TY - JOUR
T1 - Defining the CREB regulon
T2 - A genome-wide analysis of transcription factor regulatory regions
AU - Impey, Soren
AU - McCorkle, Sean R.
AU - Cha-Molstad, Hyunjoo
AU - Dwyer, Jami M.
AU - Yochum, Gregory S.
AU - Boss, Jeremy M.
AU - McWeeney, Shannon
AU - Dunn, John J.
AU - Mandel, Gail
AU - Goodman, Richard H.
N1 - Funding Information:
We thank David Ginty for anti-CREB antisera used in preliminary experiments and Yasuhiro Yoshimatsu and Ryan Cleland for analysis and discussion. We also thank Qinghong Zhang and Karl Obrietan for their comments on the manuscript. This work was supported by grants from the NIH, DOE, and Howard Hughes Medical Institute.
PY - 2004/12/29
Y1 - 2004/12/29
N2 - 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 ∼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.
AB - 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 ∼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.
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U2 - 10.1016/j.cell.2004.10.032
DO - 10.1016/j.cell.2004.10.032
M3 - Article
C2 - 15620361
AN - SCOPUS:19944367254
SN - 0092-8674
VL - 119
SP - 1041
EP - 1054
JO - Cell
JF - Cell
IS - 7
ER -