The RNA Methylome Blackboard.

Abstract

HomeCirculationVol. 139, No. 4The RNA Methylome Blackboard Free AccessEditorialPDF/EPUBAboutView PDFView EPUBSections ToolsAdd to favoritesDownload citationsTrack citationsPermissions ShareShare onFacebookTwitterLinked InMendeleyReddit Jump toFree AccessEditorialPDF/EPUBThe RNA Methylome BlackboardMETTL3 and FTO, Epigenetic Writers and Erasers Regulating Cardiac Homeostasis Through Epitranscriptome Modification Christina Pagiatakis, PhD and Gianluigi Condorelli, MD, PhD Christina PagiatakisChristina Pagiatakis Department of Cardiovascular Medicine, Humanitas Clinical and Research Center – IRCCS, Rozzano, Milan, Italy (C.P., G.C.). Search for more papers by this author and Gianluigi CondorelliGianluigi Condorelli Gianluigi Condorelli, MD, PhD, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, Milan, 20090, Italy. Email E-mail Address: [email protected] Department of Cardiovascular Medicine, Humanitas Clinical and Research Center – IRCCS, Rozzano, Milan, Italy (C.P., G.C.). Humanitas University, Pieve Emanuele, Milan, Italy (G.C.). Institute of Genetics and Biomedical Research (Milan Unit), National Research Council of Italy, Rozzano, Milan, Italy (G.C.). Search for more papers by this author Originally published21 Jan 2019https://doi.org/10.1161/CIRCULATIONAHA.118.038166Circulation. 2019;139:546–548This article is a commentary on the followingFTO-Dependent N6-Methyladenosine Regulates Cardiac Function During Remodeling and RepairThe N6-Methyladenosine mRNA Methylase METTL3 Controls Cardiac Homeostasis and HypertrophyArticles, see p 518 and p 533The field of epigenetics focuses on the regulatory networks governing gene expression at a posttranscriptional and posttranslational level. The consequences of the dysregulation of these networks reverberate on intracellular signaling and on chromatin state, which in turn regulate gene expression. During the past decade, a considerable amount of knowledge has been generated on the understanding of how epigenetic events regulate cardiovascular development and their implication in the pathogenesis of cardiovascular diseases. Although the molecular and epigenetic mechanisms governing cardiac development, homeostasis, and disease are still not fully understood, significant progress has been made in elucidating the role of histones, the proteins around which DNA is wound, their acetylation and methylation, and also DNA and protein methylation. In aggregate, these studies have unveiled an intricate and dynamic multilayer network of regulation of enzymes and proteins with writer, reader, and eraser functions.1,2 Whether RNA could be subject to epigenetic modifications remained a mystery for decades. Although there exists a myriad of chemical modifications that can be found on RNA,3,4 RNA methylation (N6-methyladenosine, m6A) is the most abundant modification in eukaryotic messenger RNAs, being present also in intronic regions of prespliced messenger RNA, transfer RNA, ribosomal RNA, and noncoding RNAs.5 In the past several years, transcriptome-wide analyses of the m6A methylome in many species have revealed that this chemical modification is enriched in long exons, near stop codons, and in the 3′-untranslated regions of RNA. Similar to many histone and DNA modifications, RNA methylation is dynamic, mediated by writers (enzymes that add chemical modifications), readers (effector proteins that bind to modified macromolecules), and erasers (enzymes that delete chemical modifications), whose roles have been studied in many biological contexts.5,6Within the multiprotein complex responsible for the deposition of m6A marks, the methyltransferases-like 3 (METTL3) and METTL14, writers, and several other accessory proteins, as well, have been identified.6METTL3 knockout has been shown to be embryonically lethal, indicating a critical role for m6A during development. Conversely, m6A demethylases (erasers) contribute to the dynamic nature of the m6A mark, and, to date, only 2 such enzymes have been identified (FTO [fat mass and obesity-associated protein] and ALKBH5 [Alk homologue 5]).7 Regardless of the recent remarkable progress in this field, the complex network of cellular events and signaling pathways contributing to the deposition of this chemical modification and the subsequent downstream control of gene expression in specific cell types, including cardiomyocytes, still remains largely unknown. Studying the epigenetic mechanisms controlling these processes will allow for better understanding of cardiac homeostasis and disease pathogenesis.In this issue, studies by Dorn et al8 and Mathiyalagan et al9 add another layer to the understanding of RNA methylation in the context of cardiac homeostasis and disease: the first by showing that RNA methylation is necessary for the maintenance of cardiac homeostasis whereby inhibition of the m6A writer METTL3 blocks the hypertrophic response, and the second by describing the mechanism by which the expression of the m6A eraser FTO is decreased in failing mammalian hearts, reducing the contractile function of cardiomyocytes.More specifically, the study by Dorn et al8 reveals the dynamic nature of m6A in cardiomyocytes, showing that these modifications are enhanced in a class of protein kinases involved in the hypertrophic response. Using a METTL3 transgenic mouse to overexpress METTL3 in adult mice, the authors uncover a significant increase in m6A coupled with hypertrophic growth of the heart. It is interesting to note that transgenic overexpression induced compensated hypertrophic remodeling without affecting the functionality of the heart. To corroborate these findings, the authors used a cardiomyocyte-specific METTL3 knockout mouse, which, although manifesting decreased levels of m6A, did not manifest any effect on cardiac development. However, with aging and after stress-induced pressure overload, these mice presented with a decrease in overall cardiac function. In vitro, small interfering RNA knockdown of METTL3 completely blocked the hypertrophic response, whereas METTL3-deficient mice undergoing pressure overload–induced hypertrophy (transverse aortic constriction) revealed that the absence of METTL3 accelerates heart failure progression by altering cardiac remodeling postinjury. These findings strongly suggest a key role for METTL3 in the maintenance of cardiac homeostasis and in disease.Because the cardiomyocyte-specific knockout of METTL3 does not have an effect on the phenotype, at least grossly, it cannot be excluded that, in vivo, cofactors other than the m6A complex, such as METTL14, play a compensatory role and could thus be critical regulators of RNA methylation. For instance, Wang et al10 have shown that METTL3 and METTL14 function as dimers, and alone each of these factors has weak methyltransferase activity. Thus, knowledge on tissue-specific accessory factors that could potentiate (or inhibit) the activity of METTL3 in the heart or cardiomyocytes is yet to be fully explored. Dorn et al8 also demonstrate that aged METTL3 knockout mice begin to show cardiac abnormalities consistent with heart failure progression; a follow-up of the model for an extended time beyond 12 months, performing m6A sequencing coupled with a bioinformatic analysis aimed at determining possible differentially enriched m6A deposition throughout the whole messenger RNA landscape, could lead to the identification of METTL3 function in cardiac aging.Dorn et al focused on writers; what about the erasers? The work of Mathiyalagan et al9 provides further insights on the role of m6A in cardiac homeostasis by focusing on the demethylation of RNA, unveiling that FTO regulates the cardiac epitranscriptome by demethylating genes involved in cardiomyocyte function.Mathiyalagan et al use several models of post–myocardial infarction ischemic hearts to show that increased levels of m6A are correlated with chronic heart failure. It is interesting to note that they find that FTO is significantly decreased in the failing left ventricle, and that the loss of FTO under ischemic conditions could be the major contributor to the aberrant levels of m6A in the failing heart. Using gain- and loss-of-function methods, both in vitro and in vivo, the authors unveil the necessity of FTO for intracellular calcium handling and sarcomere dynamics, which appears to be regulated by the hypoxic response. Overexpression of FTO regulates levels of m6A and improves cardiac function post–myocardial infarction. In line with these results, overexpression of FTO resulted in a significant reduction of fibrosis, concurrent with an increased angiogenic response at the infarct border zone. Transcriptome-wide analysis revealed that FTO preferentially targets transcripts that are associated with cardiac hypertrophy, muscle contraction, and sarcomere organization, such as the Ca2+-ATPase pump SERCA2a, further corroborating the data that this RNA demethylase is required for cardiac homeostasis.Just as with the m6A writers, several unanswered questions still remain about the mechanism by which FTO functions in the heart. The authors used several animal models with adeno-associated vectors for inducing or inhibiting FTO expression. This approach is relevant, because it allows one to determine whether a gene has therapeutic potential. Nonetheless, a cardiomyocyte-specific conditional knockout of FTO could have answered the question of whether FTO has a unique function, or whether there are other genes playing a similar role in the heart. Understanding the role of FTO in aging and whether perturbations in its expression or activity affect cardiac-specific transcriptome-wide methylation levels are questions that remain to be answered. Because FTO expression is regulated under hypoxic stress, it will be of interest to understand whether FTO activity serves to stabilize transcripts of canonical and noncanonical hypoxic stress response pathways, such as hypoxia-inducible factor 1α and its downstream target genes.As a whole, the studies by Dorn et al and Mathiyalagan et al are innovative because they provide novel and relevant insights on how epigenetics, in this case epitranscriptomics, maintains cardiac homeostasis, and how perturbation of these mechanisms results in aberrant cardiac gene expression. A better understanding of the physiological or pathological stimuli by which these m6A erasers and writers are either activated or inhibited could help to define the relevance of these phenomena in cardiac disease. Similarly, a better definition of the targets, the quantity, and the dynamics of m6A deposition, and a more comprehensive panorama of messenger RNA methylation erasers, writers, and readers as well, could help determine whether METTL3, FTO, or other proteins represent viable therapeutic targets for myocardial diseases.Download figureDownload PowerPointFigure. Scheme of mRNA methylation writers and erasers during cardiac hypertrophy. m6A indicates N6-methyladenosine; and mRNA, messenger RNA.Sources of FundingProf Condorelli is supported by a European Research Council Advanced Grant (# 294609, CardioEpigen) and Proof of Concept grant (#713734); the Italian Ministry of Health (grant # PE-2013-02356818); the Cariplo Foundation (grant #2015-0573); the EXPERT project of the European Research Area Network on Cardiovascular Diseases (ERA-NET ERA CVD); and the Italian Ministry of Education, University and Research (2015583WMX).DisclosuresNone.FootnotesThe opinions expressed in this article are not necessarily those of the editors or of the American Heart Association.https://www.ahajournals.org/journal/circGianluigi Condorelli, MD, PhD, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, Milan, 20090, Italy. Email gianluigi.[email protected]eu