCC4 protein, human);9007-49-2 (DNA);Binding Sites;DNA Breaks, Double-Stranded;DNA Ligase ATP/chemistry/metabolism;DNA Repair;DNA/chemistry/metabolism;DNA-Binding Proteins/chemistry/metabolism;EC 6.5.1.1 (DNA Ligase ATP);Humans;Ligands;Models, Molecular;Molecular Conformation;Molecular Docking Simulation;Molecular Dynamics Simulation;Protein Binding;Protein Interaction Domains and Motifs;Reproducibility of Results;Structure-Activity Relationship}, pages = {22878}, volume = {6}, issn = {2045-2322}, journal = {Scientific reports}, doi = {10.1038/srep22878} } @article{MIYAOKAETAL..2016, abstract = {srep , (2016). doi:10.1038/srep23549}, author = {Miyaoka, Yuichiro and Berman, Jennifer R. and Cooper, Samantha B. and Mayerl, Steven J. and Chan, Amanda H. and Zhang, Bin and Karlin-Neumann, George A. and Conklin, Bruce R.}, year = {2016}, title = {Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing}, keywords = {Biological Assay;Cell Line;CRISPR-Cas Systems;DNA Breaks, Double-Stranded;DNA Breaks, Single-Stranded;DNA End-Joining Repair;EC 3.1.- (Transcription Activator-Like Effector Nucleases);Gene Editing;Genetic Loci;Genome, Human;HEK293 Cells;HeLa Cells;Humans;Induced Pluripotent Stem Cells/cytology/metabolism;Plasmids/chemistry/metabolism;Polymerase Chain Reaction;Recombinational DNA Repair;Transcription Activator-Like Effector Nucleases/genetics/metabolism;Transfection}, pages = {23549}, volume = {6}, issn = {2045-2322}, journal = {Scientific reports}, doi = {10.1038/srep23549} } @article{NICKMCELHINNYETAL..2000, author = {{Nick McElhinny}, S. A. and Snowden, C. M. and McCarville, J. and Ramsden, D. A.}, year = {2000}, title = {Ku Recruits the XRCC4-Ligase IV Complex to DNA Ends}, pages = {2996--3003}, volume = {20}, number = {9}, issn = {0270-7306}, journal = {Molecular and cellular biology}, doi = {10.1128/MCB.20.9.2996-3003.2000} } @article{NICKMCELHINNYETAL..2000b, author = {{Nick McElhinny}, S. A. and Snowden, C. M. and McCarville, J. and Ramsden, D. A.}, year = {2000}, title = {Ku Recruits the XRCC4-Ligase IV Complex to DNA Ends}, pages = {2996--3003}, volume = {20}, number = {9}, issn = {0270-7306}, journal = {Molecular and cellular biology}, doi = {10.1128/MCB.20.9.2996-3003.2000} } @article{NISHIMASUETAL..2014, abstract = {The CRISPR-associated endonuclease Cas9 can be targeted to specific genomic loci by single guide RNAs (sgRNAs). Here, we report the crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 A resolution. The structure revealed a bilobed architecture composed of target recognition and nuclease lobes, accommodating the sgRNA:DNA heteroduplex in a positively charged groove at their interface. Whereas the recognition lobe is essential for binding sgRNA and DNA, the nuclease lobe contains the HNH and RuvC nuclease domains, which are properly positioned for cleavage of the complementary and noncomplementary strands of the target DNA, respectively. The nuclease lobe also contains a carboxyl-terminal domain responsible for the interaction with the protospacer adjacent motif (PAM). This high-resolution structure and accompanying functional analyses have revealed the molecular mechanism of RNA-guided DNA targeting by Cas9, thus paving the way for the rational design of new, versatile genome-editing technologies.}, author = {Nishimasu, Hiroshi and Ran, F. Ann and Hsu, Patrick D. and Konermann, Silvana and Shehata, Soraya I. and Dohmae, Naoshi and Ishitani, Ryuichiro and Zhang, Feng and Nureki, Osamu}, year = {2014}, title = {Crystal structure of Cas9 in complex with guide RNA and target DNA}, keywords = {0 (CRISPR-Associated Proteins);0 (DNA, Bacterial);0 (RNA, Bacterial);0 (RNA, Guide);Amino Acid Sequence;Bacteria/enzymology;CRISPR-Associated Proteins/chemistry/metabolism;Crystallography, X-Ray;DNA, Bacterial/chemistry/metabolism;EC 3.1.- (Endonucleases);Endonucleases/chemistry/metabolism;Models, Molecular;Molecular Sequence Data;Protein Structure, Tertiary;RNA, Bacterial/chemistry/metabolism;RNA, Guide/chemistry/metabolism;Sequence Alignment;Streptococcus pyogenes/chemistry/enzymology/metabolism}, pages = {935--949}, volume = {156}, number = {5}, issn = {0092-8674}, journal = {Cell}, doi = {10.1016/j.cell.2014.02.001} } @article{ORTHWEINETAL..2015, abstract = {Nature 528, 422 (2015). doi:10.1038/nature16142}, author = {Orthwein, Alexandre and Noordermeer, Sylvie M. and Wilson, Marcus D. and Landry, Sebastien and Enchev, Radoslav I. and Sherker, Alana and Munro, Meagan and Pinder, Jordan and Salsman, Jayme and Dellaire, Graham and Xia, Bing and Peter, Matthias and Durocher, Daniel}, year = {2015}, title = {A mechanism for the suppression of homologous recombination in G1 cells}, keywords = {0 (BRCA1 Protein);0 (BRCA1 protein, human);0 (BRCA2 Protein);0 (BRCA2 protein, human);0 (Carrier Proteins);0 (CUL3 protein, human);0 (Cullin Proteins);0 (Intracellular Signaling Peptides and Proteins);0 (KEAP1 protein, human);0 (Kelch-Like ECH-Associated Protein 1);0 (Multiprotein Complexes);0 (Nuclear Proteins);0 (PALB2 protein, human);0 (RBX1 protein, human);0 (Tumor Suppressor Proteins);9007-49-2 (DNA);Amino Acid Sequence;BRCA1 Protein/metabolism;BRCA2 Protein/metabolism;Carrier Proteins/metabolism;Cell Line;CRISPR-Cas Systems/genetics;Cullin Proteins/metabolism;DNA Damage;DNA Repair;DNA/metabolism;EC 2.3.2.27 (Ubiquitin-Protein Ligases);EC 2.7.7.- (RAD51 protein, human);EC 2.7.7.- (Rad51 Recombinase);EC 3.1.2.- (Thiolester Hydrolases);EC 3.1.2.15 (USP11 protein, human);G1 Phase;G2 Phase;Gene Targeting;Homologous Recombination;Humans;Intracellular Signaling Peptides and Proteins/metabolism;Kelch-Like ECH-Associated Protein 1;Molecular Sequence Data;Multiprotein Complexes/chemistry/metabolism;Nuclear Proteins/chemistry/metabolism;Protein Binding;Rad51 Recombinase/metabolism;S Phase;Thiolester Hydrolases/metabolism;Tumor Suppressor Proteins/chemistry/metabolism;Ubiquitination;Ubiquitin-Protein Ligases/metabolism}, pages = {422--426}, volume = {528}, number = {7582}, issn = {0028-0836}, journal = {Nature}, doi = {10.1038/nature16142} } @article{PANIERETAL..2014, abstract = {Nature Reviews Molecular Cell Biology 15, 7 (2013). doi:10.1038/nrm3719}, author = {Panier, Stephanie and Boulton, Simon J.}, year = {2014}, title = {Double-strand break repair: 53BP1 comes into focus}, keywords = {0 (Chromatin);0 (Histones);0 (Intracellular Signaling Peptides and Proteins);0 (TP53BP1 protein, human);0 (Tumor Suppressor p53-Binding Protein 1);Animals;Chromatin/genetics/metabolism;DNA Breaks, Double-Stranded;DNA End-Joining Repair;DNA Repair;Histones/metabolism;Humans;Intracellular Signaling Peptides and Proteins/physiology;Protein Transport;Signal Transduction;Tumor Suppressor p53-Binding Protein 1}, pages = {7--18}, volume = {15}, number = {1}, issn = {1471-0072}, journal = {Nature reviews. Molecular cell biology}, doi = {10.1038/nrm3719} } @article{PAQUETETAL..2016, abstract = {Nature 533, 125 (2016). doi:10.1038/nature17664}, author = {Paquet, Dominik and Kwart, Dylan and Chen, Antonia and Sproul, Andrew and Jacob, Samson and Teo, Shaun and Olsen, Kimberly Moore and Gregg, Andrew and Noggle, Scott and Tessier-Lavigne, Marc}, year = {2016}, title = {Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9}, keywords = {0 (Amyloid beta-Protein Precursor);0 (Presenilins);0 (RNA, Guide);Adolescent;Age of Onset;Alleles;Alzheimer Disease/genetics;Amyloid beta-Protein Precursor/genetics/secretion;Animals;Base Sequence;CRISPR-Cas Systems/genetics;DNA Breaks, Double-Stranded;DNA Cleavage;DNA Repair/genetics;Female;Genes, Dominant/genetics;Genetic Association Studies;Genetic Engineering/methods;Heterozygote;Homozygote;Humans;Induced Pluripotent Stem Cells/metabolism;Male;Mice;Mutagenesis/genetics;Mutation/genetics;Presenilins/genetics;RNA, Guide/genetics;Sequence Homology;Substrate Specificity;Templates, Genetic}, pages = {125--129}, volume = {533}, number = {7601}, issn = {0028-0836}, journal = {Nature}, doi = {10.1038/nature17664} } @article{PAWELCZAKETAL..2011, abstract = {DNA double-strand breaks (DSB), particularly those induced by ionizing radiation (IR), are complex lesions that can be cytotoxic if not properly repaired. IR-induced DSB often have DNA termini modifications, including thymine glycols, ring fragmentation, 3'-phosphoglycolates, 5'-hydroxyl groups, and abasic sites. Nonhomologous end joining (NHEJ) is a major pathway responsible for the repair of these complex breaks. Proteins involved in NHEJ include the Ku 70/80 heterodimer, DNA-PKcs, processing proteins including Artemis and DNA polymerases mu and lambda, XRCC4, DNA ligase IV, and XLF. We will discuss the role of the physical and functional interactions of DNA-PK as a result of activation, with an emphasis on DNA structure, chemistry, and sequence. With the diversity of IR induced DSB, it is becoming increasingly clear that multiple DNA processing enzymes are likely necessary for effective repair of a break. We will explore the roles of several important processing enzymes, with a focus on the nuclease Artemis and its role in processing diverse DSB. The effect of DNA termini on both DNA-PK and Artemis activity will be analyzed from a structural and biochemical view.}, author = {Pawelczak, Katherine S. and Bennett, Sara M. and Turchi, John J.}, year = {2011}, title = {Coordination of DNA-PK activation and nuclease processing of DNA termini in NHEJ}, keywords = {0 (Antigens, Nuclear);0 (DCLRE1C protein, human);0 (DNA-Binding Proteins);0 (Nuclear Proteins);9007-49-2 (DNA);Antigens, Nuclear/genetics/metabolism;DNA Breaks, Double-Stranded;DNA Repair;DNA/genetics/metabolism;DNA-Activated Protein Kinase/genetics/metabolism;DNA-Binding Proteins/genetics/metabolism;EC 2.7.11.1 (DNA-Activated Protein Kinase);EC 3.1.- (Endonucleases);EC 3.6.4.12 (Xrcc6 protein, human);EC 4.2.99.- (Ku Autoantigen);Endonucleases/metabolism;Enzyme Activation;Ku Autoantigen;Nuclear Proteins/metabolism}, pages = {2531--2543}, volume = {14}, number = {12}, issn = {1523-0864}, journal = {Antioxidants {\&} redox signaling}, doi = {10.1089/ars.2010.3368} } @article{QIETAL..2013, abstract = {Targeted gene regulation on a genome-wide scale is~a powerful strategy for interrogating, perturbing, and engineering cellular systems. Here, we develop a method for controlling gene expression based on Cas9, an RNA-guided DNA endonuclease from a type II CRISPR system. We show that a catalytically dead Cas9 lacking endonuclease activity, when coexpressed with a guide RNA, generates a DNA recognition complex that can specifically interfere with transcriptional elongation, RNA polymerase binding, or transcription factor binding. This system, which we call CRISPR interference (CRISPRi), can efficiently repress expression of targeted genes in Escherichia coli, with no detectable off-target effects. CRISPRi can be used to repress multiple target genes simultaneously, and its effects are reversible. We also show evidence that the system can be adapted for gene repression in mammalian cells. This RNA-guided DNA recognition platform provides a simple approach for selectively perturbing gene expression on a genome-wide scale.}, author = {Qi, Lei S. and Larson, Matthew H. and Gilbert, Luke A. and Doudna, Jennifer A. and Weissman, Jonathan S. and Arkin, Adam P. and Lim, Wendell A.}, year = {2013}, title = {Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression}, pages = {1173--1183}, volume = {152}, number = {5}, issn = {0092-8674}, journal = {Cell}, doi = {10.1016/j.cell.2013.02.022} } @article{QUINNETAL..2016, abstract = {Nature Reviews Genetics 17, 47 (2015). doi:10.1038/nrg.2015.10}, author = {Quinn, Jeffrey J. and Chang, Howard Y.}, year = {2016}, title = {Unique features of long non-coding RNA biogenesis and function}, keywords = {0 (Chromatin);0 (RNA, Long Noncoding);Animals;Chromatin/genetics/metabolism;Gene Expression;Gene Expression Regulation;Genomic Imprinting;Humans;RNA Processing, Post-Transcriptional;RNA Stability;RNA Transport;RNA, Long Noncoding/biosynthesis/genetics}, pages = {47--62}, volume = {17}, number = {1}, issn = {1471-0056}, journal = {Nature reviews. Genetics}, doi = {10.1038/nrg.2015.10} } @article{RANETAL..2013, abstract = {Targeted nucleases are powerful tools for mediating genome alteration with high precision. The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA. Here we describe a set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells, as well as generation of modified cell lines for downstream functional studies. To minimize off-target cleavage, we further describe a double-nicking strategy using the Cas9 nickase mutant with paired guide RNAs. This protocol provides experimentally derived guidelines for the selection of target sites, evaluation of cleavage efficiency and analysis of off-target activity. Beginning with target design, gene modifications can be achieved within as little as 1-2 weeks, and modified clonal cell lines can be derived within 2-3 weeks.}, author = {Ran, F. Ann and Hsu, Patrick D. and Wright, Jason and Agarwala, Vineeta and Scott, David A. and Zhang, Feng}, year = {2013}, title = {Genome engineering using the CRISPR-Cas9 system}, keywords = {Base Sequence;Cell Culture Techniques;Cell Line;Clustered Regularly Interspaced Short Palindromic Repeats;Deoxyribonucleases/chemistry/genetics;DNA End-Joining Repair;DNA Mutational Analysis;DNA Repair;EC 3.1.- (Deoxyribonucleases);Genetic Engineering/methods;Genome;Genotyping Techniques;HEK293 Cells;Humans;Molecular Sequence Data;Mutagenesis;Transfection}, pages = {2281--2308}, volume = {8}, number = {11}, issn = {1750-2799}, journal = {Nature protocols}, doi = {10.1038/nprot.2013.143} } @article{ROBERTETAL..2015, abstract = {Genome Medicine, 2015, doi:10.1186/s13073-015-0215-6}, author = {Robert, Francis and Barbeau, Mathilde and Ethier, Sylvain and Dostie, Josee and Pelletier, Jerry}, year = {2015}, title = {Pharmacological inhibition of DNA-PK stimulates Cas9-mediated genome editing}, keywords = {0 (2-(4-ethylpiperazin-1-yl)-N-(4-(2-morpholino-4-oxo-4H-chromen-8-yl)dibenzo(b,d)t hiophen-1-yl)acetamide);0 (8-dibenzothiophen-4-yl-2-morpholin-4-yl-chromen-4-one);0 (Chromones);0 (Morpholines);0 (Nuclear Proteins);0 (Protein Kinase Inhibitors);0 (Thiophenes);Animals;Cell Line;Chromones/pharmacology;CRISPR-Cas Systems;DNA-Activated Protein Kinase/antagonists {\&} inhibitors;EC 2.7.11.1 (DNA-Activated Protein Kinase);EC 2.7.11.1 (PRKDC protein, human);HEK293 Cells;Humans;Mice;Morpholines/pharmacology;Nuclear Proteins/antagonists {\&} inhibitors;Protein Kinase Inhibitors/pharmacology;Thiophenes/pharmacology}, pages = {93}, volume = {7}, issn = {1756-994X}, journal = {Genome medicine}, doi = {10.1186/s13073-015-0215-6} } @article{SAHAETAL..2016, abstract = {Heritable mutations in the tumor suppressor gene BRCA1 increase a woman's lifetime risk of developing breast and ovarian cancer. BRCA1's tumor suppressor function is directly linked to its myriad of functions in the cellular response to DNA double-strand breaks (DSBs). BRCA1 interacts with an extensive array of DNA damage responsive proteins and plays important roles in DSB repair, mediated by the homologous recombination pathway, and in the activation of cell cycle checkpoints. However, the role of BRCA1 in the other two DSB repair pathways, classical non-homologous end-joining (C-NHEJ) and alternative NHEJ (A-NHEJ), remains unclear. In this review, we will discuss the current literature on BRCA1's potential role(s) in modulating both C-NHEJ and A-NHEJ. We also present a model showing that BRCA1 contributes to genomic maintenance by promoting precise DNA repair across all cell cycle phases via the direct modulation of DNA end-joining.}, author = {Saha, Janapriya and Davis, Anthony J.}, year = {2016}, title = {Unsolved mystery: the role of BRCA1 in DNA end-joining}, pages = {i18-i24}, volume = {57 Suppl 1}, issn = {0449-3060}, journal = {Journal of radiation research}, doi = {10.1093/jrr/rrw032} } @article{SARTORIETAL..2007, abstract = {In the S and G2 phases of the cell cycle, DNA double-strand breaks (DSBs) are processed into single-stranded DNA, triggering ATR-dependent checkpoint signalling and DSB repair by homologous recombination. Previous work has implicated the MRE11 complex in such DSB-processing events. Here, we show that the human CtIP (RBBP8) protein confers resistance to DSB-inducing agents and is recruited to DSBs exclusively in the S and G2 cell-cycle phases. Moreover, we reveal that CtIP is required for DSB resection, and thereby for recruitment of replication protein A (RPA) and the protein kinase ATR to DSBs, and for the ensuing ATR activation. Furthermore, we establish that CtIP physically and functionally interacts with the MRE11 complex, and that both CtIP and MRE11 are required for efficient homologous recombination. Finally, we reveal that CtIP has sequence homology with Sae2, which is involved in MRE11-dependent DSB processing in yeast. These findings establish evolutionarily conserved roles for CtIP-like proteins in controlling DSB resection, checkpoint signalling and homologous recombination.}, author = {Sartori, Alessandro A. and Lukas, Claudia and Coates, Julia and Mistrik, Martin and Fu, Shuang and Bartek, Jiri and Baer, Richard and Lukas, Jiri and Jackson, Stephen P.}, year = {2007}, title = {Human CtIP promotes DNA end resection}, keywords = {0 (Carrier Proteins);0 (Cell Cycle Proteins);0 (DNA, Single-Stranded);0 (DNA-Binding Proteins);0 (MRE11A protein, human);0 (Nuclear Proteins);0 (RBBP8 protein, human);0 (Saccharomyces cerevisiae Proteins);0 (SAE2 protein, S cerevisiae);9007-49-2 (DNA);Ataxia Telangiectasia Mutated Proteins;Carrier Proteins/genetics/metabolism;Cell Cycle Proteins/metabolism;Cell Line, Tumor;Conserved Sequence;DNA Breaks, Double-Stranded/drug effects;DNA Repair/drug effects;DNA, Single-Stranded/metabolism;DNA/metabolism;DNA-Binding Proteins/metabolism;EC 2.7.11.1 (Ataxia Telangiectasia Mutated Proteins);EC 2.7.11.1 (ATR protein, human);EC 2.7.11.1 (Protein-Serine-Threonine Kinases);EC 3.1.- (Endonucleases);Endonucleases;Evolution, Molecular;G2 Phase;Humans;Nuclear Proteins/deficiency/genetics/metabolism;Protein-Serine-Threonine Kinases/metabolism;Recombination, Genetic/drug effects;S Phase;Saccharomyces cerevisiae Proteins/chemistry}, pages = {509--514}, volume = {450}, number = {7169}, issn = {0028-0836}, journal = {Nature}, doi = {10.1038/nature06337} } @article{SHRIVASTAVETAL..2008, abstract = {DNA double-strand breaks (DSBs) are critical lesions that can result in cell death or a wide variety of genetic alterations including large- or small-scale deletions, loss of heterozygosity, translocations, and chromosome loss. DSBs are repaired by non-homologous end-joining (NHEJ) and homologous recombination (HR), and defects in these pathways cause genome instability and promote tumorigenesis. DSBs arise from endogenous sources including reactive oxygen species generated during cellular metabolism, collapsed replication forks, and nucleases, and from exogenous sources including ionizing radiation and chemicals that directly or indirectly damage DNA and are commonly used in cancer therapy. The DSB repair pathways appear to compete for DSBs, but the balance between them differs widely among species, between different cell types of a single species, and during different cell cycle phases of a single cell type. Here we review the regulatory factors that regulate DSB repair by NHEJ and HR in yeast and higher eukaryotes. These factors include regulated expression and phosphorylation of repair proteins, chromatin modulation of repair factor accessibility, and the availability of homologous repair templates. While most DSB repair proteins appear to function exclusively in NHEJ or HR, a number of proteins influence both pathways, including the MRE11/RAD50/NBS1(XRS2) complex, BRCA1, histone H2AX, PARP-1, RAD18, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and ATM. DNA-PKcs plays a role in mammalian NHEJ, but it also influences HR through a complex regulatory network that may involve crosstalk with ATM, and the regulation of at least 12 proteins involved in HR that are phosphorylated by DNA-PKcs and/or ATM.}, author = {Shrivastav, Meena and de Haro, Leyma P. and Nickoloff, Jac A.}, year = {2008}, title = {Regulation of DNA double-strand break repair pathway choice}, keywords = {0 (Cell Cycle Proteins);0 (DNA-Binding Proteins);0 (Nuclear Proteins);0 (Tumor Suppressor Proteins);Animals;Ataxia Telangiectasia Mutated Proteins;Cell Cycle Proteins/physiology;Cell Cycle/genetics/physiology;Chromosome Aberrations;DNA Breaks, Double-Stranded;DNA Repair/physiology;DNA-Activated Protein Kinase/physiology;DNA-Binding Proteins/physiology;EC 2.7.11.1 (Ataxia Telangiectasia Mutated Proteins);EC 2.7.11.1 (ATM protein, human);EC 2.7.11.1 (DNA-Activated Protein Kinase);EC 2.7.11.1 (PRKDC protein, human);EC 2.7.11.1 (Protein-Serine-Threonine Kinases);Eukaryotic Cells/metabolism;Genomic Instability;Humans;Models, Biological;Nuclear Proteins/physiology;Protein-Serine-Threonine Kinases/physiology;Recombination, Genetic/physiology;Signal Transduction/genetics;Species Specificity;Tumor Suppressor Proteins/physiology;Yeasts/genetics}, pages = {134--147}, volume = {18}, number = {1}, issn = {1001-0602}, journal = {Cell research}, doi = {10.1038/cr.2007.111} } @article{SIBANDAETAL..2001, abstract = {A complex of two proteins, Xrcc4 and DNA ligase IV, plays a fundamental role in DNA non-homologous end joining (NHEJ), a cellular function required for double-strand break repair and V(D)J recombination. Here we report the crystal structure of human Xrcc4 bound to a polypeptide that corresponds to the DNA ligase IV sequence linking its two BRCA1 C-terminal (BRCT) domains. In the complex, a single ligase chain binds asymmetrically to an Xrcc4 dimer. The helical tails of Xrcc4 undergo a substantial conformational change relative to the uncomplexed protein, forming a coiled coil that unwinds upon ligase binding, leading to a flat interaction surface. A buried network of charged hydrogen bonds surrounded by extensive hydrophobic contacts explains the observed tightness of the interaction. The strong conservation of residues at the interface between the two proteins provides evidence that the observed mode of interaction has been maintained in NHEJ throughout evolution.}, author = {Sibanda, B. L. and Critchlow, S. E. and Begun, J. and Pei, X. Y. and Jackson, S. P. and Blundell, T. L. and Pellegrini, L.}, year = {2001}, title = {Crystal structure of an Xrcc4-DNA ligase IV complex}, keywords = {0 (DNA-Binding Proteins);0 (LIG4 protein, human);0 (Macromolecular Substances);0 (XRCC4 protein, human);Amino Acid Sequence;Binding Sites;Crystallography, X-Ray;Dimerization;DNA Ligase ATP;DNA Ligases/chemistry/metabolism;DNA-Binding Proteins/chemistry/metabolism;EC 6.5.1.- (DNA Ligases);EC 6.5.1.1 (DNA Ligase ATP);Humans;Hydrogen Bonding;Macromolecular Substances;Models, Molecular;Molecular Sequence Data;Protein Binding;Protein Structure, Quaternary;Protein Structure, Secondary;Protein Structure, Tertiary;Sequence Alignment;Static Electricity}, pages = {1015--1019}, volume = {8}, number = {12}, issn = {1072-8368}, journal = {Nature structural biology}, doi = {10.1038/nsb725} } @article{SUETAL..2016, abstract = {During DNA double-strand break and replication fork repair by homologous recombination, the RAD51 recombinase catalyzes the DNA strand exchange reaction via a helical polymer assembled on single-stranded DNA, termed the presynaptic filament. Our published work has demonstrated a dual function of the SWI5-SFR1 complex in RAD51-mediated DNA strand exchange, namely, by stabilizing the presynaptic filament and maintaining the catalytically active ATP-bound state of the filament via enhancement of ADP release. In this study, we have strived to determine the basis for physical and functional interactions between Mus musculus SWI5-SFR1 and RAD51. We found that SWI5-SFR1 preferentially associates with the oligomeric form of RAD51. Specifically, a C-terminal domain within SWI5 contributes to RAD51 interaction. With specific RAD51 interaction defective mutants of SWI5-SFR1 that we have isolated, we show that the physical interaction is indispensable for the stimulation of the recombinase activity of RAD51. Our results thus help establish the functional relevance of the trimeric RAD51-SWI5-SFR1 complex and provide insights into the mechanistic underpinnings of homology-directed DNA repair in mammalian cells.}, author = {Su, Guan-Chin and Yeh, Hsin-Yi and Lin, Sheng-Wei and Chung, Chan-I and Huang, Yu-Shan and Liu, Yi-Chung and Lyu, Ping-Chiang and Chi, Peter}, year = {2016}, title = {Role of the RAD51-SWI5-SFR1 Ensemble in homologous recombination}, pages = {6242--6251}, volume = {44}, number = {13}, issn = {0305-1048}, journal = {Nucleic acids research}, doi = {10.1093/nar/gkw375} } @article{TAGUCHIETAL..2011, abstract = {The Keap1-Nrf2 regulatory pathway plays a central role in the protection of cells against oxidative and xenobiotic damage. Under unstressed conditions, Nrf2 is constantly ubiquitinated by the Cul3-Keap1 ubiquitin E3 ligase complex and rapidly degraded in proteasomes. Upon exposure to electrophilic and oxidative stresses, reactive cysteine residues of Keap1 become modified, leading to a decline in the E3 ligase activity, stabilization of Nrf2 and robust induction of a battery of cytoprotective genes. Biochemical and structural analyses have revealed that the intact Keap1 homodimer forms a cherry-bob structure in which one molecule of Nrf2 associates with two molecules of Keap1 by using two binding sites within the Neh2 domain of Nrf2. This two-site binding appears critical for Nrf2 ubiquitination. In many human cancers, missense mutations in KEAP1 and NRF2 genes have been identified. These mutations disrupt the Keap1-Nrf2 complex activity involved in ubiquitination and degradation of Nrf2 and result in constitutive activation of Nrf2. Elevated expression of Nrf2 target genes confers advantages in terms of stress resistance and cell proliferation in normal and cancer cells. Discovery and development of selective Nrf2 inhibitors should make a critical contribution to improved cancer therapy.}, author = {Taguchi, Keiko and Motohashi, Hozumi and Yamamoto, Masayuki}, year = {2011}, title = {Molecular mechanisms of the Keap1-Nrf2 pathway in stress response and cancer evolution}, keywords = {0 (Antineoplastic Agents);0 (Intracellular Signaling Peptides and Proteins);0 (KEAP1 protein, human);0 (Kelch-Like ECH-Associated Protein 1);0 (NFE2L2 protein, human);0 (NF-E2-Related Factor 2);0 (Xenobiotics);Animals;Antineoplastic Agents/chemistry/therapeutic use;Drug Discovery;EC 2.3.2.27 (Ubiquitin-Protein Ligases);EC 3.4.25.1 (Proteasome Endopeptidase Complex);Humans;Intracellular Signaling Peptides and Proteins/genetics/metabolism;Kelch-Like ECH-Associated Protein 1;Mice;Mutation, Missense;Neoplasms/drug therapy/genetics/metabolism;NF-E2-Related Factor 2/antagonists {\&} inhibitors/genetics/metabolism;Oxidative Stress;Proteasome Endopeptidase Complex/metabolism;Protein Binding;Protein Structure, Tertiary;Signal Transduction;Ubiquitination;Ubiquitin-Protein Ligases/metabolism;Xenobiotics/toxicity}, pages = {123--140}, volume = {16}, number = {2}, issn = {1356-9597}, journal = {Genes to cells : devoted to molecular {\&} cellular mechanisms}, doi = {10.1111/j.1365-2443.2010.01473.x} } @article{THOMSONETAL..2010, abstract = {The repair of lesions and gaps in DNA follows different pathways, each mediated by specific proteins and complexes. Post-translational modifications in many of these proteins govern their activities and interactions, ultimately determining whether a particular pathway is followed. Prominent among these modifications are the addition of phosphate or ubiquitin (and ubiquitin-like) moieties that confer new binding surfaces and conformational states on the modified proteins. The present review summarizes some of consequences of ubiquitin and ubiquitin-like modifications and interactions that regulate nucleotide excision repair, translesion synthesis, double-strand break repair and interstrand cross-link repair, with the discussion of relevant examples in each pathway.}, author = {Thomson, Timothy M. and Guerra-Rebollo, Marta}, year = {2010}, title = {Ubiquitin and SUMO signalling in DNA repair}, keywords = {0 (BRCA1 Protein);0 (Cullin Proteins);0 (DNA-Binding Proteins);0 (Multiprotein Complexes);0 (Proliferating Cell Nuclear Antigen);0 (Small Ubiquitin-Related Modifier Proteins);0 (Ubiquitin);Animals;BRCA1 Protein/genetics/metabolism;Cullin Proteins/metabolism;DNA Breaks, Double-Stranded;DNA Repair;DNA Repair Enzymes/metabolism;DNA-Binding Proteins/metabolism;EC 6.5.1.- (DNA Repair Enzymes);Fanconi Anemia/genetics/physiopathology;Genes, cdc;Humans;Multiprotein Complexes/metabolism;Phosphorylation;Proliferating Cell Nuclear Antigen/metabolism;Signal Transduction/physiology;Small Ubiquitin-Related Modifier Proteins/metabolism;Ubiquitin/metabolism;Ubiquitination}, pages = {116--131}, volume = {38}, number = {Pt 1}, issn = {0300-5127}, journal = {Biochemical Society transactions}, doi = {10.1042/BST0380116} } @article{TRUONGETAL..2015, abstract = {Using CRISPR/Cas9, it is possible to target virtually any gene in any organism. A major limitation to its application in gene therapy is the size of Cas9 ({\textgreater}4 kb), impeding its efficient delivery via recombinant adeno-associated virus (rAAV). Therefore, we developed a split-Cas9 system, bypassing the packaging limit using split-inteins. Each Cas9 half was fused to the corresponding split-intein moiety and, only upon co-expression, the intein-mediated trans-splicing occurs and the full Cas9 protein is reconstituted. We demonstrated that the nuclease activity of our split-intein system is comparable to wild-type Cas9, shown by a genome-integrated surrogate reporter and by targeting three different endogenous genes. An analogously designed split-Cas9D10A nickase version showed similar activity as Cas9D10A. Moreover, we showed that the double nick strategy increased the homologous directed recombination (HDR). In addition, we explored the possibility of delivering the repair template accommodated on the same dual-plasmid system, by transient transfection, showing an efficient HDR. Most importantly, we revealed for the first time that intein-mediated split-Cas9 can be packaged, delivered and its nuclease activity reconstituted efficiently, in cells via rAAV.}, author = {Truong, Dong-Jiunn Jeffery and Kuhner, Karin and Kuhn, Ralf and Werfel, Stanislas and Engelhardt, Stefan and Wurst, Wolfgang and Ortiz, Oskar}, year = {2015}, title = {Development of an intein-mediated split-Cas9 system for gene therapy}, keywords = {0 (CRISPR-Associated Proteins);Cell Line;CRISPR-Associated Proteins/genetics;CRISPR-Cas Systems;Deoxyribonucleases/genetics;Dependovirus/genetics;EC 3.1.- (Deoxyribonucleases);Gene Targeting;Genetic Therapy/methods;Humans;Inteins;Plasmids/genetics;Streptococcus pyogenes/enzymology;Transfection}, pages = {6450--6458}, volume = {43}, number = {13}, issn = {0305-1048}, journal = {Nucleic acids research}, doi = {10.1093/nar/gkv601} } @article{TSAIETAL..2016, abstract = {Nature Reviews Genetics 17, 300 (2016). doi:10.1038/nrg.2016.28}, author = {Tsai, Shengdar Q. and Joung, J. Keith}, year = {2016}, title = {Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases}, keywords = {9007-49-2 (DNA);CRISPR-Cas Systems/genetics;DNA/genetics;EC 3.1.- (Endonucleases);Endonucleases/metabolism;Genetic Engineering;Genome, Human;Humans}, pages = {300--312}, volume = {17}, number = {5}, issn = {1471-0056}, journal = {Nature reviews. Genetics}, doi = {10.1038/nrg.2016.28} } @article{TSAIETAL..2016b, abstract = {Nature Reviews Genetics 17, 300 (2016). doi:10.1038/nrg.2016.28}, author = {Tsai, Shengdar Q. and Joung, J. Keith}, year = {2016}, title = {Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases}, keywords = {9007-49-2 (DNA);CRISPR-Cas Systems/genetics;DNA/genetics;EC 3.1.- (Endonucleases);Endonucleases/metabolism;Genetic Engineering;Genome, Human;Humans}, pages = {300--312}, volume = {17}, number = {5}, issn = {1471-0056}, journal = {Nature reviews. Genetics}, doi = {10.1038/nrg.2016.28} } @article{VANCHUETAL..2015, abstract = {The insertion of precise genetic modifications by genome editing tools such as CRISPR-Cas9 is limited by the relatively low efficiency of homology-directed repair (HDR) compared with the higher efficiency of the nonhomologous end-joining (NHEJ) pathway. To enhance HDR, enabling the insertion of precise genetic modifications, we suppressed the NHEJ key molecules KU70, KU80 or DNA ligase IV by gene silencing, the ligase IV inhibitor SCR7 or the coexpression of adenovirus 4 E1B55K and E4orf6 proteins in a 'traffic light' and other reporter systems. Suppression of KU70 and DNA ligase IV promotes the efficiency of HDR 4-5-fold. When co-expressed with the Cas9 system, E1B55K and E4orf6 improved the efficiency of HDR up to eightfold and essentially abolished NHEJ activity in both human and mouse cell lines. Our findings provide useful tools to improve the frequency of precise gene modifications in mammalian cells.}, author = {{van Chu}, Trung and Weber, Timm and Wefers, Benedikt and Wurst, Wolfgang and Sander, Sandrine and Rajewsky, Klaus and Kuhn, Ralf}, year = {2015}, title = {Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells}, keywords = {0 (Adenovirus E4 Proteins);0 (E1B55K protein, adenovirus);0 (E4orf6 protein, adenovirus);0 (LIG4 protein, human);0 (Viral Proteins);Adenoviridae/genetics;Adenovirus E4 Proteins/biosynthesis/genetics;Animals;Cell Line;CRISPR-Cas Systems/genetics;DNA Breaks, Double-Stranded;DNA End-Joining Repair/genetics;DNA Ligase ATP;DNA Ligases/genetics;EC 6.5.1.- (DNA Ligases);EC 6.5.1.1 (DNA Ligase ATP);Gene Expression Regulation;Genetic Engineering/methods;Genome, Human;Homologous Recombination/genetics;Humans;Mice;Viral Proteins/biosynthesis/genetics}, pages = {543--548}, volume = {33}, number = {5}, issn = {1087-0156}, journal = {Nature biotechnology}, doi = {10.1038/nbt.3198} } @article{WANGETAL..2013, abstract = {CtIP plays an important role in homologous recombination (HR)-mediated DNA double-stranded break (DSB) repair and interacts with Nbs1 and BRCA1, which are linked to Nijmegen breakage syndrome (NBS) and familial breast cancer, respectively. We identified new CDK phosphorylation sites on CtIP and found that phosphorylation of these newly identified CDK sites induces association of CtIP with the N-terminus FHA and BRCT domains of Nbs1. We further showed that these CDK-dependent phosphorylation events are a prerequisite for ATM to phosphorylate CtIP upon DNA damage, which is important for end resection to activate HR by promoting recruitment of BLM and Exo1 to DSBs. Most notably, this CDK-dependent CtIP and Nbs1 interaction facilitates ATM to phosphorylate CtIP in a substrate-specific manner. These studies reveal one important mechanism to regulate cell-cycle-dependent activation of HR upon DNA damage by coupling CDK- and ATM-mediated phosphorylation of CtIP through modulating the interaction of CtIP with Nbs1, which significantly helps to understand how DSB repair is regulated in mammalian cells to maintain genome stability.}, author = {Wang, Hailong and Shi, Linda Z. and Wong, Catherine C. L. and Han, Xuemei and Hwang, Patty Yi-Hwa and Truong, Lan N. and Zhu, Qingyuan and Shao, Zhengping and Chen, David J. and Berns, Michael W. and Yates, John R. 3rd and Chen, Longchuan and Wu, Xiaohua}, year = {2013}, title = {The interaction of CtIP and Nbs1 connects CDK and ATM to regulate HR-mediated double-strand break repair}, keywords = {0 (BRCA1 Protein);0 (BRCA1 protein, human);0 (Carrier Proteins);0 (Cell Cycle Proteins);0 (DNA-Binding Proteins);0 (NBN protein, human);0 (Nuclear Proteins);0 (RBBP8 protein, human);0 (Tumor Suppressor Proteins);Ataxia Telangiectasia Mutated Proteins;BRCA1 Protein/genetics/metabolism;Carrier Proteins/genetics/metabolism;Cell Cycle Proteins/genetics/metabolism;Cell Cycle/genetics;Cyclin-Dependent Kinases/genetics;DNA Breaks, Double-Stranded;DNA Repair/genetics;DNA-Binding Proteins/genetics/metabolism;EC 2.7.11.1 (Ataxia Telangiectasia Mutated Proteins);EC 2.7.11.1 (ATM protein, human);EC 2.7.11.1 (Protein-Serine-Threonine Kinases);EC 2.7.11.22 (Cyclin-Dependent Kinases);Genomic Instability;HEK293 Cells;HeLa Cells;Homologous Recombination;Humans;Nuclear Proteins/genetics/metabolism;Phosphorylation;Protein-Serine-Threonine Kinases/genetics/metabolism;Tumor Suppressor Proteins/genetics/metabolism}, pages = {e1003277}, volume = {9}, number = {2}, issn = {1553-7390}, journal = {PLoS genetics}, doi = {10.1371/journal.pgen.1003277} } @article{WETERINGSETAL..2008, abstract = {DNA double-strand breaks (DSBs) are introduced in cells by ionizing radiation and reactive oxygen species. In addition, they are commonly generated during V(D)J recombination, an essential aspect of the developing immune system. Failure to effectively repair these DSBs can result in chromosome breakage, cell death, onset of cancer, and defects in the immune system of higher vertebrates. Fortunately, all mammalian cells possess two enzymatic pathways that mediate the repair of DSBs: homologous recombination and non-homologous end-joining (NHEJ). The NHEJ process utilizes enzymes that capture both ends of the broken DNA molecule, bring them together in a synaptic DNA-protein complex, and finally repair the DNA break. In this review, all the known enzymes that play a role in the NHEJ process are discussed and a working model for the co-operation of these enzymes during DSB repair is presented.}, author = {Weterings, Eric and Chen, David J.}, year = {2008}, title = {The endless tale of non-homologous end-joining}, keywords = {Animals;DNA Breaks, Double-Stranded;DNA Repair/physiology;Gene Rearrangement/immunology/physiology;Humans;Models, Biological;Recombination, Genetic/immunology;VDJ Exons/genetics}, pages = {114--124}, volume = {18}, number = {1}, issn = {1001-0602}, journal = {Cell research}, doi = {10.1038/cr.2008.3} } @article{WIEDENHEFTETAL..2012, abstract = {Clustered regularly interspaced short palindromic repeat (CRISPR) are essential components of nucleic-acid-based adaptive immune systems that are widespread in bacteria and archaea. Similar to RNA interference (RNAi) pathways in eukaryotes, CRISPR-mediated immune systems rely on small RNAs for sequence-specific detection and silencing of foreign nucleic acids, including viruses and plasmids. However, the mechanism of RNA-based bacterial immunity is distinct from RNAi. Understanding how small RNAs are used to find and destroy foreign nucleic acids will provide new insights into the diverse mechanisms of RNA-controlled genetic silencing systems.}, author = {Wiedenheft, Blake and Sternberg, Samuel H. and Doudna, Jennifer A.}, year = {2012}, title = {RNA-guided genetic silencing systems in bacteria and archaea}, keywords = {0 (RNA, Archaeal);0 (RNA, Bacterial);Archaea/genetics;Bacteria/genetics;Gene Expression Regulation, Bacterial;Gene Silencing;Models, Molecular;RNA Interference;RNA, Archaeal/biosynthesis/chemistry/genetics/metabolism;RNA, Bacterial/biosynthesis/chemistry/genetics/metabolism}, pages = {331--338}, volume = {482}, number = {7385}, issn = {0028-0836}, journal = {Nature}, doi = {10.1038/nature10886} } @article{WIJSHAKEETAL..2014, abstract = {Mouse transgenesis has been instrumental in determining the function of genes in the pathophysiology of human diseases and modification of genes by homologous recombination in mouse embryonic stem cells remains a widely used technology. However, this approach harbors a number of disadvantages, as it is time-consuming and quite laborious. Over the last decade a number of new genome editing technologies have been developed, including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas). These systems are characterized by a designed DNA binding protein or RNA sequence fused or co-expressed with a non-specific endonuclease, respectively. The engineered DNA binding protein or RNA sequence guides the nuclease to a specific target sequence in the genome to induce a double strand break. The subsequent activation of the DNA repair machinery then enables the introduction of gene modifications at the target site, such as gene disruption, correction or insertion. Nuclease-mediated genome editing has numerous advantages over conventional gene targeting, including increased efficiency in gene editing, reduced generation time of mutant mice, and the ability to mutagenize multiple genes simultaneously. Although nuclease-driven modifications in the genome are a powerful tool to generate mutant mice, there are concerns about off-target cleavage, especially when using the CRISPR/Cas system. Here, we describe the basic principles of these new strategies in mouse genome manipulation, their inherent advantages, and their potential disadvantages compared to current technologies used to study gene function in mouse models. This article is part of a Special Issue entitled: From Genome to Function.}, author = {Wijshake, Tobias and Baker, Darren J. and {van de Sluis}, Bart}, year = {2014}, title = {Endonucleases: new tools to edit the mouse genome}, pages = {1942--1950}, volume = {1842}, number = {10}, issn = {0006-3002}, journal = {Biochimica et biophysica acta}, doi = {10.1016/j.bbadis.2014.04.020} } @article{WUETAL..2009, abstract = {Nonhomologous end-joining represents the major pathway used by human cells to repair DNA double-strand breaks. It relies on the XRCC4/DNA ligase IV complex to reseal DNA strands. Here we report the high-resolution crystal structure of human XRCC4 bound to the carboxy-terminal tandem BRCT repeat of DNA ligase IV. The structure differs from the homologous Saccharomyces cerevisiae complex and reveals an extensive DNA ligase IV binding interface formed by a helix-loop-helix structure within the inter-BRCT linker region, as well as significant interactions involving the second BRCT domain, which induces a kink in the tail region of XRCC4. We further demonstrate that interaction with the second BRCT domain of DNA ligase IV is necessary for stable binding to XRCC4 in cells, as well as to achieve efficient dominant-negative effects resulting in radiosensitization after ectopic overexpression of DNA ligase IV fragments in human fibroblasts. Together our findings provide unanticipated insight for understanding the physical and functional architecture of the nonhomologous end-joining ligation complex.}, author = {Wu, Pei-Yu and Frit, Philippe and Meesala, SriLakshmi and Dauvillier, Stephanie and Modesti, Mauro and Andres, Sara N. and Huang, Ying and Sekiguchi, JoAnn and Calsou, Patrick and Salles, Bernard and Junop, Murray S.}, year = {2009}, title = {Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4}, keywords = {0 (DNA-Binding Proteins);0 (DNL4 protein, S cerevisiae);0 (LIG4 protein, human);0 (NHEJ1 protein, human);0 (XRCC4 protein, human);Amino Acid Sequence;Binding, Competitive;Cell Line;DNA Breaks, Double-Stranded;DNA Ligase ATP;DNA Ligases/chemistry/metabolism;DNA Repair;DNA Repair Enzymes/metabolism;DNA-Binding Proteins/chemistry/metabolism;Down-Regulation;EC 6.5.1.- (DNA Ligases);EC 6.5.1.- (DNA Repair Enzymes);EC 6.5.1.1 (DNA Ligase ATP);Humans;Molecular Sequence Data;Protein Binding;Protein Stability;Protein Structure, Secondary;Protein Structure, Tertiary;Radiation Tolerance;Recombination, Genetic/genetics;Structural Homology, Protein;Structure-Activity Relationship}, pages = {3163--3172}, volume = {29}, number = {11}, issn = {0270-7306}, journal = {Molecular and cellular biology}, doi = {10.1128/MCB.01895-08} } @article{YAMANOETAL..2016, abstract = {Cell, 165 (2016) 949-962. doi:10.1016/j.cell.2016.04.003}, author = {Yamano, Takashi and Nishimasu, Hiroshi and Zetsche, Bernd and Hirano, Hisato and Slaymaker, Ian M. and Li, Yinqing and Fedorova, Iana and Nakane, Takanori and Makarova, Kira S. and Koonin, Eugene V. and Ishitani, Ryuichiro and Zhang, Feng and Nureki, Osamu}, year = {2016}, title = {Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA}, keywords = {0 (Bacterial Proteins);0 (Nucleic Acid Heteroduplexes);0 (RNA, Guide);9007-49-2 (DNA);Acidaminococcus/chemistry;Bacterial Proteins/chemistry/metabolism;Crystallography, X-Ray;DNA/chemistry/metabolism;Genetic Techniques;Models, Molecular;Nucleic Acid Heteroduplexes/metabolism;RNA, Guide/chemistry/metabolism}, pages = {949--962}, volume = {165}, number = {4}, issn = {0092-8674}, journal = {Cell}, doi = {10.1016/j.cell.2016.04.003} } @article{YANGETAL..2014, abstract = {Mice with specific gene modifications are valuable tools for studying development and disease. Traditional gene targeting in mice using embryonic stem (ES) cells, although suitable for generating sophisticated genetic modifications in endogenous genes, is complex and time-consuming. We have recently described CRISPR/Cas-mediated genome engineering for the generation of mice carrying mutations in multiple genes, endogenous reporters, conditional alleles or defined deletions. Here we provide a detailed protocol for embryo manipulation by piezo-driven injection of nucleic acids into the cytoplasm to create gene-modified mice. Beginning with target design, the generation of gene-modified mice can be achieved in as little as 4 weeks. We also describe the application of the CRISPR/Cas technology for the simultaneous editing of multiple genes (five genes or more) after a single transfection of ES cells. The principles described in this protocol have already been applied in rats and primates, and they are applicable to sophisticated genome engineering in species in which ES cells are not available.}, author = {Yang, Hui and Wang, Haoyi and Jaenisch, Rudolf}, year = {2014}, title = {Generating genetically modified mice using CRISPR/Cas-mediated genome engineering}, keywords = {Animals;Cell Culture Techniques;Clustered Regularly Interspaced Short Palindromic Repeats;Embryonic Stem Cells;Gene Targeting/methods;Genetic Engineering/methods;Genotyping Techniques;Mice;Mice, Inbred C57BL;Mice, Transgenic}, pages = {1956--1968}, volume = {9}, number = {8}, issn = {1750-2799}, journal = {Nature protocols}, doi = {10.1038/nprot.2014.134} } @article{YUANETAL..2009, abstract = {DNA double-strand breaks (DSBs) represent one of the most lethal types of DNA damage cells encounter. CtIP (also known as RBBP8) acts together with the MRN (MRE11-RAD50-NBS1) complex to promote DNA end resection and the generation of single-stranded DNA, which is critically important for homologous recombination repair. However, it is not yet clear exactly how CtIP participates in this process. Here, we demonstrate that besides the known conserved C terminus, the N terminus of CtIP protein is also required in DSB end resection and DNA damage-induced G(2)/M checkpoint control. We further show that both termini of CtIP can interact with the MRN complex and that the N terminus of CtIP, especially residues 22-45, binds to MRN and plays a critical role in targeting CtIP to sites of DNA breaks. Collectively, our results highlight the importance of the N terminus of CtIP in directing its localization and function in DSB repair.}, author = {Yuan, Jingsong and Chen, Junjie}, year = {2009}, title = {N terminus of CtIP is critical for homologous recombination-mediated double-strand break repair}, keywords = {0 (Carrier Proteins);0 (Cell Cycle Proteins);0 (DNA-Binding Proteins);0 (MRE11A protein, human);0 (NBN protein, human);0 (Nuclear Proteins);0 (Rad50 protein, human);0 (RBBP8 protein, human);0 (RNA, Small Interfering);9007-49-2 (DNA);Bone Neoplasms/genetics/metabolism/pathology;Carrier Proteins/genetics/metabolism;Cell Cycle Proteins/antagonists {\&} inhibitors/genetics/metabolism;Cell Division;Cells, Cultured;DNA Breaks, Double-Stranded;DNA Repair;DNA Repair Enzymes/antagonists {\&} inhibitors/genetics/metabolism;DNA/genetics;DNA-Binding Proteins/antagonists {\&} inhibitors/genetics/metabolism;EC 6.5.1.- (DNA Repair Enzymes);G2 Phase;Humans;Immunoblotting;Kidney/metabolism/pathology;Nuclear Proteins/antagonists {\&} inhibitors/genetics/metabolism;Osteosarcoma/genetics/metabolism/pathology;Recombination, Genetic;RNA, Small Interfering/pharmacology;Transfection}, pages = {31746--31752}, volume = {284}, number = {46}, issn = {0021-9258}, journal = {The Journal of biological chemistry}, doi = {10.1074/jbc.M109.023424} } @article{YUETAL..2004, abstract = {The BRCA1 C-terminal (BRCT) domain has recently been implicated as a phospho-protein binding domain. We demonstrate here that a CTBP-interacting protein CtIP interacts with BRCA1 BRCT domains in a phosphorylation-dependent manner. The CtIP/BRCA1 complex only exists in G(2) phase and is required for DNA damage-induced Chk1 phosphorylation and the G(2)/M transition checkpoint. However, the CtIP/BRCA1 complex is not required for the damage-induced G(2) accumulation checkpoint, which is controlled by a separate BRCA1/BACH1 complex. Taken together, these data not only implicate CtIP as a critical player in cell cycle checkpoint control but also provide molecular mechanisms by which BRCA1 controls multiple cell cycle transitions after DNA damage.}, author = {Yu, Xiaochun and Chen, Junjie}, year = {2004}, title = {DNA damage-induced cell cycle checkpoint control requires CtIP, a phosphorylation-dependent binding partner of BRCA1 C-terminal domains}, keywords = {0 (BRCA1 Protein);0 (Carrier Proteins);0 (Multiprotein Complexes);0 (Nuclear Proteins);0 (RBBP8 protein, human);Animals;BRCA1 Protein/chemistry/genetics/metabolism;Carrier Proteins/genetics/metabolism;Cell Cycle;Cell Division;Cell Line;Checkpoint Kinase 1;DNA Damage;EC 2.7.- (Protein Kinases);EC 2.7.11.1 (Checkpoint Kinase 1);EC 2.7.11.1 (CHEK1 protein, human);Enzyme Activation;G2 Phase;Humans;Multiprotein Complexes;Mutagenesis, Site-Directed;Nuclear Proteins/genetics/metabolism;Phosphorylation;Protein Binding;Protein Kinases/metabolism;Protein Structure, Tertiary;RNA Interference}, pages = {9478--9486}, volume = {24}, number = {21}, issn = {0270-7306}, journal = {Molecular and cellular biology}, doi = {10.1128/MCB.24.21.9478-9486.2004} } @article{YUETAL..2006, abstract = {BRCA1 (Breast Cancer Susceptibility Gene 1) possesses an N-terminal Ring domain and tandem C-terminal BRCT motifs. While the Ring domain has E3 ubiquitin ligase activity, the BRCA1 BRCT domains specifically recognize phospho-serine motifs. Here, we demonstrate that BRCA1 Ring domain catalyzes CtIP ubiquitination in a manner that depends on a phosphorylation-mediated interaction between CtIP and BRCA1 BRCT domains. The BRCA1-dependent ubiquitination of CtIP does not target CtIP for degradation. Instead, ubiquitinated CtIP associates with chromatin following DNA damage and participates in G2/M checkpoint control. Thus, we propose that BRCA1 can regulate the functions of its substrates through nonproteasomal pathways that do not involve substrate degradation.}, author = {Yu, Xiaochun and Fu, Shuang and Lai, Maoyi and Baer, Richard and Chen, Junjie}, year = {2006}, title = {BRCA1 ubiquitinates its phosphorylation-dependent binding partner CtIP}, keywords = {0 (BRCA1 Protein);0 (Carrier Proteins);0 (Chromatin);0 (Nuclear Proteins);0 (RBBP8 protein, human);452VLY9402 (Serine);BRCA1 Protein/metabolism;Carrier Proteins/metabolism;Catalysis;Cell Cycle/physiology;Cell Line;Chromatin/metabolism;DNA Damage;EC 2.3.2.27 (Ubiquitin-Protein Ligases);EC 3.4.25.1 (Proteasome Endopeptidase Complex);Humans;Nuclear Proteins/metabolism;Phosphorylation;Proteasome Endopeptidase Complex/metabolism;Protein Binding;Protein Structure, Tertiary;Serine/metabolism;Signal Transduction;Ubiquitin-Protein Ligases/metabolism}, pages = {1721--1726}, volume = {20}, number = {13}, issn = {0890-9369}, journal = {Genes {\&} development}, doi = {10.1101/gad.1431006} } @article{ZETSCHEETAL..2015, abstract = {Cell, 163 (2015) 759-771. doi:10.1016/j.cell.2015.09.038}, author = {Zetsche, Bernd and Gootenberg, Jonathan S. and Abudayyeh, Omar O. and Slaymaker, Ian M. and Makarova, Kira S. and Essletzbichler, Patrick and Volz, Sara E. and Joung, Julia and {van der Oost}, John and Regev, Aviv and Koonin, Eugene V. and Zhang, Feng}, year = {2015}, title = {Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system}, keywords = {0 (RNA, Guide);Amino Acid Sequence;CRISPR-Cas Systems;EC 3.1.- (Endonucleases);Endonucleases/chemistry/genetics;Francisella/enzymology/genetics;Genetic Engineering/methods;HEK293 Cells;Humans;Molecular Sequence Data;Nucleic Acid Conformation;RNA, Guide/genetics;Sequence Alignment}, pages = {759--771}, volume = {163}, number = {3}, issn = {0092-8674}, journal = {Cell}, doi = {10.1016/j.cell.2015.09.038} } @article{ZHANGETAL..2009, abstract = {BRCA1 and BRCA2 are often mutated in familial breast and ovarian cancer. Both tumor suppressors play key roles in the DNA-damage response. However, it remains unclear whether these two tumor suppressor function together in the same DNA-damage response pathway. Here, we show that BRCA1 associates with BRCA2 through PALB2/FANCN, a major binding partner of BRCA2. The interaction between BRCA1 and BRCA2 is abrogated in PALB2-deficient Fanconi anemia cells and in the cells depleted of PALB2 by small interfering RNA. Moreover, we show that BRCA1 promotes the concentration of PALB2 and BRCA2 at DNA-damage sites and the interaction between BRCA1 and PALB2 is important for the homologous recombination repair. Taken together, our results indicate that BRCA1 is an upstream regulator of BRCA2 in the DNA-damage response, and PALB2 is the linker between BRCA1 and BRCA2.}, author = {Zhang, Feng and Ma, Jianglin and Wu, Jiaxue and Ye, Lin and Cai, Hong and Xia, Bing and Yu, Xiaochun}, year = {2009}, title = {PALB2 links BRCA1 and BRCA2 in the DNA-damage response}, keywords = {0 (Apoptosis Regulatory Proteins);0 (BLID protein, human);0 (BRCA1 Protein);0 (BRCA1 protein, human);0 (BRCA2 Protein);0 (BRCA2 protein, human);0 (Nuclear Proteins);0 (PALB2 protein, human);0 (Tumor Suppressor Proteins);Apoptosis Regulatory Proteins;BRCA1 Protein/deficiency/genetics/metabolism;BRCA2 Protein/deficiency/genetics/metabolism;Breast Neoplasms/genetics;DNA;DNA Damage;DNA Repair;Fanconi Anemia/genetics;Female;Genes, BRCA1;Genes, BRCA2;Genetic Linkage/genetics;Humans;Mutation;Nuclear Proteins/deficiency/genetics/metabolism;Ovarian Neoplasms/genetics;Tumor Suppressor Proteins/deficiency/genetics/metabolism}, pages = {524--529}, volume = {19}, number = {6}, issn = {0960-9822}, journal = {Current biology : CB}, doi = {10.1016/j.cub.2009.02.018} } @article{ZHANGETAL..2016, abstract = {Nature Communications 7, (2016). doi:10.1038/ncomms10201}, author = {Zhang, Haoxing and Liu, Hailong and Chen, Yali and Yang, Xu and Wang, Panfei and Liu, Tongzheng and Deng, Min and Qin, Bo and Correia, Cristina and Lee, Seungbaek and Kim, Jungjin and Sparks, Melanie and Nair, Asha A. and Evans, Debra L. and Kalari, Krishna R. and Zhang, Pumin and Wang, Liewei and You, Zhongsheng and Kaufmann, Scott H. and Lou, Zhenkun and Pei, Huadong}, year = {2016}, title = {A cell cycle-dependent BRCA1-UHRF1 cascade regulates DNA double-strand break repair pathway choice}, keywords = {0 (BRCA1 Protein);0 (BRCA1 protein, human);0 (CCAAT-Enhancer-Binding Proteins);0 (UHRF1 protein, human);BRCA1 Protein/genetics/metabolism;CCAAT-Enhancer-Binding Proteins/genetics/metabolism;Cell Cycle;DNA Breaks, Double-Stranded;DNA Repair/physiology;Gene Expression Regulation/physiology;HEK293 Cells;Humans;Mutation}, pages = {10201}, volume = {7}, issn = {2041-1723}, journal = {Nature communications}, doi = {10.1038/ncomms10201} } @article{RN143, author = {LeCun, Yann and Bengio, Yoshua and Hinton, Geoffrey}, title = {Deep learning}, journal = {Nature}, volume = {521}, number = {7553}, pages = {436-444}, ISSN = {0028-0836}, DOI = {10.1038/nature14539}, url = {http://dx.doi.org/10.1038/nature14539}, year = {2015}, type = {Journal Article} } @article{RN35, author = {Badran, A. H. and Guzov, V. M. and Huai, Q. and Kemp, M. M. and Vishwanath, P. and Kain, W. and Nance, A. M. and Evdokimov, A. and Moshiri, F. and Turner, K. H. and Wang, P. and Malvar, T. and Liu, D. R.}, title = {Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance}, journal = {Nature}, volume = {533}, number = {7601}, pages = {58-63}, ISSN = {1476-4687 (Electronic) 0028-0836 (Linking)}, DOI = {10.1038/nature17938}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27120167 http://www.nature.com/nature/journal/v533/n7601/pdf/nature17938.pdf}, year = {2016}, type = {Journal Article} } @article{RN95, author = {Jain, Miten and Olsen, Hugh E. and Paten, Benedict and Akeson, Mark}, title = {The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community}, journal = {Genome Biology}, volume = {17}, number = {1}, pages = {239}, ISSN = {1474-760X}, DOI = {10.1186/s13059-016-1103-0}, url = {http://dx.doi.org/10.1186/s13059-016-1103-0 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5124260/pdf/13059_2016_Article_1103.pdf}, year = {2016}, type = {Journal Article} } @article{RN141, author = {Norris, A. L. and Workman, R. E. and Fan, Y. and Eshleman, J. R. and Timp, W.}, title = {Nanopore sequencing detects structural variants in cancer}, journal = {Cancer Biol Ther}, volume = {17}, DOI = {10.1080/15384047.2016.1139236}, url = {http://dx.doi.org/10.1080/15384047.2016.1139236}, year = {2016}, type = {Journal Article} } @article{RN136, author = {Wescoe, Z. L. and Schreiber, J. and Akeson, M.}, title = {Nanopores discriminate among five C5-cytosine variants in DNA}, journal = {J Am Chem Soc}, volume = {136}, DOI = {10.1021/ja508527b}, url = {http://dx.doi.org/10.1021/ja508527b}, year = {2014}, type = {Journal Article} } @article{RN134, author = {Wei, S. and Williams, Z.}, title = {Rapid short-read sequencing and aneuploidy detection using MinION nanopore technology}, journal = {Genetics}, volume = {202}, DOI = {10.1534/genetics.115.182311}, url = {http://dx.doi.org/10.1534/genetics.115.182311}, year = {2016}, type = {Journal Article} } @article{RN133, author = {Watson, M. and Thomson, M. and Risse, J. and Talbot, R. and Santoyo-Lopez, J. and Gharbi, K.}, title = {poRe: an R package for the visualization and analysis of nanopore sequencing data}, journal = {Bioinformatics}, volume = {31}, DOI = {10.1093/bioinformatics/btu590}, url = {http://dx.doi.org/10.1093/bioinformatics/btu590}, year = {2015}, type = {Journal Article} } @article{RN132, author = {Ward, A. C. and Kim, W.}, title = {MinIONTM: new, long read, portable nucleic acid sequencing device}, journal = {J Bacteriol Virol}, volume = {45}, DOI = {10.4167/jbv.2015.45.4.285}, url = {http://dx.doi.org/10.4167/jbv.2015.45.4.285}, year = {2015}, type = {Journal Article} } @article{RN135, author = {Schreiber, J. and Wescoe, Z. L. and Abu-Shumays, R. and Vivian, J. T. and Baatar, B. and Karplus, K.}, title = {Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands}, journal = {Proc Natl Acad Sci U S A}, volume = {110}, DOI = {10.1073/pnas.1310615110}, url = {http://dx.doi.org/10.1073/pnas.1310615110}, year = {2013}, type = {Journal Article} } @article{RN139, author = {Loose, M. and Malla, S. and Stout, M.}, title = {Real time selective sequencing using nanopore technology}, journal = {Nat Methods}, volume = {13}, DOI = {10.1038/nmeth.3930}, url = {http://dx.doi.org/10.1038/nmeth.3930}, year = {2016}, type = {Journal Article} } @misc{RN138, type = {Generic} } @misc{RN137, type = {Generic} } @article{RN130, author = {Wang, J. and Moore, N. E. and Deng, Y. -. M. and Eccles, D. A. and Hall, R. J.}, title = {MinION nanopore sequencing of an influenza genome}, journal = {Front Microbiol}, volume = {6}, year = {2015}, type = {Journal Article} } @article{RN129, author = {Risse, J. and Thomson, M. and Patrick, S. and Blakely, G. and Koutsovoulos, G. and Blaxter, M.}, title = {A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data}, journal = {Gigascience}, volume = {4}, DOI = {10.1186/s13742-015-0101-6}, url = {http://dx.doi.org/10.1186/s13742-015-0101-6}, year = {2015}, type = {Journal Article} } @article{RN128, author = {Ramgren, A. C. and Newhall, H. S. and James, K. E.}, title = {DNA barcoding and metabarcoding with the Oxford Nanopore MinION}, journal = {Genome}, volume = {58}, year = {2015}, type = {Journal Article} } @article{RN127, author = {Quick, J. and Quinlan, A. R. and Loman, N. J.}, title = {A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer}, journal = {Gigascience}, volume = {3}, DOI = {10.1186/2047-217x-3-22}, url = {http://dx.doi.org/10.1186/2047-217X-3-22}, year = {2014}, type = {Journal Article} } @article{RN126, author = {Quick, J. and Loman, N. J. and Duraffour, S. and Simpson, J. T. and Severi, E. and Cowley, L.}, title = {Real-time, portable genome sequencing for ebola surveillance}, journal = {Nature}, volume = {530}, DOI = {10.1038/nature16996}, url = {http://dx.doi.org/10.1038/nature16996}, year = {2016}, type = {Journal Article} } @article{RN124, author = {Quick, J. and Ashton, P. and Calus, S. and Chatt, C. and Gossain, S. and Hawker, J.}, title = {Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella}, journal = {Genome Biol}, volume = {16}, DOI = {10.1186/s13059-015-0677-2}, url = {http://dx.doi.org/10.1186/s13059-015-0677-2}, year = {2015}, type = {Journal Article} } @article{RN123, author = {Pallen, M. J.}, title = {Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections}, journal = {Parasitology}, volume = {141}, DOI = {10.1017/s0031182014000134}, url = {http://dx.doi.org/10.1017/S0031182014000134}, year = {2014}, type = {Journal Article} } @article{RN122, author = {Miller, R. R. and Montoya, V. and Gardy, J. L. and Patrick, D. M. and Tang, P.}, title = {Metagenomics for pathogen detection in public health}, journal = {Genome Med}, volume = {5}, DOI = {10.1186/gm485}, url = {http://dx.doi.org/10.1186/gm485}, year = {2013}, type = {Journal Article} } @article{RN121, author = {Miles, G. and Hoisington-Lopez, J. and Duncavage, E.}, title = {Nanopore sequencing of a DNA library prepared from formalin-fixed paraffin-embedded tissue}, journal = {Lab Invest}, volume = {95}, year = {2015}, type = {Journal Article} } @misc{RN131, type = {Generic} } @misc{RN125, type = {Generic} } @article{RN108, author = {Sović, I. and Šikić, M. and Wilm, A. and Fenlon, S. N. and Chen, S. and Nagarajan, N.}, title = {Fast and sensitive mapping of nanopore sequencing reads with GraphMap}, journal = {Nat Commun}, volume = {7}, DOI = {10.1038/ncomms11307}, url = {http://dx.doi.org/10.1038/ncomms11307}, year = {2016}, type = {Journal Article} } @article{RN106, author = {Quick, J. and Quinlan, A. and Loman, N.}, title = {A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer}, journal = {GigaScience}, volume = {3}, DOI = {10.1186/2047-217x-3-22}, url = {http://dx.doi.org/10.1186/2047-217X-3-22}, year = {2014}, type = {Journal Article} } @article{RN120, author = {Mikheyev, A. S. and Tin, M. M. Y.}, title = {A first look at the Oxford Nanopore MinION sequencer}, journal = {Mol Ecol Resour}, volume = {14}, DOI = {10.1111/1755-0998.12324}, url = {http://dx.doi.org/10.1111/1755-0998.12324}, year = {2014}, type = {Journal Article} } @article{RN119, author = {Madoui, M. -. A. and Engelen, S. and Cruaud, C. and Belser, C. and Bertrand, L. and Alberti, A.}, title = {Genome assembly using Nanopore-guided long and error-free DNA reads}, journal = {BMC Genomics}, volume = {16}, DOI = {10.1186/s12864-015-1519-z}, url = {http://dx.doi.org/10.1186/s12864-015-1519-z}, year = {2015}, type = {Journal Article} } @article{RN118, author = {Loman, N. J. and Quinlan, A. R.}, title = {Poretools: a toolkit for analyzing nanopore sequence data}, journal = {Bioinformatics}, volume = {30}, DOI = {10.1093/bioinformatics/btu555}, url = {http://dx.doi.org/10.1093/bioinformatics/btu555}, year = {2014}, type = {Journal Article} } @article{RN117, author = {Loman, N. J. and Pallen, M. J.}, title = {Twenty years of bacterial genome sequencing}, journal = {Nat Rev Microbiol}, volume = {13}, DOI = {10.1038/nrmicro3565}, url = {http://dx.doi.org/10.1038/nrmicro3565}, year = {2015}, type = {Journal Article} } @article{RN116, author = {Leggett, R. M. and Heavens, D. and Caccamo, M. and Clark, M. D. and Davey, R. P.}, title = {NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles}, journal = {Bioinformatics}, volume = {32}, year = {2016}, type = {Journal Article} } @article{RN107, author = {Kilianski, A. and Haas, J. L. and Corriveau, E. J. and Liem, A. T. and Willis, K. L. and Kadavy, D. R.}, title = {Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer}, journal = {Gigascience}, volume = {4}, DOI = {10.1186/s13742-015-0051-z}, url = {http://dx.doi.org/10.1186/s13742-015-0051-z}, year = {2015}, type = {Journal Article} } @article{RN114, author = {Karlsson, E. and Lärkeryd, A. and Sjödin, A. and Forsman, M. and Stenberg, P.}, title = {Scaffolding of a bacterial genome using MinION nanopore sequencing}, journal = {Sci Rep}, volume = {5}, DOI = {10.1038/srep11996}, url = {http://dx.doi.org/10.1038/srep11996}, year = {2015}, type = {Journal Article} } @article{RN113, author = {Judge, K. and Harris, S. R. and Reuter, S. and Parkhill, J. and Peacock, S. J.}, title = {Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes}, journal = {J Antimicrob Chemother}, volume = {70}, DOI = {10.1093/jac/dkv206}, url = {http://dx.doi.org/10.1093/jac/dkv206}, year = {2015}, type = {Journal Article} } @article{RN105, author = {Jain, M. and Fiddes, I. T. and Miga, K. H. and Olsen, H. E. and Paten, B. and Akeson, M.}, title = {Improved data analysis for the MinION nanopore sequencer}, journal = {Nat Methods}, volume = {12}, DOI = {10.1038/nmeth.3290}, url = {http://dx.doi.org/10.1038/nmeth.3290}, year = {2015}, type = {Journal Article} } @article{RN111, author = {Hargreaves, A. D. and Mulley, J. F.}, title = {Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing}, journal = {Peer J}, volume = {3}, DOI = {10.7717/peerj.1441}, url = {http://dx.doi.org/10.7717/peerj.1441}, year = {2015}, type = {Journal Article} } @article{RN110, author = {Greninger, A. L. and Naccache, S. N. and Federman, S. and Yu, G. and Mbala, P. and Bres, V.}, title = {Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis}, journal = {Genome Med}, volume = {7}, DOI = {10.1186/s13073-015-0220-9}, url = {http://dx.doi.org/10.1186/s13073-015-0220-9}, year = {2015}, type = {Journal Article} } @article{RN109, author = {Goodwin, S. and Gurtowski, J. and Ethe-Sayers, S. and Deshpande, P. and Schatz, M. C. and McCombie, W. R.}, title = {Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome}, journal = {Genome Res}, volume = {25}, DOI = {10.1101/gr.191395.115}, url = {http://dx.doi.org/10.1101/gr.191395.115}, year = {2015}, type = {Journal Article} } @article{RN112, author = {Cao, M. D. and Ganesamoorthy, D. and Elliott, A. and Zhang, H. and Cooper, M. A. and Coin, L. J. M.}, title = {Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION™ sequencing}, journal = {GigaScience}, volume = {5}, DOI = {10.1186/s13742-016-0137-2}, url = {http://dx.doi.org/10.1186/s13742-016-0137-2}, year = {2016}, type = {Journal Article} } @misc{RN115, type = {Generic} } @article{RN104, author = {Bolisetty, M. T. and Rajadinakaran, G. and Graveley, B. R.}, title = {Determining exon connectivity in complex mRNAs by nanopore sequencing}, journal = {Genome Biol}, volume = {16}, DOI = {10.1186/s13059-015-0777-z}, url = {http://dx.doi.org/10.1186/s13059-015-0777-z}, year = {2015}, type = {Journal Article} } @article{RN101, author = {Manrao, E. A. and Derrington, I. M. and Laszlo, A. H. and Langford, K. W. and Hopper, M. K. and Nathaniel, G.}, title = {Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase}, journal = {Nat Biotechnol}, volume = {30}, DOI = {10.1038/nbt.2171}, url = {http://dx.doi.org/10.1038/nbt.2171}, year = {2012}, type = {Journal Article} } @article{RN102, author = {Ashton, P. M. and Nair, S. and Dallman, T. and Rubino, S. and Rabsch, W. and Mwaigwisya, S.}, title = {MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island}, journal = {Nat Biotechnol}, volume = {33}, DOI = {10.1038/nbt.3103}, url = {http://dx.doi.org/10.1038/nbt.3103}, year = {2015}, type = {Journal Article} } @article{RN99, author = {Cherf, G. M. and Lieberman, K. R. and Hytham, R. and Lam, C. E. and Kevin, K. and Mark, A.}, title = {Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision}, journal = {Nat Biotechnol}, volume = {30}, DOI = {10.1038/nbt.2147}, url = {http://dx.doi.org/10.1038/nbt.2147}, year = {2012}, type = {Journal Article} } @article{RN100, author = {Ayub, M. and Bayley, H.}, title = {Individual RNA base recognition in immobilized oligonucleotides using a protein nanopore}, journal = {Nano Lett}, volume = {12}, DOI = {10.1021/nl3027873}, url = {http://dx.doi.org/10.1021/nl3027873}, year = {2012}, type = {Journal Article} } @article{RN98, author = {Kasianowicz, J. J. and Brandin, E. and Branton, D. and Deamer, D. W.}, title = {Characterization of individual polynucleotide molecules using a membrane channel}, journal = {Proc Natl Acad Sci U S A}, volume = {93}, DOI = {10.1073/pnas.93.24.13770}, url = {http://dx.doi.org/10.1073/pnas.93.24.13770}, year = {1996}, type = {Journal Article} } @article{RN97, author = {Deamer, D. and Akeson, M. and Branton, D.}, title = {Three decades of nanopore sequencing}, journal = {Nat Biotechnol}, volume = {34}, DOI = {10.1038/nbt.3423}, url = {http://dx.doi.org/10.1038/nbt.3423}, year = {2016}, type = {Journal Article} } @article{RN96, author = {Branton, D. and Daniel, B. and Deamer, D. W. and Andre, M. and Hagan, B. and Benner, S. A.}, title = {The potential and challenges of nanopore sequencing}, journal = {Nat Biotechnol}, volume = {26}, DOI = {10.1038/nbt.1495}, url = {http://dx.doi.org/10.1038/nbt.1495}, year = {2008}, type = {Journal Article} } @article{RN93, author = {Ondov, B. D. and Treangen, T. J. and Melsted, P. and Mallonee, A. B. and Bergman, N. 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