Figure 1.

(a) The genomic regulatory block model of transcriptional regulation. Genes involved in the regulation of developmental processes are themselves regulated by enhancers located in a variety of locations, both upstream and downstream. Developmentally regulated genes tend to have CpG islands (CGIs) that overlap with its promoter and extend into the body of the gene. Genes with Type II and III promoters typically feature a broad TSS distribution, as detected by CAGE. (b) Regulatory elements within the genome can be identified by distinct patterns of histone modifications and TF binding. Promoters are enriched for H3K4me3, with active promoters showing evidence of PolII binding. The presence of the repressive mark at promoters and depletion of H3K4me3 is associated with inactive repressed promoters. Promoters having both H3K4me3 and H3K27me3 are termed bivalent promoters; they are repressed but poised for activation. Both poised and active enhancers are marked by the histone modification H3K4me1 and show depletion of H3K4me3. In addition, active enhancers are marked by H3K27ac and the binding of P300, whereas poised enhancers lack H3K27ac and may be marked by H3K27me3.