Chromatin remodelling and epigenetic state regulation by non-coding RNAs in the diseased heart

Epigenetics refers to all the changes in phenotype and gene expression which are not due to alterations in the DNA sequence. These mechanisms have a pivotal role not only in the development but also in the maintenance during adulthood of a physiological phenotype of the heart. Because of the crucial role of epigenetic modifications, their alteration can lead to the arise of pathological conditions. Heart failure affects an estimated 23 million people worldwide and leads to substantial numbers of hospitalizations and health care costs: ischemic heart disease, hypertension, rheumatic fever and other valve diseases, cardiomyopathy, cardiopulmonary disease, congenital heart disease and other factors may all lead to heart failure, either alone or in concert with other risk factors. Epigenetic alterations have recently been included among these risk factors as they can affect gene expression in response to external stimuli. In this review, we provide an overview of all the major classes of chromatin remodellers, providing examples of how their disregulation in the adult heart alters specific gene programs with subsequent development of major cardiomyopathies. Understanding the functional significance of the different epigenetic marks as points of genetic control may be useful for developing promising future therapeutic tools.

[1]  M. Lange,et al.  Combinatorial assembly and function of chromatin regulatory complexes. , 2011, Epigenomics.

[2]  G. Ruvkun,et al.  Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans , 1993, Cell.

[3]  A. Berezin Epigenetics in heart failure phenotypes☆ , 2016, BBA clinical.

[4]  Manolis Kellis,et al.  Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila , 2007, Cell.

[5]  R. Guigó,et al.  CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis. , 2015, Journal of molecular and cellular cardiology.

[6]  T. Arnesen,et al.  The world of protein acetylation. , 2016, Biochimica et biophysica acta.

[7]  T. Thum Facts and updates about cardiovascular non‐coding RNAs in heart failure , 2015, ESC heart failure.

[8]  B. Zhao,et al.  A circular RNA protects the heart from pathological hypertrophy and heart failure by targeting miR-223. , 2016, European heart journal.

[9]  E. Seto,et al.  Erasers of histone acetylation: the histone deacetylase enzymes. , 2014, Cold Spring Harbor perspectives in biology.

[10]  Ali Hamiche,et al.  A chromatin remodelling complex involved in transcription and DNA processing , 2000, Nature.

[11]  P. Insel,et al.  Cardiac-Specific Overexpression of Caveolin-3 Induces Endogenous Cardiac Protection by Mimicking Ischemic Preconditioning , 2008, Circulation.

[12]  J. Jalife,et al.  Loss of H3K4 methylation destabilizes gene expression patterns and physiological functions in adult murine cardiomyocytes. , 2011, The Journal of clinical investigation.

[13]  F. Neumann,et al.  Cardiac Myocyte De Novo DNA Methyltransferases 3a/3b Are Dispensable for Cardiac Function and Remodeling after Chronic Pressure Overload in Mice , 2015, PloS one.

[14]  Manolis Kellis,et al.  The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. , 2013, Developmental cell.

[15]  Mark T Bedford,et al.  Arginine methylation an emerging regulator of protein function. , 2005, Molecular cell.

[16]  Lubo Zhang,et al.  Epigenetic mechanisms in heart development and disease. , 2015, Drug discovery today.

[17]  T. D. di Salvo,et al.  Epigenetic Regulation in Heart Failure: Part I RNA. , 2015, Cardiology in review.

[18]  Remco Loos,et al.  Citrullination regulates pluripotency and histone H1 binding to chromatin , 2014, Nature.

[19]  S. Khochbin,et al.  Histone Acylation beyond Acetylation: Terra Incognita in Chromatin Biology , 2015, Cell journal.

[20]  E. Ashley,et al.  A long non-coding RNA protects the heart from pathological hypertrophy , 2014, Nature.

[21]  Richard A Young,et al.  The long noncoding RNA Wisper controls cardiac fibrosis and remodeling , 2017, Science Translational Medicine.

[22]  M. Pilato,et al.  PIWI-interacting RNA (piRNA) signatures in human cardiac progenitor cells. , 2016, The international journal of biochemistry & cell biology.

[23]  Tsuyoshi Murata,et al.  {m , 1934, ACML.

[24]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[25]  B. Trimarco,et al.  Epigenetic Switch at Atp2a2 and Myh7 Gene Promoters in Pressure Overload-Induced Heart Failure , 2014, PloS one.

[26]  N. Silverman,et al.  Abnormal mitochondrial respiration in failed human myocardium. , 2000, Journal of molecular and cellular cardiology.

[27]  A. Birkmann,et al.  The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high‐molecular‐weight protein complex , 1999, Molecular microbiology.

[28]  Joe C. Liang,et al.  Engineering biological systems with synthetic RNA molecules. , 2011, Molecular cell.

[29]  K. Shimada,et al.  Genome‐wide histone methylation profile for heart failure , 2009, Genes to cells : devoted to molecular & cellular mechanisms.

[30]  J. Newell-Price,et al.  DNA Methylation and Silencing of Gene Expression , 2000, Trends in Endocrinology & Metabolism.

[31]  R. Mark Henkelman,et al.  Chromatin remodelling complex dosage modulates transcription factor function in heart development , 2011, Nature communications.

[32]  N. Brockdorff,et al.  The interplay of histone modifications – writers that read , 2015, EMBO reports.

[33]  G. Felsenfeld A brief history of epigenetics. , 2014, Cold Spring Harbor perspectives in biology.

[34]  V. Beneš,et al.  Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease , 2014, Nature Communications.

[35]  B. Cairns,et al.  The biology of chromatin remodeling complexes. , 2009, Annual review of biochemistry.

[36]  P. Scacheri,et al.  Knockdown of fbxl10/kdm2bb rescues chd7 morphant phenotype in a zebrafish model of CHARGE syndrome. , 2013, Developmental biology.

[37]  C. Croce,et al.  Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Lubo Zhang,et al.  Inhibition of DNA methylation reverses norepinephrine-induced cardiac hypertrophy in rats. , 2014, Cardiovascular research.

[39]  E. Ashley,et al.  Chromatin regulation by Brg1 underlies heart muscle development and disease , 2010, Nature.

[40]  K. Murray,et al.  BRG1 and BRM SWI/SNF ATPases redundantly maintain cardiomyocyte homeostasis by regulating cardiomyocyte mitophagy and mitochondrial dynamics in vivo. , 2016, Cardiovascular pathology : the official journal of the Society for Cardiovascular Pathology.

[41]  P. Wade,et al.  WSTF–ISWI chromatin remodeling complex targets heterochromatic replication foci , 2002, The EMBO journal.

[42]  M. Berger,et al.  Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA , 2015, Nucleic acids research.

[43]  Ming-Ming Zhou,et al.  Mechanism and Regulation of Acetylated Histone Binding by the Tandem PHD Finger of DPF3b , 2010, Nature.

[44]  Benjamin Meder,et al.  Alterations in cardiac DNA methylation in human dilated cardiomyopathy , 2013, EMBO molecular medicine.

[45]  W. Rottbauer,et al.  Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. , 2008, Genes & development.

[46]  Michael Weber,et al.  Mechanisms of DNA methylation and demethylation in mammals. , 2012, Biochimie.

[47]  M. Jeong,et al.  Inhibition of Histone Deacetylation Blocks Cardiac Hypertrophy Induced by Angiotensin II Infusion and Aortic Banding , 2005, Circulation.

[48]  Michael Weber,et al.  Functions of DNA methylation and hydroxymethylation in mammalian development. , 2013, Current topics in developmental biology.

[49]  P. Ellinor,et al.  RBM20, a gene for hereditary cardiomyopathy, regulates titin splicing , 2012, Nature Medicine.

[50]  Vincent L. Butty,et al.  Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment , 2013, Cell.

[51]  Y. Geng,et al.  Inhibition of Gata4 and Tbx5 by Nicotine-Mediated DNA Methylation in Myocardial Differentiation , 2017, Stem cell reports.

[52]  Martin Vingron,et al.  Genome-Wide Array Analysis of Normal and Malformed Human Hearts , 2003, Circulation.

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

[54]  M. Kühl,et al.  Cloning and developmental expression of WSTF during Xenopus laevis embryogenesis. , 2006, Gene expression patterns : GEP.

[55]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[56]  G. Condorelli,et al.  Long noncoding RNAs and microRNAs in cardiovascular pathophysiology. , 2015, Circulation research.

[57]  Donna M. Martin,et al.  Loss of Chd7 function in gene-trapped reporter mice is embryonic lethal and associated with severe defects in multiple developing tissues , 2007, Mammalian Genome.

[58]  C. Napoli,et al.  Epigenetic-related therapeutic challenges in cardiovascular disease. , 2015, Trends in pharmacological sciences.

[59]  Jim Selfridge,et al.  The role of MeCP2 in the brain. , 2009, Annual review of cell and developmental biology.

[60]  Ching-Pin Chang,et al.  Epigenetics and cardiovascular development. , 2012, Annual review of physiology.

[61]  A. Schambach,et al.  Long noncoding RNA Chast promotes cardiac remodeling , 2016, Science Translational Medicine.

[62]  Miss A.O. Penney (b) , 1974, The New Yale Book of Quotations.

[63]  S. Tyagi,et al.  MicroRNA-133a regulates DNA methylation in diabetic cardiomyocytes. , 2012, Biochemical and biophysical research communications.

[64]  G. Lofland,et al.  Noncoding RNA Expression in Myocardium From Infants With Tetralogy of Fallot , 2012, Circulation. Cardiovascular genetics.

[65]  C A Morris,et al.  Natural history of Williams syndrome: physical characteristics. , 1988, The Journal of pediatrics.

[66]  R. Conaway,et al.  The INO80 chromatin remodeling complex in transcription, replication and repair. , 2009, Trends in biochemical sciences.

[67]  David A. Knowles,et al.  Distinct Epigenomic Features in End-Stage Failing Human Hearts , 2011, Circulation.

[68]  Dean Y. Li,et al.  Epigenetic response to environmental stress: Assembly of BRG1-G9a/GLP-DNMT3 repressive chromatin complex on Myh6 promoter in pathologically stressed hearts. , 2016, Biochimica et biophysica acta.

[69]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[70]  Loss of WSTF results in spontaneous fluctuations of heterochromatin formation and resolution, combined with substantial changes to gene expression , 2013, BMC Genomics.

[71]  Majid Ezzati,et al.  Worldwide risk factors for heart failure: a systematic review and pooled analysis. , 2013, International journal of cardiology.

[72]  B. Long,et al.  CARL lncRNA inhibits anoxia-induced mitochondrial fission and apoptosis in cardiomyocytes by impairing miR-539-dependent PHB2 downregulation , 2014, Nature Communications.

[73]  Ravi Sachidanandam,et al.  A germline-specific class of small RNAs binds mammalian Piwi proteins , 2006, Nature.

[74]  P. Zhang,et al.  A Long Non-Coding RNA Defines an Epigenetic Checkpoint in Cardiac Hypertrophy , 2016 .

[75]  Donna M. Martin,et al.  Chromodomain helicase DNA-binding proteins in stem cells and human developmental diseases. , 2015, Stem cells and development.

[76]  E. Creemers,et al.  Circular RNAs in heart failure , 2017, European journal of heart failure.

[77]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[78]  G. Kreiman,et al.  Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.

[79]  L. D. de Windt,et al.  MicroRNAs in control of cardiac hypertrophy. , 2012, Cardiovascular research.

[80]  Peter A. Jones,et al.  The Role of DNA Methylation in Mammalian Epigenetics , 2001, Science.

[81]  O. Kretz,et al.  Adrenergic Repression of the Epigenetic Reader MeCP2 Facilitates Cardiac Adaptation in Chronic Heart Failure , 2015, Circulation research.

[82]  Giovanni Stefani,et al.  piRNA involvement in genome stability and human cancer , 2015, Journal of Hematology & Oncology.

[83]  R. Castro,et al.  Epigenetic modifications: basic mechanisms and role in cardiovascular disease. , 2011, Circulation.

[84]  D. Moazed,et al.  Heterochromatin and Epigenetic Control of Gene Expression , 2003, Science.

[85]  G. Crabtree,et al.  Chromatin remodelling during development , 2010, Nature.

[86]  F. Lienert,et al.  Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family , 2013, Cell.

[87]  William Stanley,et al.  Cardiac mitochondria in heart failure: decrease in respirasomes and oxidative phosphorylation , 2008, Cardiovascular research.

[88]  M. Latronico,et al.  microRNAs in cardiovascular diseases: current knowledge and the road ahead. , 2014, Journal of the American College of Cardiology.

[89]  K. S. Rajan,et al.  miRNA and piRNA mediated Akt pathway in heart: antisense expands to survive. , 2014, The international journal of biochemistry & cell biology.

[90]  R. Pfundt,et al.  Loss-of-Function Mutations in YY1AP1 Lead to Grange Syndrome and a Fibromuscular Dysplasia-Like Vascular Disease. , 2017, American journal of human genetics.

[91]  K. Steel,et al.  Multiple mutations in mouse Chd7 provide models for CHARGE syndrome. , 2005, Human molecular genetics.

[92]  T. Down,et al.  Differential DNA Methylation Correlates with Differential Expression of Angiogenic Factors in Human Heart Failure , 2010, PloS one.

[93]  Yolan J. Reckman,et al.  RBM20 Regulates Circular RNA Production From the Titin Gene. , 2016, Circulation research.

[94]  C. Sander,et al.  A novel class of small RNAs bind to MILI protein in mouse testes , 2006, Nature.

[95]  Jeffrey A. Jones,et al.  HDACs Regulate miR-133a Expression in Pressure Overload–Induced Cardiac Fibrosis , 2015, Circulation. Heart failure.

[96]  Andrew J. Bannister,et al.  Histone methylation: recognizing the methyl mark. , 2004, Methods in enzymology.