ChIP, library preparation, and sequencing

ChIP-seq (32) was performed from HeLa cells using the ChIP-IT High Sensitivity Kit from Active Motif (reference 53040) according to the manufacturer’s instructions. Sonication was performed using the Qsonica Q700 Sonicator with microtip of 1/8 inches (reference 4418) at 11% amplitude and 13 min of processing time (30-s “ON” and 30-s “OFF”). Each ChIP used 30 μg of chromatin along with 4 μg of antibody detecting MRE11, NBS1, RNAPII, or phospo-Ser² RNAPII (table S3). ChIP-seq libraries were constructed using the Next Gen DNA Library Kit (Active Motif, 53216 and 53264). Library quality was assessed using Agilent 2100 Bioanalyzer and Agilent High Sensitivity DNA assay. High-throughput sequencing was performed by sequence-by-synthesis technique using a NextSeq 500 (Illumina) at the Genom’ic Facility, Institut Cochin, Paris.