@article{c728168e4e5544969d5da53d2be5318b,
title = "Mapping the genetic landscape of DNA double-strand break repair",
abstract = "Cells repair DNA double-strand breaks (DSBs) through a complex set of pathways critical for maintaining genomic integrity. To systematically map these pathways, we developed a high-throughput screening approach called Repair-seq that measures the effects of thousands of genetic perturbations on mutations introduced at targeted DNA lesions. Using Repair-seq, we profiled DSB repair products induced by two programmable nucleases (Cas9 and Cas12a) in the presence or absence of oligonucleotides for homology-directed repair (HDR) after knockdown of 476 genes involved in DSB repair or associated processes. The resulting data enabled principled, data-driven inference of DSB end joining and HDR pathways. Systematic interrogation of this data uncovered unexpected relationships among DSB repair genes and demonstrated that repair outcomes with superficially similar sequence architectures can have markedly different genetic dependencies. This work provides a foundation for mapping DNA repair pathways and for optimizing genome editing across diverse modalities.",
keywords = "CRISPR-Cas9, DNA repair, double-strand breaks, functional genomics, genome editing",
author = "Hussmann, {Jeffrey A.} and Jia Ling and Purnima Ravisankar and Jun Yan and Ann Cirincione and Albert Xu and Danny Simpson and Dian Yang and Anne Bothmer and Cecilia Cotta-Ramusino and Weissman, {Jonathan S.} and Britt Adamson",
note = "Funding Information: We thank M. Jost, J. Replogle, M. Leonetti, H. Canaj, B. Conklin, M. Levine, S.J. Elledge, J. Haber, and members of the Adamson and Weissman labs for helpful discussions. We thank M. Demozzi, K.W. Gareau, H.S. Abdulkerim, C. Wilson, and M. Donepudi (Editas Medicine). We thank E. Chow (UCSF Center for Advanced Technology), M. Tan (Chan Zuckerberg Biohub), W. Wang (Genomics Core Facility of Princeton University), and C. DeCoste and K. Rittenbach ( Princeton University Flow Cytometry Resource Facility; NCI-CCSG P30CA072720-5921 ). Research was supported by the National Institutes of Health (NIH) under award numbers 1RM1HG009490 (J.S.W.), 1R35GM138167 (B.A.), and T32HG003284 ( Princeton QCB training grant), as well as Rutgers Cancer Institute of New Jersey via an NIH Cancer Center Support Grant ( P30CA072720 ) and the Searle Scholars Program. J.S.W. is supported by HHMI. A.C. is supported by the National Science Foundation GRFP ( DGE-2039656 ). J.A.H. was the Rebecca Ridley Kry Fellow of the Damon Runyon Cancer Research Foundation ( DRG-2262-16 ). J.Y. is supported by a fellowship provided by the China Scholarship Council (CSC) based on the April 2015 Memorandum of Understanding between the CSC and Princeton University. Funding Information: We thank M. Jost, J. Replogle, M. Leonetti, H. Canaj, B. Conklin, M. Levine, S.J. Elledge, J. Haber, and members of the Adamson and Weissman labs for helpful discussions. We thank M. Demozzi, K.W. Gareau, H.S. Abdulkerim, C. Wilson, and M. Donepudi (Editas Medicine). We thank E. Chow (UCSF Center for Advanced Technology), M. Tan (Chan Zuckerberg Biohub), W. Wang (Genomics Core Facility of Princeton University), and C. DeCoste and K. Rittenbach (Princeton University Flow Cytometry Resource Facility; NCI-CCSG P30CA072720-5921). Research was supported by the National Institutes of Health (NIH) under award numbers 1RM1HG009490 (J.S.W.), 1R35GM138167 (B.A.), and T32HG003284 (Princeton QCB training grant), as well as Rutgers Cancer Institute of New Jersey via an NIH Cancer Center Support Grant (P30CA072720) and the Searle Scholars Program. J.S.W. is supported by HHMI. A.C. is supported by the National Science Foundation GRFP (DGE-2039656). J.A.H. was the Rebecca Ridley Kry Fellow of the Damon Runyon Cancer Research Foundation (DRG-2262-16). J.Y. is supported by a fellowship provided by the China Scholarship Council (CSC) based on the April 2015 Memorandum of Understanding between the CSC and Princeton University. Conception, J.A.H. C.C.R. J.S.W. and B.A.; methodology, B.A.; software, J.A.H.; screen and reagent optimization, P.R. A.X. and A.B.; library cloning, P.R. A.C. A.X. and B.A.; screens, J.A.H. J.L. P.R. A.C. D.S. and B.A. with assistance from A.X. and D.Y.; ddPCR, J.Y.; validation, J.L. P.R. and B.A.; formal analysis, J.A.H.; interpretation, J.A.H. J.L. C.C.-R. J.S.W. and B.A.; writing, J.A.H. J.L. C.C.-R. J.S.W. and B.A. with input from all authors; supervision, C.C.-R. J.S.W. and B.A.; project administration, B.A. funding acquisition, C.C.-R. J.S.W. and B.A. Editas Medicine was involved in this work and provided reagents. B.A. was a member of a ThinkLab Advisory Board for, and holds equity in, Celsius Therapeutics. J.A.H. is a consultant for Tessera Therapeutics. J.S.W. declares outside interest in 5 AM Venture, Amgen, Chroma Medicine, KSQ Therapeutics, Maze Therapeutics, Tenaya Therapeutics, Tessera Therapeutics, and Third Rock Ventures. A.B. and C.C.-R. are former employees and shareholders of Editas Medicine and were employed by Editas at the time this work was conducted. J.A.H. and B.A. have filed patent applications on related work. Publisher Copyright: {\textcopyright} 2021 The Authors",
year = "2021",
month = oct,
day = "28",
doi = "10.1016/j.cell.2021.10.002",
language = "English (US)",
volume = "184",
pages = "5653--5669.e25",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "22",
}