Chromatin remodeling in Embryonic stem cells: Regulating the balance between pluripotency and differentiation

Embryonic stem cells have an unlimited potential for self‐renewal yet are pluripotent, capable of differentiating into three different germ layers and ultimately into multiple cell lineages. Key pluripotency specific factors maintain an undifferentiated ES cell phenotype while lineage specific factors work in opposition to promote cell specialization. In addition to these important transcriptional regulators, epigenetic modifiers play a defining role in regulating the balance between pluripotency and differentiation by promoting changes in chromatin structure. J. Cell. Physiol. 219: 1–7, 2009. © 2008 Wiley‐Liss, Inc.

[1]  C. Chen,et al.  Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of theHPRT Promoter , 2001, Molecular and Cellular Biology.

[2]  Ryo Matoba,et al.  BAF250B‐Associated SWI/SNF Chromatin‐Remodeling Complex Is Required to Maintain Undifferentiated Mouse Embryonic Stem Cells , 2008, Stem cells.

[3]  S. Henikoff,et al.  Assembly of variant histones into chromatin. , 2005, Annual review of cell and developmental biology.

[4]  G. Natoli,et al.  The Histone H3 Lysine-27 Demethylase Jmjd3 Links Inflammation to Inhibition of Polycomb-Mediated Gene Silencing , 2007, Cell.

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

[6]  S. Elgin,et al.  The role of a positioned nucleosome at the Drosophila melanogaster hsp26 promoter. , 1995, The EMBO journal.

[7]  K. Helin,et al.  Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. , 2008, Genes & development.

[8]  M. Yaniv,et al.  ras transformation is associated with decreased expression of the brm/SNF2α ATPase from the mammalian SWI–SNF complex , 1998, The EMBO journal.

[9]  E. Morii,et al.  Inhibitory effect of the transcription factor encoded by the mutant mi microphthalmia allele on transactivation of mouse mast cell protease 7 gene. , 2001, Blood.

[10]  K. Helin,et al.  RBP2 Belongs to a Family of Demethylases, Specific for Tri-and Dimethylated Lysine 4 on Histone 3 , 2007, Cell.

[11]  I. Issaeva,et al.  UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development , 2007, Nature.

[12]  G. Lyons,et al.  The Polycomb Ezh2 methyltransferase regulates muscle gene expression and skeletal muscle differentiation. , 2004, Genes & development.

[13]  B. Amati,et al.  Tip60 in DNA damage response and growth control: many tricks in one HAT. , 2006, Trends in cell biology.

[14]  Jun S. Song,et al.  High-throughput mapping of the chromatin structure of human promoters , 2007, Nature Biotechnology.

[15]  Giacomo Cavalli,et al.  Chromatin and epigenetics in development: blending cellular memory with cell fate plasticity , 2006, Development.

[16]  K. Zaret,et al.  An active tissue-specific enhancer and bound transcription factors existing in a precisely positioned nucleosomal array , 1993, Cell.

[17]  Bing Li,et al.  The Role of Chromatin during Transcription , 2007, Cell.

[18]  R Blossey,et al.  Regulating chromatin: On code and dynamic models , 2006, The European physical journal. E, Soft matter.

[19]  Haruhiko Koseki,et al.  Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. , 2004, Developmental cell.

[20]  T. Magnuson,et al.  Imprinted X inactivation maintained by a mouse Polycomb group gene , 2001, Nature Genetics.

[21]  N. Schork,et al.  The Polycomb-group gene eed is required for normal morphogenetic movements during gastrulation in the mouse embryo. , 1998, Development.

[22]  G. Daley,et al.  Molecular basis of pluripotency. , 2008, Human molecular genetics.

[23]  Rudolf Jaenisch,et al.  Molecular control of pluripotency. , 2006, Current opinion in genetics & development.

[24]  C. Robson,et al.  Cellular functions of TIP60. , 2006, The international journal of biochemistry & cell biology.

[25]  Stormy J. Chamberlain,et al.  The Murine Polycomb Group Protein Eed Is Required for Global Histone H3 Lysine-27 Methylation , 2005, Current Biology.

[26]  Stephan Sauer,et al.  Chromatin signatures of pluripotent cell lines , 2006, Nature Cell Biology.

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

[28]  E. Ballestar,et al.  Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation , 1999, Nature Genetics.

[29]  Jeffrey L. Wrana,et al.  Baf60c is essential for function of BAF chromatin remodelling complexes in heart development , 2004, Nature.

[30]  K. Helin,et al.  Polycomb Group Proteins in Cell Cycle Progression and Cancer , 2004, Cell cycle.

[31]  R. B. Redmon,et al.  Identity , 2021, Notre Dame J. Formal Log..

[32]  R. Tjian,et al.  Polybromo protein BAF180 functions in mammalian cardiac chamber maturation. , 2004, Genes & development.

[33]  D. Reinberg,et al.  Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. , 2004, Genes & development.

[34]  Suresh Cuddapah,et al.  The genomic landscape of histone modifications in human T cells , 2006, Proceedings of the National Academy of Sciences.

[35]  Daniel Chourrout,et al.  Genome Regulation by Polycomb and Trithorax Proteins , 2007, Cell.

[36]  X. Chen,et al.  The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells , 2006, Nature Genetics.

[37]  Yasuyuki Ohkawa,et al.  Chromatin remodelling in mammalian differentiation: lessons from ATP-dependent remodellers , 2006, Nature Reviews Genetics.

[38]  Kristian Helin,et al.  The Polycomb Group Protein Suz12 Is Required for Embryonic Stem Cell Differentiation , 2007, Molecular and Cellular Biology.

[39]  W. Bickmore,et al.  Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. , 2004, Genes & development.

[40]  C. Niehrs,et al.  Nuclear Reprogramming of Human Somatic Cells by Xenopus Egg Extract Requires BRG1 , 2004, Current Biology.

[41]  Michael Y Tolstorukov,et al.  Nucleosome positioning in human HOX gene clusters. , 2008, Genome research.

[42]  J. Seavitt,et al.  The chromatin remodeler Mi-2beta is required for CD4 expression and T cell development. , 2004, Immunity.

[43]  Wendy A Bickmore,et al.  Nuclear re-organisation of the Hoxb complex during mouse embryonic development , 2005, Development.

[44]  B. Panning,et al.  An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity , 2008, Cell.

[45]  M. Surani,et al.  The Polycomb-Group GeneEzh2 Is Required for Early Mouse Development , 2001, Molecular and Cellular Biology.

[46]  Wendy A Bickmore,et al.  Does looping and clustering in the nucleus regulate gene expression? , 2004, Current opinion in cell biology.

[47]  K. Helin,et al.  Coordinated regulation of transcriptional repression by the RBP2 H3K4 demethylase and Polycomb-Repressive Complex 2. , 2008, Genes & development.

[48]  A. Sands,et al.  Disruption of Ini1 Leads to Peri-Implantation Lethality and Tumorigenesis in Mice , 2001, Molecular and Cellular Biology.

[49]  G. Keller,et al.  Embryonic stem cell differentiation: emergence of a new era in biology and medicine. , 2005, Genes & development.

[50]  J. Yates,et al.  BRD7, a Novel PBAF-specific SWI/SNF Subunit, Is Required for Target Gene Activation and Repression in Embryonic Stem Cells* , 2008, Journal of Biological Chemistry.

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

[52]  T. Kouzarides.  Chromatin Modifications and Their Function , 2007, Cell.

[53]  K. Helin,et al.  Bypass of senescence by the polycomb group protein CBX8 through direct binding to the INK4A‐ARF locus , 2007, The EMBO journal.

[54]  Michael O. Dorschner,et al.  Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells. , 2008, Genes & development.

[55]  J. Workman,et al.  Activation domains drive nucleosome eviction by SWI/SNF , 2007, The EMBO journal.

[56]  Jun Qin,et al.  Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells , 2008, Nature Cell Biology.

[57]  Megan F. Cole,et al.  Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells , 2006, Cell.

[58]  Dustin E. Schones,et al.  Dynamic Regulation of Nucleosome Positioning in the Human Genome , 2008, Cell.

[59]  T. Luckenbach,et al.  Evidence for Histone Eviction in trans upon Induction of the Yeast PHO5 Promoter , 2004, Molecular and Cellular Biology.

[60]  T. Misteli,et al.  Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus , 2006, Journal of Cell Science.

[61]  R. Tjian,et al.  ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a , 2008, Proceedings of the National Academy of Sciences.

[62]  Dimitris Thanos,et al.  Nucleosome Sliding via TBP DNA Binding In Vivo , 2001, Cell.

[63]  S. Denslow,et al.  The human Mi-2/NuRD complex and gene regulation , 2007, Oncogene.

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

[65]  Sharmistha Pal,et al.  The Protein Arginine Methyltransferase Prmt5 Is Required for Myogenesis because It Facilitates ATP-Dependent Chromatin Remodeling , 2006, Molecular and Cellular Biology.

[66]  C. Peterson,et al.  Heterochromatin assembly: A new twist on an old model , 2006, Chromosome Research.

[67]  Ianessa Morantte,et al.  Functional interdependence at the chromatin level between the MKK6/p38 and IGF1/PI3K/AKT pathways during muscle differentiation. , 2007, Molecular cell.

[68]  Xiaomei Wang,et al.  Distinct mammalian SWI/SNF chromatin remodeling complexes with opposing roles in cell‐cycle control , 2007, The EMBO journal.

[69]  Jiangwen Zhang,et al.  The role of the chromatin remodeler Mi-2beta in hematopoietic stem cell self-renewal and multilineage differentiation. , 2008, Genes & development.

[70]  Kristian Helin,et al.  Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. , 2006, Genes & development.

[71]  Tom Misteli,et al.  Chromatin in pluripotent embryonic stem cells and differentiation , 2006, Nature Reviews Molecular Cell Biology.

[72]  J. Nichols,et al.  The NuRD component Mbd3 is required for pluripotency of embryonic stem cells , 2006, Nature Cell Biology.

[73]  Stephen N. Jones,et al.  Loss of the INI1 tumor suppressor does not impair the expression of multiple BRG1-dependent genes or the assembly of SWI/SNF enzymes , 2004, Oncogene.

[74]  Min Gyu Lee,et al.  Demethylation of H3K27 Regulates Polycomb Recruitment and H2A Ubiquitination , 2007, Science.

[75]  M. Yaniv,et al.  The murine SNF5/INI1 chromatin remodeling factor is essential for embryonic development and tumor suppression , 2000, EMBO reports.

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

[77]  S. Sif.  ATP‐dependent nucleosome remodeling complexes: Enzymes tailored to deal with chromatin , 2004, Journal of cellular biochemistry.

[78]  R. DePinho,et al.  The oncogene and Polycomb-group gene bmi-1 regulates cell proliferation and senescence through the ink4a locus , 1999, Nature.

[79]  M. Vidal,et al.  Role of histone H2A ubiquitination in Polycomb silencing , 2004, Nature.

[80]  C. Roberts,et al.  Haploinsufficiency of Snf5 (integrase interactor 1) predisposes to malignant rhabdoid tumors in mice. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[81]  F Randazzo,et al.  A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes. , 2000, Molecular cell.

[82]  Debashis Ghosh,et al.  EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[83]  T. Rasmussen,et al.  Global Epiproteomic Signatures Distinguish Embryonic Stem Cells from Differentiated Cells , 2007, Stem cells.