Mapping the genetic landscape of DNA double-strand break repair.

TitleMapping the genetic landscape of DNA double-strand break repair.
Publication TypeJournal Article
Year of Publication2021
AuthorsHussmann, JA, Ling, J, Ravisankar, P, Yan, J, Cirincione, A, Xu, A, Simpson, D, Yang, D, Bothmer, A, Cotta-Ramusino, C, Weissman, JS, Adamson, B
JournalCell
Volume184
Issue22
Pagination5653-5669.e25
Date Published2021 10 28
ISSN1097-4172
KeywordsCell Line, Cluster Analysis, CRISPR-Associated Protein 9, DNA Breaks, Double-Stranded, DNA Repair, Gene Editing, Gene Expression Regulation, Genome, Human, Genomics, Humans, Phenotype, Reproducibility of Results, RNA, Guide
Abstract

<p>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.</p>

DOI10.1016/j.cell.2021.10.002
Alternate JournalCell
PubMed ID34672952
PubMed Central IDPMC9074467
Grant ListR35 GM138167 / GM / NIGMS NIH HHS / United States
P30 CA072720 / CA / NCI NIH HHS / United States
RM1 HG009490 / HG / NHGRI NIH HHS / United States
/ HHMI / Howard Hughes Medical Institute / United States
T32 HG003284 / HG / NHGRI NIH HHS / United States