title: Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion.
abstract: The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes the accumulation of local H3K9me2 and subsequent Dnmt3a-mediated DNA methylation. Upon binding DNA, Oct4 recruits the histone lysine demethylase Jmjd1c. Chromatin immunoprecipitation (ChIP) time course experiments identify a stepwise Oct4 mechanism involving Jmjd1c recruitment and H3K9me2 demethylation, transient FACT (facilitates chromatin transactions) complex recruitment, and nucleosome depletion. Genome-wide and targeted ChIP confirms binding of newly synthesized Oct4, together with Jmjd1c and FACT, to the Pou5f1 enhancer and a small number of other Oct4 targets, including the Nanog promoter. Histone demethylation is required for both FACT recruitment and H3 depletion. Jmjd1c is required to induce endogenous Oct4 expression and fully reprogram fibroblasts to pluripotency, indicating that the assay system identifies functional Oct4 cofactors. These findings indicate that Oct4 sequentially recruits activities that catalyze histone demethylation and depletion.
authors.affiliation: Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA.
authors.forename: Arvind
authors.initials: A
authors.lastname: Shakya
authors.affiliation: Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA.
authors.forename: Catherine
authors.initials: C
authors.lastname: Callister
authors.affiliation: Broad Technology Labs, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Alon
authors.initials: A
authors.lastname: Goren
authors.affiliation: Department of Electrical Engineering and Computer Science, Center for Computational Biology, University of California, Berkeley, California, USA.
authors.forename: Nir
authors.initials: N
authors.lastname: Yosef
authors.affiliation: Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA.
authors.forename: Neha
authors.initials: N
authors.lastname: Garg
authors.affiliation: Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA.
authors.forename: Vahid
authors.initials: V
authors.lastname: Khoddami
authors.affiliation: Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA.
authors.forename: David
authors.initials: D
authors.lastname: Nix
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.affiliation: Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA dean.tantin@path.utah.edu.
authors.forename: Dean
authors.initials: D
authors.lastname: Tantin
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics; D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation / Q000379:methods; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000378:metabolism; D005347:Fibroblasts / Q000378:metabolism; D006657:Histones / Q000235:genetics / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D056484:Jumonji Domain-Containing Histone Demethylases / Q000235:genetics / Q000378:metabolism; D051379:Mice; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism*; D050814:Octamer Transcription Factor-3 / Q000235:genetics / Q000378:metabolism*; D039904:Pluripotent Stem Cells / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics
chemical_list: D004268:DNA-Binding Proteins; D006657:Histones; D018398:Homeodomain Proteins; D009707:Nucleosomes; D050814:Octamer Transcription Factor-3; D056484:Jumonji Domain-Containing Histone Demethylases; D004248:DNA (Cytosine-5-)-Methyltransferases