Extended Data Fig. 2: Cohesin recruitment and loop extrusion occurs at DSBs.
From: Loop extrusion as a mechanism for formation of DNA damage repair foci
a, Calibrated SCC1 ChIP–seq tracks before (grey) and after (black) DSB induction (n = 1). SCC1 enrichment at DSB site is indicated by a red arrow. b, Average profile of SCC1 ChIP–seq signal centred on the 80 best-induced DSBs (left) or centred on all CTCF peaks of the genome (right) on a 10-kb window. c, Calibrated ChIP–qPCR of SCC1 in the indicated conditions at three DSB sites or a negative control region. Insets, western blots validating depletion of the proteins NIPBL (n = 1) and MRE11 (n = 2) by the corresponding siRNAs. For gel source data, see Supplementary Fig. 1. Mean ± s.e.m. for technical replicates (n = 4) of a representative experiment (out of n = 2 biological replicates). d, Averaged Hi-C matrix before (−DSB) and after DSB induction (+DSB) (observed/expected) and of the log2 ratio between damaged and undamaged cells centred on the 80 best-induced DSBs (top) or centred on eighty random TAD borders (bottom) (50-kb resolution, 5-Mb window; combined replicates). e, Averaged Hi-C contact matrix of log2[+DSB/−DSB] centred on the eighty best-induced DSBs in the two independent biological replicates. f, APA plot on a 200-kb window (10-kb resolution) before (−DSB) and after DSB induction (+DSB) in biological replicate no. 2 (replicate no. 1 shown in Fig. 2c). APAs are calculated between the DSBs and loop anchors (n = 552 pairs). The fold change between the signal (central pixel) and the background (upper left corner 5 × 5 pixels) is indicated. g, For comparison with f, APA plot on a 200-kb window (10-kb resolution) before DSB induction computed between classical loop anchors that are near DSB sites (<500 kb; n = 674 pairs for replicate 1 and n = 737 pairs for replicate 2). The fold change between the signal (central pixel) and the background (upper left corner 5 × 5 pixels) is indicated. The loop strength (quantified by the fold change between signal and background on the APA plot) is higher at loop anchors (g, replicate 1 fold-change = 5.4; replicate 2 fold-change = 5.8) than the loop strength observed at DSBs after break induction (Fig. 2c, replicate 1, fold-change = 2; f, replicate 2, fold-change = 2.3).
