Figure 3
Similar genome-wide binding patterns of 15 HAT marks at binding sites of HATs. Raw chromatin immunoprecipitation sequencing (ChIP-seq) data were extracted from [12, 13]. (a) Co-occurrence of 15 acetylation marks on CBP binding sites: average binding densities of 15 HAT marks (marked in black), control (immunoglobulin G (IgG)) (marked in dashed black) and CBP (marked in red) surrounding ± 5-kb region of a collection of 10,360 CBP binding sites. From the raw data sets, enrichment clusters representing CBP binding sites were determined. Around each CBP binding site, four hundred 25-bp bins were created, and densities were collected for each bin for the 15 acetylation tracks. The mean was calculated for each bin and used to represent average acetylation densities around the CBP binding sites. (b) Co-occurrence of 18 acetylation marks on all the genome-wide CBP binding sites: binding densities of regions (± 5) surrounding the 10,360 binding sites of CBP. Densities are shown for control (IgG), CBP and 18 HAT marks (as indicated). In the heat map, each line represents a genomic location of a binding site with its surrounding ± 5-kb region. CBP binding sites were used as references to collect ChIP-seq tag densities over a 10-kb (± 5 kb) window. This matrix was subjected to k-means clustering. The heat map representing the clustered density matrix is displayed. In (a) and (b), similar results were obtained with the other four other HATs (data not shown).