Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues

Abstract

Hormones and nutrients often induce genetic programs via signaling pathways that interface with gene-specific activators. Activation of the cAMP pathway, for example, stimulates cellular gene expression by means of the PKA-mediated phosphorylation of cAMP-response element binding protein (CREB) at Ser-133. Here, we use genome-wide approaches to characterize target genes that are regulated by CREB in different cellular contexts. CREB was found to occupy Ϸ4,000 promoter sites in vivo, depending on the presence and methylation state of consensus cAMP response elements near the promoter. The profiles for CREB occupancy were very similar in different human tissues, and exposure to a cAMP agonist stimulated CREB phosphorylation over a majority of these sites. Only a small proportion of CREB target genes was induced by cAMP in any cell type, however, due in part to the preferential recruitment of the coactivator CREB-binding protein to those promoters. These results indicate that CREB phosphorylation alone is not a reliable predictor of target gene activation and that additional CREB regulatory partners are required for recruitment of the transcriptional apparatus to the promoter.cAMP ͉ cAMP-response element binding protein-binding protein ͉ DNA methylation T he concept of a transcription code that dictates gene expression by means of the concerted action of multiple promoter elements has served as a useful paradigm for understanding specificity in gene regulation. The ability of multiple transcription factors to recruit RNA polymerase II to the promoter by means of low affinity interactions with components of the transcriptional machinery has been documented extensively (1).By contrast with this model, other studies suggest that some activators per se are sufficient to mediate transcriptional responses to hormonal signals depending on the occupancy of relevant sites (1). Indeed, genome-wide studies comparing binding patterns of hepatic nuclear factors in the liver and endocrine pancreas indicate that selective occupancy may often explain how different genetic programs are activated in distinct cell types (2).The cAMP-response element binding protein (CREB) family of activators stimulates cellular gene expression after phosphorylation at a conserved serine (Ser-133 in CREB1) in response to cAMP (3). Ser-133 phosphorylation promotes target gene activation in part by means of recruitment of the coactivator paralogs CREB-binding protein (CBP)͞p300 (4). Recruitment of CBP by phospho-CREB (P-CREB) appears sufficient for induction of cellular genes in response to cAMP (5, 6); in vitro transcription studies indicate that P-CREB is capable of promoting assembly of the transcriptional apparatus independent of other regulatory inputs (7).By contrast, some reports suggest that other upstream activators in addition to CREB are required for cellular gene induction by cAMP (8). Indeed, the notion that CREB coordinates with other transcription factors is supported by recent animal studies in which CREB appeared to elicit the expressi...

A Key Role for Cyclic AMP-Responsive Element Binding Protein in Hypoxia-Mediated Activation of the Angiogenesis Factor CCN1 (CYR61) in Tumor Cells

“…This suggests that phosphorylation of CREB and activation of a subset of hypoxiaresponsive genes may be an adaptive cellular response to a reduction in O 2 levels. Our results are in accordance with other studies that report increased sustained phosphorylation of CREB in response to hypoxia (11,35,48,52).…”

“…cAMP and Prostaglandin E2 Increase CCN1 Promoter Activity via the PKA Signal Transduction Pathway Bioinformatics analysis suggested two putative half CRE sites designated Cre1 and Cre2 at positions À801 and À64, respectively, in the CCN1 promoter region (32,35). As yet, no direct proof for cAMP-and CREB-mediated control of mouse CCN1 was shown.…”

“…As yet, no direct proof for cAMP-and CREB-mediated control of mouse CCN1 was shown. To test the effect of cAMP on activation of the CCN1 promoter, the plasmid vector, pCYRluc, harboring the CCN1 promoter from position À2062 to +65 (32,35), fused to the luc gene, was transfected into Rev-2-T-6 cells derived from the S49 T-cell lymphoma (36). Following transfection, cells were treated at different times (2-24 hours) with either 8-bromo-cAMP (0.1-2 mmol/L) or with 1 to 1,000 nmol/L prostaglandin E2 (PGE2), known to elevate intracellular cAMP (37).…”

Deviant effects in molecular reaction pathways

“…Notably, this and similar mechanisms are readily found in a wide assortment of natural settings, including, among others, the dynamic elements of branching-chain chemical reactions 1 , cAMP-induced PKA control 13,14 , simple models of transcriptional autoregulation (n > 1), Rep-family replication initiator protein regulation 15 Figure 1 Characteristic CME distribution examples. Schematic representation of characteristic cases of possible instantaneous CME system state probability distributions and their effects on the fidelity of CCK description.…”

Regulation of VEGF-A Expression in Endothelial Cells by Transcriptional Gene Activation or Transcriptional Gene Silencing: Analysis of Genome Wide Transcriptional Response

“…The targeting strand of this shRNA contains one mismatch (G to T) in the middle part of the sequence and this area in the murine VEGF-A promoter contains a conserved cAMP response element (CRE). CREB, which binds to CRE [23], regulates the H3K27 acetylation by binding CREB binding protein (CBP)/p300 and CREB Regulated Transcription Coactivator (CRTC) [24]. When cells were treated with CBP-CREB interaction inhibitor, the shRNA-mediated VEGF-A upregulation was reduced to the level of shRNA control [9].…”