Mapping the genetic landscape of DNA double-strand break repair

Jeffrey A. Hussmann, Jia Ling, Purnima Ravisankar, Jun Yan, Ann Cirincione, Albert Xu, Danny Simpson, Dian Yang, Anne Bothmer, Cecilia Cotta-Ramusino, Jonathan S. Weissman, Britt Adamson

Research output: Contribution to journalArticlepeer-review

71 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)5653-5669.e25
Issue number22
StatePublished - Oct 28 2021

All Science Journal Classification (ASJC) codes

  • General Biochemistry, Genetics and Molecular Biology


  • CRISPR-Cas9
  • DNA repair
  • double-strand breaks
  • functional genomics
  • genome editing


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