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

Genome Res. 2011 Jul;21(7):1055-64. doi: 10.1101/gr.115824.110. Epub 2011 Apr 28.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Binding Sites / genetics
  • Blotting, Western
  • Cells, Cultured
  • Chromatin Immunoprecipitation
  • Chromosome Mapping
  • Electrophoresis, Polyacrylamide Gel
  • Gene Expression Regulation, Developmental
  • Genome*
  • High-Throughput Nucleotide Sequencing
  • Homeodomain Proteins / genetics*
  • Homeodomain Proteins / metabolism
  • Humans
  • Octamer Transcription Factor-1 / genetics*
  • Octamer Transcription Factor-1 / metabolism
  • Octamer Transcription Factor-3 / genetics*
  • Octamer Transcription Factor-3 / metabolism
  • Promoter Regions, Genetic
  • Protein Binding / genetics
  • SOXB1 Transcription Factors / genetics
  • SOXB1 Transcription Factors / metabolism


  • Homeodomain Proteins
  • Octamer Transcription Factor-1
  • Octamer Transcription Factor-3
  • SOXB1 Transcription Factors

Associated data

  • GEO/GSE27535