Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins.
Previously, 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 (X(4)-N(1-30)-X(4)) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif ((C/G)CCGGAAGCGGAA) and the ETS⇔CRE motif ((C/G)CGGAAGTGACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETS⇔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 GABPα and the B-ZIP protein CREB preferentially bind to the ETS⇔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 ETS⇔CRE. The 11-mer (CGGAAGTGACG), the conserved part of the ETS⇔CRE motif, occurs 226 times in the human genome and 83% are in known regulatory regions. In vivo GABPα and CREB ChIP-seq peaks identified the ETS⇔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.
Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Raghunath
R
Chatterjee
Jianfei
J
Zhao
Ximiao
X
He
Andrey
A
Shlyakhtenko
Ishminder
I
Mann
Joshua J
JJ
Waterfall
Paul
P
Meltzer
B K
BK
Sathyanarayana
Peter C
PC
FitzGerald
Charles
C
Vinson
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D017362:Cyclic AMP Response Element-Binding Protein / Q000737:chemistry / Q000378:metabolism*; D019175:DNA Methylation; D051268:GA-Binding Protein Transcription Factor / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D051379:Mice; D062105:Molecular Docking Simulation; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D011487:Protein Conformation; D050783:Proto-Oncogene Proteins c-ets / Q000737:chemistry / Q000235:genetics*
D017362:Cyclic AMP Response Element-Binding Protein; D051268:GA-Binding Protein Transcription Factor; C495661:GABPA protein, human; D050783:Proto-Oncogene Proteins c-ets