Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions.

Polycomb repressive complex 2 (PRC2) plays crucial roles in transcriptional regulation and stem cell development. However, the context-specific functions associated with alternative subunits remain largely unexplored. Here we show that the related enzymatic subunits EZH1 and EZH2 undergo an expression switch during blood cell development. An erythroid-specific enhancer mediates transcriptional activation of EZH1, and a switch from GATA2 to GATA1 controls the developmental EZH1/2 switch by differential association with EZH1 enhancers. We further examine the in vivo stoichiometry of the PRC2 complexes by quantitative proteomics and reveal the existence of an EZH1-SUZ12 subcomplex lacking EED. EZH1 together with SUZ12 form a non-canonical PRC2 complex, occupy active chromatin, and positively regulate gene expression. Loss of EZH2 expression leads to repositioning of EZH1 to EZH2 targets. Thus, the lineage- and developmental stage-specific regulation of PRC2 subunit composition leads to a switch from canonical silencing to non-canonical functions during blood stem cell specification.

[1]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[2]  D. Reinberg,et al.  Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. , 2008, Molecular cell.

[3]  Christopher D. Brown,et al.  Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis. , 2012, Blood.

[4]  D. Schwarzer,et al.  Chromatin regulated interchange between polycomb repressive complex 2 (PRC2)-Ezh2 and PRC2-Ezh1 complexes controls myogenin activation in skeletal muscle cells , 2011, Epigenetics & Chromatin.

[5]  Brigitte Wild,et al.  Histone Methyltransferase Activity of a Drosophila Polycomb Group Repressor Complex , 2002, Cell.

[6]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[7]  Masayuki Yamamoto,et al.  GATA factor switching during erythroid differentiation , 2010, Current opinion in hematology.

[8]  M. Montecino,et al.  Ezh1 and Ezh2 differentially regulate PSD-95 gene transcription in developing hippocampal neurons , 2013, Molecular and Cellular Neuroscience.

[9]  S. Orkin,et al.  Transcriptional silencing of {gamma}-globin by BCL11A involves long-range interactions and cooperation with SOX6. , 2010, Genes & development.

[10]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[11]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

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

[13]  V. Sartorelli,et al.  Polycomb protein Ezh1 promotes RNA polymerase II elongation. , 2012, Molecular cell.

[14]  S. Orkin,et al.  Polycomb repressive complex 2 regulates normal hematopoietic stem cell function in a developmental-stage-specific manner. , 2014, Cell stem cell.

[15]  K. Helin,et al.  Transcriptional regulation by Polycomb group proteins , 2013, Nature Structural &Molecular Biology.

[16]  Hao Wang,et al.  Global regulation of erythroid gene expression by transcription factor GATA-1. , 2004, Blood.

[17]  A. Jankowska,et al.  Novel homo- and hemizygous mutations in EZH2 in myeloid malignancies , 2010, Leukemia.

[18]  V. Pirrotta,et al.  Drosophila Enhancer of Zeste/ESC Complexes Have a Histone H3 Methyltransferase Activity that Marks Chromosomal Polycomb Sites , 2002, Cell.

[19]  H. Mikkola,et al.  The first trimester human placenta is a site for terminal maturation of primitive erythroid cells. , 2010, Blood.

[20]  S. González,et al.  Ezh1 is required for hematopoietic stem cell maintenance and prevents senescence-like cell cycle arrest. , 2012, Cell stem cell.

[21]  R. Aebersold,et al.  An Essential Switch in Subunit Composition of a Chromatin Remodeling Complex during Neural Development , 2007, Neuron.

[22]  Qiang Yu,et al.  Context-specific regulation of NF-κB target gene expression by EZH2 in breast cancers. , 2011, Molecular cell.

[23]  Tohru Fujiwara,et al.  Context-dependent function of "GATA switch" sites in vivo. , 2011, Blood.

[24]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[25]  H. Drexler,et al.  Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders , 2010, Nature Genetics.

[26]  Yan Liu,et al.  EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations , 2012, Nature.

[27]  S. Dhanasekaran,et al.  The polycomb group protein EZH2 is involved in progression of prostate cancer , 2002, Nature.

[28]  C. Nislow,et al.  Mammalian homologues of the Polycomb‐group gene Enhancer of zeste mediate gene silencing in Drosophila heterochromatin and at S.cerevisiae telomeres , 1997, The EMBO journal.

[29]  Yong Jiang,et al.  Mutation of A677 in histone methyltransferase EZH2 in human B-cell lymphoma promotes hypertrimethylation of histone H3 on lysine 27 (H3K27) , 2012, Proceedings of the National Academy of Sciences.

[30]  Dustin E. Schones,et al.  Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. , 2009, Cell stem cell.

[31]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[32]  S. Orkin,et al.  Targeted Disruption of the EZH2/EED Complex Inhibits EZH2-dependent Cancer , 2013, Nature chemical biology.

[33]  D. Reinberg,et al.  Nucleosome-binding activities within JARID2 and EZH1 regulate the function of PRC2 on chromatin , 2013, Genes & development.

[34]  H. Pasolli,et al.  EZH1 and EZH2 cogovern histone H3K27 trimethylation and are essential for hair follicle homeostasis and wound repair. , 2011, Genes & development.

[35]  D. Reinberg,et al.  The Polycomb complex PRC2 and its mark in life , 2011, Nature.

[36]  Hengbin Wang,et al.  Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing , 2002, Science.

[37]  Tim J. Wigle,et al.  A selective inhibitor of EZH2 blocks H3K27 methylation and kills mutant lymphoma cells. , 2012, Nature chemical biology.

[38]  D. Reinberg,et al.  Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. , 2002, Genes & development.

[39]  G. Crabtree,et al.  Reversible Disruption of mSWI/SNF (BAF) Complexes by the SS18-SSX Oncogenic Fusion in Synovial Sarcoma , 2013, Cell.

[40]  Guo-Cheng Yuan,et al.  EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. , 2008, Molecular cell.

[41]  Jonghwan Kim,et al.  Use of in vivo biotinylation to study protein–protein and protein–DNA interactions in mouse embryonic stem cells , 2009, Nature Protocols.

[42]  S. Orkin,et al.  Jumonji Modulates Polycomb Activity and Self-Renewal versus Differentiation of Stem Cells , 2009, Cell.

[43]  Ruedi Aebersold,et al.  Molecular architecture of human polycomb repressive complex 2 , 2012, eLife.

[44]  Jacob D. Jaffe,et al.  Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia , 2013, Nature Genetics.

[45]  Guy Sauvageau,et al.  Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer. , 2010, Cell stem cell.

[46]  W. Huber,et al.  Differential expression analysis for sequence count data , 2010 .

[47]  Luca Pinello,et al.  Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. , 2012, Developmental cell.

[48]  Debashis Sahoo,et al.  Gene Expression Commons: An Open Platform for Absolute Gene Expression Profiling , 2012, PloS one.

[49]  Emery H. Bresnick,et al.  GATA Switches as Developmental Drivers* , 2010, The Journal of Biological Chemistry.

[50]  A. Iwama,et al.  Dependency on the polycomb gene Ezh2 distinguishes fetal from adult hematopoietic stem cells. , 2011, Blood.