Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

摘要

pPreviously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promoters and grouped them into known transcription factor binding sites (TFBS). We now examine split 8-mers consisting of two 4-mers separated by 1-bp to 30-bps (Xsub4/sub-Nsub1-30/sub-Xsub4/sub) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETSa?”ETS motif (supC/sup/subG/subCCGGAAbG/bCGGAA) and the ETSa?”CRE motif (supC/sup/subG/subCGGAAbGTG/bACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETSa?”CRE motif can be bound simultaneously by both the ETS and the B-ZIP domains without protein-protein clashes. The electrophoretic mobility shift assay (EMSA) shows that the ETS protein GABP?± and the B-ZIP protein CREB preferentially bind to the ETSa?”CRE motif only when the two TFBS overlap precisely. In contrast, the ETS domain of ETV5 and CREB interfere with each other for binding the ETSa?”CRE. The 11-mer (CGGAAbGTG/bACG), the conserved part of the ETSa?”CRE motif, occurs 226 times in the human genome and 83% are in known regulatory regions. iIn vivo/i GABP?± and CREB ChIP-seq peaks identified the ETSa?”CRE as the most enriched motif occurring in promoters of genes involved in mRNA processing, cellular catabolic processes, and stress response, suggesting that a specific class of genes is regulated by this composite motif./p