Chd1 regulates open chromatin and pluripotency of embryonic stem cells

An open chromatin largely devoid of heterochromatin is a hallmark of stem cells. It remains unknown whether an open chromatin is necessary for the differentiation potential of stem cells, and which molecules are needed to maintain open chromatin. Here we show that the chromatin remodelling factor Chd1 is required to maintain the open chromatin of pluripotent mouse embryonic stem cells. Chd1 is a euchromatin protein that associates with the promoters of active genes, and downregulation of Chd1 leads to accumulation of heterochromatin. Chd1-deficient embryonic stem cells are no longer pluripotent, because they are incapable of giving rise to primitive endoderm and have a high propensity for neural differentiation. Furthermore, Chd1 is required for efficient reprogramming of fibroblasts to the pluripotent stem cell state. Our results indicate that Chd1 is essential for open chromatin and pluripotency of embryonic stem cells, and for somatic cell reprogramming to the pluripotent state.

[1]  J. Utikal,et al.  Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. , 2007, Cell stem cell.

[2]  P. Reddien,et al.  Fundamentals of planarian regeneration. , 2004, Annual review of cell and developmental biology.

[3]  James A. Cuff,et al.  A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells , 2006, Cell.

[4]  Christina Chaivorapol,et al.  Systematic Identification of cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells , 2007, PLoS genetics.

[5]  R. Perry,et al.  CHD1 is concentrated in interbands and puffed regions of Drosophila polytene chromosomes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[6]  J. Zeitlinger,et al.  Polycomb complexes repress developmental regulators in murine embryonic stem cells , 2006, Nature.

[7]  T. Jenuwein,et al.  The many faces of histone lysine methylation. , 2002, Current opinion in cell biology.

[8]  Xi Chen,et al.  Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. , 2007, Genes & development.

[9]  S. Yamanaka,et al.  Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.

[10]  Radu Dobrin,et al.  Dissecting self-renewal in stem cells with RNA interference , 2006, Nature.

[11]  R. Jaenisch,et al.  In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state , 2007, Nature.

[12]  V. Pirrotta,et al.  CHD1 Motor Protein Is Required for Deposition of Histone Variant H3.3 into Chromatin in Vivo , 2007, Science.

[13]  G. Horgan,et al.  Relative expression software tool (REST©) for group-wise comparison and statistical analysis of relative expression results in real-time PCR , 2002 .

[14]  Paul Tempst,et al.  Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. , 2007, Molecular cell.

[15]  Daniel J. Hoeppner,et al.  Global transcription in pluripotent embryonic stem cells. , 2008, Cell stem cell.

[16]  F. Collins,et al.  Characterization of the CHD family of proteins. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[17]  N. D. Clarke,et al.  Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells , 2008, Cell.

[18]  Mike J. Mason,et al.  Role of the Murine Reprogramming Factors in the Induction of Pluripotency , 2009, Cell.

[19]  Danny Reinberg,et al.  Human but Not Yeast CHD1 Binds Directly and Selectively to Histone H3 Methylated at Lysine 4 via Its Tandem Chromodomains* , 2005, Journal of Biological Chemistry.

[20]  Hien G. Tran,et al.  Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes , 2003, The EMBO journal.

[21]  P. Lansdorp,et al.  Sequential generations of hematopoietic colonies derived from single nonlineage-committed CD34+CD38- progenitor cells. , 1991, Blood.

[22]  E. Morrisey,et al.  GATA6 regulates HNF4 and is required for differentiation of visceral endoderm in the mouse embryo. , 1998, Genes & development.

[23]  J. Miyazaki,et al.  Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells , 2000, Nature Genetics.

[24]  I. Weissman,et al.  Purification and characterization of mouse hematopoietic stem cells. , 1988, Science.

[25]  A. Tong,et al.  Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z , 2007, Proceedings of the National Academy of Sciences.

[26]  M. Ramalho-Santos,et al.  Generation of induced pluripotent stem cells in the absence of drug selection. , 2007, Cell stem cell.

[27]  T. Mikkelsen,et al.  Dissecting direct reprogramming through integrative genomic analysis , 2008, Nature.

[28]  D. Melton,et al.  "Stemness": Transcriptional Profiling of Embryonic and Adult Stem Cells , 2002, Science.

[29]  Marius Wernig,et al.  A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types , 2008, Nature Biotechnology.

[30]  Steven C. Lawlor,et al.  MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data , 2003, Genome Biology.

[31]  P. Sharp,et al.  Cre-lox-regulated conditional RNA interference from transgenes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[32]  A. Reynolds,et al.  Rational siRNA design for RNA interference , 2004, Nature Biotechnology.

[33]  B. Wang,et al.  Changing potency by spontaneous fusion , 2022 .

[34]  Philip R. Gafken,et al.  Histone H3.3 is enriched in covalent modifications associated with active chromatin. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[35]  R. Lahesmaa,et al.  Gene Expression Signatures of Seven Individual Human Embryonic Stem Cell Lines , 2005, Stem cells.

[36]  A. Kimura,et al.  Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing , 2002, Nature Genetics.

[37]  T. Ichisaka,et al.  Generation of germline-competent induced pluripotent stem cells , 2007, Nature.

[38]  T. Misteli,et al.  Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. , 2006, Developmental cell.

[39]  C. Li,et al.  Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. , 2001, Proceedings of the National Academy of Sciences of the United States of America.