m6A-mRNA methylation regulates cardiac gene expression and cellular growth

This study provides evidence that m6A methylation is dynamically regulated during human and murine cardiac disease and highlights an important role of the m6A methylase Mettl3 in regulating cardiac growth by gene expression control. Conceptually similar to modifications of DNA, mRNAs undergo chemical modifications, which can affect their activity, localization, and stability. The most prevalent internal modification in mRNA is the methylation of adenosine at the N6-position (m6A). This returns mRNA to a role as a central hub of information within the cell, serving as an information carrier, modifier, and attenuator for many biological processes. Still, the precise role of internal mRNA modifications such as m6A in human and murine-dilated cardiac tissue remains unknown. Transcriptome-wide mapping of m6A in mRNA allowed us to catalog m6A targets in human and murine hearts. Increased m6A methylation was found in human cardiomyopathy. Knockdown and overexpression of the m6A writer enzyme Mettl3 affected cell size and cellular remodeling both in vitro and in vivo. Our data suggest that mRNA methylation is highly dynamic in cardiomyocytes undergoing stress and that changes in the mRNA methylome regulate translational efficiency by affecting transcript stability. Once elucidated, manipulations of methylation of specific m6A sites could be a powerful approach to prevent worsening of cardiac function.

[1]  G. Akusjärvi,et al.  Gene expression, regulation of , 1995 .

[2]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[3]  Francine E. Garrett-Bakelman,et al.  The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal and leukemia cells , 2017, Nature Medicine.

[4]  Davis J. McCarthy,et al.  Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.

[5]  Erez Y. Levanon,et al.  m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation , 2015, Science.

[6]  E. Graves National Hospital Discharge Survey. , 1989, Vital and health statistics. Series 13, Data from the National Health Survey.

[7]  J. Hanna,et al.  The N6-Methyladenosine mRNA Methylase METTL3 Controls Cardiac Homeostasis and Hypertrophy , 2018, Circulation.

[8]  M. Kupiec,et al.  Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq , 2012, Nature.

[9]  Paul Lehner,et al.  Fat mass and obesity-related (FTO) shuttles between the nucleus and cytoplasm , 2014, Bioscience reports.

[10]  David A. Kass,et al.  Tackling heart failure in the twenty-first century , 2008, Nature.

[11]  F. Sheikh,et al.  Functions of myosin light chain-2 (MYL2) in cardiac muscle and disease. , 2015, Gene.

[12]  Chengqi Yi,et al.  N6-Methyladenosine in Nuclear RNA is a Major Substrate of the Obesity-Associated FTO , 2011, Nature chemical biology.

[13]  S. Tavazoie,et al.  N6-methyladenosine marks primary microRNAs for processing , 2015, Nature.

[14]  O. Elemento,et al.  Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons , 2012, Cell.

[15]  C. Dieterich,et al.  Bayesian prediction of RNA translation from ribosome profiling , 2017, Nucleic acids research.

[16]  M. Latronico,et al.  Epigenetics: a new mechanism of regulation of heart failure? , 2013, Basic Research in Cardiology.

[17]  Zhike Lu,et al.  Differential m6A, m6Am, and m1A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm. , 2018, Molecular cell.

[18]  Mark A Sussman,et al.  PRAS40 prevents development of diabetic cardiomyopathy and improves hepatic insulin sensitivity in obesity , 2013, EMBO molecular medicine.

[19]  J. Ross,et al.  Segregation of atrial-specific and inducible expression of an atrial natriuretic factor transgene in an in vivo murine model of cardiac hypertrophy , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[20]  M. Boerries,et al.  Cardiac adenoviral S100A1 gene delivery rescues failing myocardium. , 2004, The Journal of clinical investigation.

[21]  C. Dieterich,et al.  Identification of circular RNAs with host gene-independent expression in human model systems for cardiac differentiation and disease. , 2017, Journal of molecular and cellular cardiology.

[22]  Carol DeFrances,et al.  2006 National Hospital Discharge Survey. , 2005, National health statistics reports.

[23]  R. Palmiter,et al.  Cell-type-specific isolation of ribosome-associated mRNA from complex tissues , 2009, Proceedings of the National Academy of Sciences.

[24]  Gunter Meister,et al.  Interactions, localization, and phosphorylation of the m6A generating METTL3–METTL14–WTAP complex , 2018, RNA.

[25]  Olivier Elemento,et al.  5′ UTR m6A Promotes Cap-Independent Translation , 2015, Cell.

[26]  Chuan He,et al.  Grand challenge commentary: RNA epigenetics? , 2010, Nature chemical biology.

[27]  M. Ehrenberg,et al.  N6-methyladenosine in mRNA disrupts tRNA selection and translation elongation dynamics , 2016, Nature Structural &Molecular Biology.

[28]  Yi Xing,et al.  m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome , 2016, Nature Methods.

[29]  Yu Zhang,et al.  m6A facilitates hippocampus-dependent learning and memory through Ythdf1 , 2018, Nature.

[30]  N J Izzo,et al.  HL-1 cells: a cardiac muscle cell line that contracts and retains phenotypic characteristics of the adult cardiomyocyte. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Nicholas T. Ingolia Ribosome Footprint Profiling of Translation throughout the Genome , 2016, Cell.

[32]  Samie R. Jaffrey,et al.  The dynamic epitranscriptome: N6-methyladenosine and gene expression control , 2014, Nature Reviews Molecular Cell Biology.

[33]  Miao Yu,et al.  A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation , 2013, Nature chemical biology.

[34]  Mark A Sussman,et al.  mTORC2 Protects the Heart from Ischemic Damage , 2013 .

[35]  Gideon Rechavi,et al.  Gene expression regulation mediated through reversible m6A RNA methylation , 2014, Nature Reviews Genetics.

[36]  Mee-Sup Yoon,et al.  XPLN is an endogenous inhibitor of mTORC2 , 2013, Proceedings of the National Academy of Sciences.

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

[38]  J. Sadoshima,et al.  New Insights Into the Role of mTOR Signaling in the Cardiovascular System. , 2018, Circulation research.

[39]  Alexandra King Heart failure: Placing an EMPHASIS on the mineralocorticoid receptor—benefit of eplerenone in mild HF , 2010, Nature Reviews Cardiology.

[40]  Jianbo Li,et al.  The gene expression fingerprint of human heart failure , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Chuan He,et al.  YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA , 2017, Cell Research.

[42]  Mark A Sussman,et al.  Pathological hypertrophy amelioration by PRAS40-mediated inhibition of mTORC1 , 2013, Proceedings of the National Academy of Sciences.

[43]  D. Kass,et al.  Reverse remodeling in heart failure—mechanisms and therapeutic opportunities , 2012, Nature Reviews Cardiology.

[44]  Chuan He,et al.  N 6 -methyladenosine Modulates Messenger RNA Translation Efficiency , 2015, Cell.

[45]  Olivier Elemento,et al.  Reversible methylation of m6Am in the 5′ cap controls mRNA stability , 2016, Nature.

[46]  Philippe Froguel,et al.  Loss-of-function mutation in the dioxygenase-encoding FTO gene causes severe growth retardation and multiple malformations. , 2009, American journal of human genetics.

[47]  R. Hajjar,et al.  FTO-Dependent N6-Methyladenosine Regulates Cardiac Function During Remodeling and Repair , 2018, Circulation.

[48]  Ran Elkon,et al.  Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation , 2017, Cell.

[49]  W. Gilbert,et al.  Messenger RNA modifications: Form, distribution, and function , 2016, Science.

[50]  Mark A Sussman,et al.  Mechanistic Target of Rapamycin Complex 2 Protects the Heart From Ischemic Damage , 2013, Circulation.

[51]  Mark A Sussman,et al.  Hrd1 and ER-Associated Protein Degradation, ERAD, are Critical Elements of the Adaptive ER Stress Response in Cardiac Myocytes. , 2015, Circulation research.

[52]  Martin Vingron,et al.  Translational regulation shapes the molecular landscape of complex disease phenotypes , 2015, Nature Communications.

[53]  L. Kadaja,et al.  Distinct organization of energy metabolism in HL-1 cardiac cell line and cardiomyocytes. , 2008, Biochimica et biophysica acta.

[54]  Karen S. Frese,et al.  Epigenome-Wide Association Study Identifies Cardiac Gene Patterning and a Novel Class of Biomarkers for Heart Failure , 2017, Circulation.