Chromatin immunoprecipitation was performed as described previously (McNee et al., 2017 (link)). Briefly, 48 h post transfection with siRNA, double-strand breaks were induced in U-2-OS-FokI cells by addition of 1 μM Shield1 ligand (Clontech) and 1 μM 4-hydroxytamoxifen (Sigma-Aldrich) for 4 h, or left untreated. Samples were crosslinked with 1 % formaldehyde and neutralized with 0.125 M glycine. Cells were lysed and DNA sheared to 300-1000 bp by sonication. Samples were pre-cleared with rabbit immunoglobulins (Dako) and chromatin was co-immunoprecipitated with antibodies to BOD1L, SETD1A, RIF1, histone H3, H3K4me1, H3K4me2 and H3K4me3. Protein-DNA complexes were washed and eluted from magnetic protein G beads, cross-links were reversed and samples treated with proteinase K. DNA was purified using a PCR purification kit (Qiagen) and quantified by qPCR using 4 primer pairs (see Figure 6 O for location of amplicons, and key resources table for sequences).
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