CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses.

ABSTRACT: Motif overrepresentation analysis of proximal promoters is a common approach to characterize the regulatory properties of co-expressed sets of genes. Here we show that these approaches perform well on mammalian CpG-depleted promoter sets that regulate expression in terminally differentiated tissues such as liver and heart. In contrast, CpG-rich promoters show very little overrepresentation signal, even when associated with genes that display highly constrained spatiotemporal expression. For instance, while approximately 50% of heart specific genes possess CpG-rich promoters we find that the frequently observed enrichment of MEF2-binding sites upstream of heart-specific genes is solely due to contributions from CpG-depleted promoters. Similar results are obtained for all sets of tissue-spec

SUBMITTER: Roider HG 

PROVIDER: S-EPMC2770660 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature