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Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
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Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation

Xinmin Zhang1, Duncan T Odom, Seung-Hoi Koo

  • 1The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.

Proceedings of the National Academy of Sciences of the United States of America
|March 9, 2005
PubMed

Insights

cAMP-response element binding protein (CREB) phosphorylation alone doesn't guarantee gene activation. Additional regulatory partners are needed to recruit transcriptional machinery to target gene promoters.

Area of Science:

  • Molecular Biology
  • Genetics
  • Cellular Signaling

Background:

  • Hormones and nutrients regulate gene expression through signaling pathways.
  • Cyclic adenosine monophosphate (cAMP) pathway activation involves protein kinase A (PKA)-mediated phosphorylation of cAMP-response element binding protein (CREB) at Ser-133.
  • CREB acts as a gene-specific activator in response to cellular signals.

Purpose of the Study:

  • To comprehensively identify and characterize CREB target genes across diverse cellular contexts using genome-wide approaches.
  • To investigate the relationship between CREB binding, phosphorylation, and gene induction.
  • To elucidate the regulatory mechanisms governing CREB-mediated gene expression.

Main Methods:

  • Genome-wide occupancy profiling to map CREB binding sites in vivo.
  • Analysis of CREB binding site characteristics, including the presence and methylation of cAMP response elements.
  • Assessment of CREB phosphorylation status upon stimulation with a cAMP agonist.
  • Quantitative analysis of gene expression changes in response to cAMP stimulation.

Main Results:

  • CREB was found to bind to approximately 4,000 promoter sites genome-wide, with binding profiles largely conserved across human tissues.
  • CREB phosphorylation was induced at a majority of binding sites upon cAMP agonist exposure.
  • Only a small subset of CREB target genes showed significant induction by cAMP, irrespective of cell type.
  • Preferential recruitment of the coactivator CREB-binding protein (CBP) was observed at a subset of induced promoters.

Conclusions:

  • CREB phosphorylation is necessary but not sufficient for target gene activation.
  • Additional regulatory factors and coactivators, such as CBP, are crucial for efficient recruitment of the transcriptional machinery.
  • CREB-mediated gene regulation is a complex process involving more than just phosphorylation status.

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