Enrichment of Twist ChIP-seq summits and explanatory E-box motifs in different genic and intergenic locations. (A) Enrichment of Twist ChIP-seq and ChIP-chip summits at particular positions in the genome, relative to a genome random sample and several sequencing negative controls. The genome was segregated into four mutually exclusive categories: promoter proximal (relative to the set of promoters from S. Celniker, including 500 bp upstream), exonic, intronic, and intergenic (see Supplemental Methods). While the majority of Twist regions fall into intergenic and intronic regions, there is a significant overabundance of Twist peaks in promoters relative to the amount of promoters in the genome (24%, or 258 of the ChIP-seq peaks). Intergenic and intronic Twist occurrences are comparable to that expected from a random genomic sample (29%, or 319 intergenic, and 38%, or 420 intronic). The number of summits within exonic regions is relatively disenriched (9%, or 102). In order to assess these numbers compared to expected values, we also compared the same number of Twist ChIP-chip regions (largest by area), the input control DNA regions enriched over Twist, the aggregated input DNA, and a random sampling of sequenced reads mapping uniquely to the genome (see Supplemental Text). We also report the total amount of the genome falling into each of these categories. The aggregated control and, to a lesser degree, the random control reads draw attention to the fact that there are many sequenced reads falling into exons. The enriched control does not show the exon bias perhaps because a directionality requirement was used; there is a mild enrichment of these sequences in the gene flanking category relative to the random genomic sample but a significant depletion in the promoter proximal that is likely due to the fact that Twist peaks are enriched at promoters. (B) The frequency of explanatory E-box sequences as a function of position of Twist-bound peaks in the genome (i.e., promoter proximal, intergenic, intronic, and exonic position). The CA, CG, and GA core E-boxes show enrichment in promoter, intergenic, and intronic positions; the GC core E-box is specifically enriched in the promoter proximal position.
