Defining the CREB Regulon; A Genome-Wide Analysis of Transcription Factor Regulatory Regions

Authors:
Impey S, McCorkle SR, Cha-Molstad H, Dwyer JM, Yochum GS, Boss JM, McWeeney S, Dunn JJ, Mandel G and Goodman RH
In:
Source: Cell
Publication Date: (2004)
Issue: 119(7): 1041-1054
Research Area:
Neurobiology
Cells used in publication:
PC-12
Species: rat
Tissue Origin: adrenal
Platform:
Nucleofectorâ„¢ I/II/2b
Experiment
PC12 cells (rat pheochromocytoma cell line) were transfected by nucleofection with expression plasmids for GFP or ACREB, a dominant-negative CREB mutant.
Abstract
The CREB transcription factor regulates differentiation, survival, and synaptic plasticity. The complement of CREB targets responsible for these responses has not been identified, however. We developed a novel approach to identify CREB targets, termed serial analysis of chromatin occupancy (SACO), by combining chromatin immunoprecipitation (ChIP) with a modification of SAGE. Using a SACO library derived from rat PC12 cells, we identified approximately 41,000 genomic signature tags (GSTs) that mapped to unique genomic loci. CREB binding was confirmed for all loci supported by multiple GSTs. Of the 6302 loci identified by multiple GSTs, 40% were within 2 kb of the transcriptional start of an annotated gene, 49% were within 1 kb of a CpG island, and 72% were within 1 kb of a putative cAMP-response element (CRE). A large fraction of the SACO loci delineated bidirectional promoters and novel antisense transcripts. This study represents the most comprehensive definition of transcription factor binding sites in a metazoan species.