title: Interactions between pluripotency factors specify cis-regulation in embryonic stem cells.
abstract: We investigated how interactions between pluripotency transcription factors (TFs) affect cis-regulation. We created hundreds of synthetic cis-regulatory elements (CREs) comprised of combinations of binding sites for pluripotency TFs and measured their expression in mouse embryonic stem (ES) cells. A thermodynamic model that incorporates interactions between TFs explains a large portion (72%) of the variance in expression of these CREs. These interactions include three favorable heterotypic interactions between TFs. The model also predicts an unfavorable homotypic interaction between TFs, helping to explain the observation that homotypic chains of binding sites express at low levels. We further investigated the expression driven by CREs comprised of homotypic chains of KLF4 binding sites. Our results suggest that KLF homologs make unique contributions to regulation by these CREs. We conclude that a specific set of interactions between pluripotency TFs plays a large role in setting the levels of expression driven by CREs in ES cells.
authors.affiliation: Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Fiore
authors.affiliation: Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
authors.forename: Barak A
authors.initials: BA
authors.lastname: Cohen
mesh_terms: D000818:Animals; D001665:Binding Sites; D002478:Cells, Cultured; D015870:Gene Expression; D005786:Gene Expression Regulation; D015723:Gene Library; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors / Q000502:physiology; D051379:Mice; D008957:Models, Genetic; D000066450:Mouse Embryonic Stem Cells / Q000502:physiology*; D012045:Regulatory Sequences, Nucleic Acid; D013816:Thermodynamics; D014157:Transcription Factors / Q000502:physiology*
chemical_list: C000715468:Klf4 protein, mouse; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors; D014157:Transcription Factors