ChIP-seq Histone Modification Analysis Protocol

ChIPs were done as previously described with the modifications described below41 (link). The following histone antibodies were used: 1 μl of anti-H3K4me2 (Upstate 07-030); 0.5 μl of anti-H3K36me3 (Abcam 9050); 0.5 μl of anti-acetyl H4 (Upstate 06-598); and 2 μl of anti-H3 (Abcam 1791). All antibodies were bound to Protein A-agarose beads and used for precipitation of formaldehyde-crosslinked chromatin. For anti-H3 antibody, binding was done in FA lysis buffer containing 275 mM NaCl. For other antibodies, binding was done in FA lysis buffer containing 1 M NaCl. Precipitated DNAs were analysed in real-time using SYBR Green Supermix and CFX96 cycler (Bio-Rad). Oligonucleotides for PCR analysis are listed in Supplementary Table 2.