Figure 3.

Validation of ChIP-chip results and effects on nucleosome occupancy and H3K4me3 of butyrate-mediated histone deacetylation. ChIPs were prepared from cells that were either untreated (0 h) or treated with 5 mM Na-butyrate for 15 min (15’), 2 h, 6 h, or 12 h, and cells were exposed to butyrate for 12 h and then grown for 6 h without (12 + 6 h) using antibodies against H3ac and H4ac. ChIPs were analyzed by amplifying the regions indicated in Supplemental Table 1, which displayed histone deacetylation (A) or histone hyperacetylation (B) in our ChIP-chip analysis. A negative control region (HBG1/2) was analyzed together with some gene promoters from the literature (B). ChIPs were prepared from cells that were either nontreated (0 h) or treated with 100 ng/mL TSA for 12 h, using antibodies against H3ac and H4ac. Some of the selected targets from A and B were analyzed and presented here (C) and in Supplemental Figure 2. ChIPs were also prepared from cells that were either untreated (0 h) or treated with 5 mM Na-butyrate for 12 h using an antibody against H3-cter or against H3K4me3 (D).