Figure 5.

Dose dependent largazole effects on the epigenetic features of distal enhancer elements. (A and B) Screen shots from Genome Browser (UCSC) showing ChIP-seq and associated signal determined by FStitch (black rectangles) from HCT116 cells targeting H3K27ac (orange) starting with untreated cells (DMSO) at the bottom and followed by eight increasing largazole dose treatments on top (4.7–300 nM). ChIP-seq signal accumulation for p300 (purple) (23), total RNAPII (green), H3K4me1 (yellow), and H3K4me2 (pink) is shown for untreated HCT116 cells and for those treated with either 75 nM or 300 nM largazole concentrations (insets to the right). GRO-seq data from unstimulated HCT116 cells illustrate the presence of nascent transcripts resulting from the plus (red) and negative strand (blue) (24). (C) and (D) Schematic diagram shown illustrates the features used to identify isolated enhancers (IE) for genomic regions displaying both H3K27ac and H3K4me1 signal (determined by FStitch and MACS2 respectively). Only enhancers elements (green) located with a minimal distance of ±10 kb from neighboring H3K27ac/H3K4me1 locations from canonical (n = 8667) and poised (n = 3505) enhancers were used for further cluster analyses. (E and F) Largazole induces both the decommission and activation of transcriptional enhancers in a dose dependent manner. Shown are the fraction of IE regions with H3K27ac (left) and H3K9ac (right) signal (FStitch calls) along a ±10 kb distance centered on overlapping peak regions. Peak center locations are indicated by black triangles. Nine ChIP-seq experiments are illustrated with vehicle (DMSO) at the bottom and followed by increasing doses of largazole treatments to a maximum of 300 nM at the top. The fraction of IE elements with significant signal (FStitch) for each histone acetylation marks is illustrated by the heat-color scale: all regions (red); half of regions (green); no regions with signal detected (dark blue).