title: Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation.
abstract: Embryonic stem cells (ESCs) possess a distinct chromatin conformation maintained by specialized chromatin proteins. To identify chromatin regulators in ESCs, we developed a simple biochemical assay named D-CAP (differential chromatin-associated proteins), using brief micrococcal nuclease digestion of chromatin, followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Using D-CAP, we identified several differentially chromatin-associated proteins between undifferentiated and differentiated ESCs, including the chromatin remodeling protein SMARCD1. SMARCD1 depletion in ESCs led to altered chromatin and enhanced endodermal differentiation. Gene expression and chromatin immunoprecipitation sequencing (ChIP-seq) analyses suggested that SMARCD1 is both an activator and a repressor and is enriched at developmental regulators and that its chromatin binding coincides with H3K27me3. SMARCD1 knockdown caused H3K27me3 redistribution and increased H3K4me3 around the transcription start site (TSS). One of the identified SMARCD1 targets was Klf4. In SMARCD1-knockdown clones, KLF4, as well as H3K4me3 at the Klf4 locus, remained high and H3K27me3 was abolished. These results propose a role for SMARCD1 in restricting pluripotency and activating lineage pathways by regulating H3K27 methylation.
authors.affiliation: Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
authors.forename: Adi
authors.initials: A
authors.lastname: Alajem
authors.affiliation: Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
authors.forename: Alva
authors.initials: A
authors.lastname: Biran
authors.affiliation: Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
authors.forename: Arigela
authors.initials: A
authors.lastname: Harikumar
authors.affiliation: Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
authors.forename: Badi Sri
authors.initials: BS
authors.lastname: Sailaja
authors.affiliation: Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
authors.forename: Yair
authors.initials: Y
authors.lastname: Aaronson
authors.affiliation: Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
authors.forename: Ilana
authors.initials: I
authors.lastname: Livyatan
authors.affiliation: Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
authors.forename: Malka
authors.initials: M
authors.lastname: Nissim-Rafinia
authors.affiliation: Section of Gastroenterology, Department of Medicine, Center for Regenerative Medicine (CReM), Boston University School of Medicine, 670 Albany Street, Suite 209, Boston, MA 02118, USA.
authors.forename: Andreia Gianotti
authors.initials: AG
authors.lastname: Sommer
authors.affiliation: Section of Gastroenterology, Department of Medicine, Center for Regenerative Medicine (CReM), Boston University School of Medicine, 670 Albany Street, Suite 209, Boston, MA 02118, USA.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Mostoslavsky
authors.affiliation: Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA; Naval Medical Research Center, Silver Spring, MD 20910, USA.
authors.forename: Vincent R
authors.initials: VR
authors.lastname: Gerbasi
authors.affiliation: Merial Inc., a Sanofi Company, Duluth, GA 30096, USA.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Golden
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
authors.forename: Arnab
authors.initials: A
authors.lastname: Datta
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
authors.forename: Siu Kwan
authors.initials: SK
authors.lastname: Sze
authors.affiliation: Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel. Electronic address: meshorer@huji.ac.il.
authors.forename: Eran
authors.initials: E
authors.lastname: Meshorer
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics* / Q000502:physiology*; D002843:Chromatin / Q000378:metabolism*; D002868:Chromosomal Proteins, Non-Histone / Q000378:metabolism*; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D006657:Histones / Q000378:metabolism; D056484:Jumonji Domain-Containing Histone Demethylases / Q000235:genetics; D000090062:Kruppel-Like Factor 4; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000166:cytology* / Q000378:metabolism*
chemical_list: D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D006657:Histones; C000715468:Klf4 protein, mouse; D000090062:Kruppel-Like Factor 4; C529549:Smarcd1 protein, mouse; D056484:Jumonji Domain-Containing Histone Demethylases; C523761:Kdm6b protein, mouse