ChIP assays were performed as described [33 (link),34 (link)]. Briefly, 2.5 million cells were crosslinked with 37% w/v formaldehyde, quenched with 2.5M glycine, washed 3 times with ice cold PBS, and sonicated in a Bioruptor (Diagenode). The following primary antibodies were utilized for incubation of crosslinked chromatin overnight: HDAC1 (Abcam #31263, 3μg), HDAC2 (Abcam #12169, 3μg) pan-H4ac (Upstate #06–866, 5μg), H3K9Ac (Abcam #12179, 5μg), H3K9me3 (Abcam #8898, 5μg), SIN3A (Abcam #3479, 5μg) and as a negative control IgG Rabbit (Cell Signaling Technologies #2729S, 3 or 5μg), IgG Rabbit (Santa Cruz #2027, 3 or 5μg), or IgG Mouse (Santa Cruz #2025, 3 or 5μg,). Protein A/G magnetic beads (Pierce #88802) were added at 50 μL per ChIP sample. ChIP-qPCR primers were designed using Primer3 web tool and are listed in S5 Table.
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