Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment

Tissue mechanics drive morphogenesis, but how forces are sensed and transmitted to control stem cell fate and self-organization remains unclear. We show that a mechanosensory complex of emerin (Emd), non-muscle myosin IIA (NMIIA) and actin controls gene silencing and chromatin compaction, thereby regulating lineage commitment. Force-driven enrichment of Emd at the outer nuclear membrane of epidermal stem cells leads to defective heterochromatin anchoring to the nuclear lamina and a switch from H3K9me2,3 to H3K27me3 occupancy at constitutive heterochromatin. Emd enrichment is accompanied by the recruitment of NMIIA to promote local actin polymerization that reduces nuclear actin levels, resulting in attenuation of transcription and subsequent accumulation of H3K27me3 at facultative heterochromatin. Perturbing this mechanosensory pathway by deleting NMIIA in mouse epidermis leads to attenuated H3K27me3-mediated silencing and precocious lineage commitment, abrogating morphogenesis. Our results reveal how mechanics integrate nuclear architecture and chromatin organization to control lineage commitment and tissue morphogenesis.

[1]  Juliet A. Ellis,et al.  Molecular signatures of Emery-Dreifuss muscular dystrophy. , 2008, Biochemical Society transactions.

[2]  Ruedi Aebersold,et al.  Structure and Subunit Topology of the INO80 Chromatin Remodeler and Its Nucleosome Complex , 2013, Cell.

[3]  Keji Zhao,et al.  Rapid and Phosphoinositol-Dependent Binding of the SWI/SNF-like BAF Complex to Chromatin after T Lymphocyte Receptor Signaling , 1998, Cell.

[4]  L. Mahadevan,et al.  Tissue tectonics: morphogenetic strain rates, cell shape change and intercalation , 2009, Nature Methods.

[5]  K. Helin,et al.  Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide. , 2014, Molecular cell.

[6]  M. Mann,et al.  Stabilization of integrin‐linked kinase by the Hsp90‐CHIP axis impacts cellular force generation, migration and the fibrotic response , 2013, The EMBO journal.

[7]  F. Watt The stem cell compartment in human interfollicular epidermis. , 2002, Journal of dermatological science.

[8]  David A. Orlando,et al.  Revisiting Global Gene Expression Analysis , 2012, Cell.

[9]  R. Grosse,et al.  Nuclear Actin Network Assembly by Formins Regulates the SRF Coactivator MAL , 2013, Science.

[10]  Richard Superfine,et al.  Isolated nuclei adapt to force and reveal a mechanotransduction pathway in the nucleus , 2014, Nature Cell Biology.

[11]  V. Iyer,et al.  FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. , 2007, Genome research.

[12]  B. Suki,et al.  Alveolar epithelial surface area-volume relationship in isolated rat lungs , 1999 .

[13]  C. E. Perlman,et al.  Alveolar expansion imaged by optical sectioning microscopy. , 2007, Journal of applied physiology.

[14]  K. Wilson,et al.  The nucleoskeleton as a genome-associated dynamic 'network of networks' , 2011, Nature Reviews Molecular Cell Biology.

[15]  C. Heisenberg,et al.  Forces in Tissue Morphogenesis and Patterning , 2013, Cell.

[16]  A. Lambacher,et al.  Integrin-Linked Kinase Controls Microtubule Dynamics Required for Plasma Membrane Targeting of Caveolae , 2010, Developmental cell.

[17]  Benjamin Geiger,et al.  Adhesion-mediated mechanosensitivity: a time to experiment, and a time to theorize. , 2006, Current opinion in cell biology.

[18]  Kristian Helin,et al.  Chromatin repressive complexes in stem cells, development, and cancer. , 2014, Cell stem cell.

[19]  Y. Xu,et al.  Nuclear Translocation of β-Actin Is Involved in Transcriptional Regulation during Macrophage Differentiation of HL-60 Cells , 2010, Molecular biology of the cell.

[20]  J. Darnell,et al.  DRB-induced premature termination of late adenovirus transcription , 1978, Nature.

[21]  E. Hoffman,et al.  Loss of emerin at the nuclear envelope disrupts the Rb1/E2F and MyoD pathways during muscle regeneration. , 2006, Human molecular genetics.

[22]  David P. Kreil,et al.  Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures , 2014, Nature Communications.

[23]  T. Hope,et al.  Actin is part of pre-initiation complexes and is necessary for transcription by RNA polymerase II , 2004, Nature Cell Biology.

[24]  S. Q. Xie,et al.  Polycomb Associates Genome-wide with a Specific RNA Polymerase II Variant, and Regulates Metabolic Genes in ESCs , 2012, Cell stem cell.

[25]  Miguel Vicente-Manzanares,et al.  Non-muscle myosin II takes centre stage in cell adhesion and migration , 2009, Nature Reviews Molecular Cell Biology.

[26]  Adam J. Koch,et al.  The Nuclear Envelope Protein Emerin Binds Directly to Histone Deacetylase 3 (HDAC3) and Activates HDAC3 Activity* , 2012, The Journal of Biological Chemistry.

[27]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[28]  S. Gasser,et al.  Mechanisms of heterochromatin subnuclear localization. , 2013, Trends in biochemical sciences.

[29]  Philipp J. Thurner,et al.  Epithelial mechanobiology, skin wound healing, and the stem cell niche. , 2013, Journal of the mechanical behavior of biomedical materials.

[30]  C. Brangwynne,et al.  Mechanical Response of Cytoskeletal Networks , 2008 .

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

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

[33]  J. Lammerding,et al.  Cellular mechanosensing: getting to the nucleus of it all. , 2014, Progress in biophysics and molecular biology.

[34]  A. Regev,et al.  An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors , 2008, Nature Genetics.

[35]  Bradley E. Bernstein,et al.  Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues , 2013, Cell.

[36]  E. Hartmann,et al.  Exportin 6: a novel nuclear export receptor that is specific for profilin·actin complexes , 2003, The EMBO journal.

[37]  Brenton D. Hoffman,et al.  Dynamic molecular processes mediate cellular mechanotransduction , 2011, Nature.

[38]  Nicole Gorfinkiel,et al.  S09-03 Tissue tectonics: Morphogenetic strain rates, cell shape change and intercalation , 2009, Mechanisms of Development.

[39]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[40]  Timothy J Mitchison,et al.  Dissecting Temporal and Spatial Control of Cytokinesis with a Myosin II Inhibitor , 2003, Science.

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

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

[43]  Katherine H. Schreiber,et al.  When Lamins Go Bad: Nuclear Structure and Disease , 2013, Cell.

[44]  J. Gurdon,et al.  Nuclear actin polymerization is required for transcriptional reprogramming of Oct4 by oocytes. , 2011, Genes & development.

[45]  B. van Steensel,et al.  Genome-nuclear lamina interactions and gene regulation. , 2010, Current opinion in cell biology.

[46]  Kenneth M. Yamada,et al.  Defects in Cell Adhesion and the Visceral Endoderm following Ablation of Nonmuscle Myosin Heavy Chain II-A in Mice* , 2004, Journal of Biological Chemistry.

[47]  Kari-Pekka Skarp,et al.  Active maintenance of nuclear actin by importin 9 supports transcription , 2012, Proceedings of the National Academy of Sciences.

[48]  G. Hannon,et al.  Ezh2 Orchestrates Gene Expression for the Stepwise Differentiation of Tissue-Specific Stem Cells , 2009, Cell.

[49]  D. Discher,et al.  The nuclear lamina is mechano-responsive to ECM elasticity in mature tissue , 2014, Journal of Cell Science.

[50]  P. Giresi,et al.  Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA , 2012, Nature Protocols.

[51]  D. Reinberg,et al.  Prdm3 and Prdm16 are H3K9me1 Methyltransferases Required for Mammalian Heterochromatin Integrity , 2012, Cell.

[52]  K. Struhl,et al.  Determinants of nucleosome positioning , 2013, Nature Structural &Molecular Biology.

[53]  R. Treisman Shedding light on nuclear actin dynamics and function. , 2013, Trends in biochemical sciences.

[54]  P. Lappalainen,et al.  Mechanisms of actin stress fibre assembly , 2008, Journal of microscopy.

[55]  Werner Müller,et al.  Keratin 14 Cre transgenic mice authenticate keratin 14 as an oocyte‐expressed protein , 2004, Genesis.

[56]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[57]  Yoshiki Sasai,et al.  Cytosystems dynamics in self-organization of tissue architecture , 2013, Nature.

[58]  Martin Renqiang Min,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[59]  Kristian Helin,et al.  The histone demethylase PHF8 governs retinoic acid response in acute promyelocytic leukemia. , 2013, Cancer cell.