Combinatorial binding of transcription factors in the pluripotency control regions of the genome

Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA.
Genome Research (Impact Factor: 14.63). 04/2011; 21(7):1055-64. DOI: 10.1101/gr.115824.110
Source: PubMed


The pluripotency control regions (PluCRs) are defined as genomic regions that are bound by POU5F1, SOX2, and NANOG in vivo. We utilized a high-throughput binding assay to record more than 270,000 different DNA/protein binding measurements along incrementally tiled windows of DNA within these PluCRs. This high-resolution binding map is then used to systematically define the context of POU factor binding, and reveals patterns of cooperativity and competition in the pluripotency network. The most prominent pattern is a pervasive binding competition between POU5F1 and the forkhead transcription factors. Like many transcription factors, POU5F1 is co-expressed with a paralog, POU2F1, that shares an apparently identical binding specificity. By analyzing thousands of binding measurements, we discover context effects that discriminate POU2F1 from POU5F1 binding. Proximal NANOG binding promotes POU5F1 binding, whereas nearby SOX2 binding favors POU2F1. We demonstrate by cross-species comparison and by chromatin immunoprecipitation (ChIP) that the contextual sequence determinants learned in vitro are sufficient to predict POU2F1 binding in vivo.

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    • "However, these higher-order multi-protein mechanisms cause difficulties in constructing models, primarily due to the fact that DNA-binding models of proteins examined in isolation may not capture the binding sites utilized in vivo when cofactors are present. Here again, HT technologies are being used successfully to characterize binding of multi-protein complexes, revealing recognition codes mediated by cooperative binding (40,133) and cofactor-mediated targeting (48). The continued application of HT technologies to examine DNA binding of multi-protein complexes will undoubtedly provide increasingly refined binding models and provide new insights into gene targeting in vivo. "
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