Protocol for mapping double-stranded DNA break sites across the genome with translocation capture sequencing

Joe R Delaney; Albert R La Spada

doi:10.1016/j.xpro.2023.102205

Protocol for mapping double-stranded DNA break sites across the genome with translocation capture sequencing

STAR Protoc. 2023 Mar 30;4(2):102205. doi: 10.1016/j.xpro.2023.102205. Online ahead of print.

Authors

Joe R Delaney¹, Albert R La Spada²

Affiliations

¹ Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA. Electronic address: [email protected].
² Departments of Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurobiology & Behavior, School of Biosciences, University of California, Irvine, Irvine, CA 92697, USA; UCI Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA. Electronic address: [email protected].

Abstract

Translocation sequencing can be used to assess mechanisms of DNA repair and identify genome-wide double-strand breaks (DSBs) accessible to DNA repair machinery. Here, we present a protocol for mapping double-strand DNA break sites across the genome with translocation capture sequencing. Bait DSBs are introduced using a Cas9 nuclease and repaired by the host cell, connecting bait DSBs to other DSBs. Repair sites are detected by isolating bait site DNA, cleaving normal sequence to enrich off-site repair, and next-generation sequencing. For complete details on the use and execution of this protocol, please refer to Switonski et al. (2021).¹.

Keywords: Cell Biology; Genomics; High-throughput Screening.

Abstract

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