Chromatin Immunoprecipitation Protocols

Protocols employed for ChIP, ChIP-chip DNase-chip have been previously described [25] (link), [29] (link). Primer sequences that were not previously published [25] (link) are available upon request. We employed a slightly modified ChIP protocol for p300 ChIP. Cells were dounced in 25 mM Hepes (pH 7.8), 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1× complete protease inhibitor cocktail (Roche). Nuclei were isolated, resuspended in 0.1× SDS lysis buffer (Millipore) diluted in 1× ChIP dilution buffer (Millipore). Samples were sonicated in and subject to ChIP as previously described using ChIP assay kit (Millipore). For ChIP-chip, samples and inputs were amplified using WGA2 kit (Sigma), labeled and hybridized to custom-designed microarrays (Roche-Nimblegen). A previously described algorithm, ACME was employed for peak calling and identifying enriched regions in the ChIP-chip datasets [46] (link).