Repair of DNA double-strand breaks leaves heritable impairment to genome function

Upon DNA breakage, a genomic locus undergoes alterations in 3-D chromatin architecture to facilitate signaling and repair. While cells possess mechanisms to repair damaged DNA, it is unknown whether the surrounding chromatin is restored to its naïve state. We show that a single DNA double-strand break (DSB) within a topologically-associated domain (TAD) harboring conformation-sensitive genes causes lasting chromatin alterations, which persist after completion of DNA repair and feature structural changes, chromatin compaction and loss of local RNA species. Unexpectedly, these newly-acquired features of post-repair chromatin are transmitted to daughter cells and manifest as heritable impairments of gene expression. These findings uncover a hitherto concealed dimension of DNA breakage, which we term post-repair chromatin fatigue, and which confers heritable impairment of gene function beyond DNA repair. Overall design: Region Capture Micro-C of the c-MYC locus of untreated HeLa cells and Hela cells after Cas9 cleavages. c-MYC ORF and CTCF sites were analyzed over a time course of 72 hours, whereas upstream-TAD#1, upstream-TAD#2, downstream-TAD#1 and downstream-TAD#2 cut sites were analyzed 48 hours after DNA cleavage.