H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

[1]  H. Jo,et al.  Hemodynamics and Mechanobiology of Aortic Valve Calcification , 2016 .

[2]  A. Brunner,et al.  Cardiac myocyte miR-29 promotes pathological remodeling of the heart by activating Wnt signaling , 2017, Nature Communications.

[3]  F. Asselbergs,et al.  Systems analysis of dilated cardiomyopathy in the next generation sequencing era , 2018, Wiley interdisciplinary reviews. Systems biology and medicine.

[4]  M. Vos,et al.  Sex-specific influence on cardiac structural remodeling and therapy in cardiovascular disease , 2019, Biology of Sex Differences.

[5]  David Haussler,et al.  ENCODE Data in the UCSC Genome Browser: year 5 update , 2012, Nucleic Acids Res..

[6]  S. Teichmann,et al.  Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement , 2018, Nature Communications.

[7]  Julia A. Lasserre,et al.  Histone modification levels are predictive for gene expression , 2010, Proceedings of the National Academy of Sciences.

[8]  David P. Kreil,et al.  Sex-Specific Human Cardiomyocyte Gene Regulation in Left Ventricular Pressure Overload. , 2020, Mayo Clinic proceedings.

[9]  M. Martí-Renom,et al.  Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse , 2015, Molecular and Cellular Biology.

[10]  Á. Raya,et al.  Update on the Pathogenic Implications and Clinical Potential of microRNAs in Cardiac Disease , 2015, BioMed research international.

[11]  Y. Pinto,et al.  Molecular mechanisms that control interstitial fibrosis in the pressure-overloaded heart. , 2011, Cardiovascular research.

[12]  Timothy L. Bailey,et al.  Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data , 2010, BMC Bioinformatics.

[13]  Susan J Clark,et al.  Disruption of the 3D cancer genome blueprint. , 2017, Epigenomics.

[14]  Georgios Kararigas,et al.  Mechanistic Pathways of Sex Differences in Cardiovascular Disease. , 2017, Physiological reviews.

[15]  E. Petretto,et al.  Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy , 2017, Genome Biology.

[16]  B. Llamas,et al.  Hypertensive cardiac remodeling in males and females: from the bench to the bedside. , 2007, Hypertension.

[17]  H. Parkinson,et al.  Large scale comparison of global gene expression patterns in human and mouse , 2010, Genome Biology.

[18]  N. Kelleher,et al.  Measurement of acetylation turnover at distinct lysines in human histones identifies long-lived acetylation sites , 2013, Nature Communications.

[19]  M. Latronico,et al.  Genome-wide analysis of histone marks identifying an epigenetic signature of promoters and enhancers underlying cardiac hypertrophy , 2013, Proceedings of the National Academy of Sciences.

[20]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[21]  M. Pesce,et al.  Mechanotransduction in the Cardiovascular System: From Developmental Origins to Homeostasis and Pathology , 2019, Cells.

[22]  R. Myers,et al.  An Integrated Software System for Analyzing Chip-chip and Chip-seq Data (supplementary Information) , 2008 .

[23]  Davide Heller,et al.  STRING v10: protein–protein interaction networks, integrated over the tree of life , 2014, Nucleic Acids Res..

[24]  W. V. van IJcken,et al.  Gene reprogramming in exercise-induced cardiac hypertrophy in swine: A transcriptional genomics approach. , 2014, Journal of molecular and cellular cardiology.

[25]  A. Barabasi,et al.  Epigenomic and transcriptomic approaches in the post-genomic era: path to novel targets for diagnosis and therapy of the ischaemic heart? Position Paper of the European Society of Cardiology Working Group on Cellular Biology of the Heart , 2017, Cardiovascular research.

[26]  D. McCollum,et al.  Control of cellular responses to mechanical cues through YAP/TAZ regulation , 2019, The Journal of Biological Chemistry.

[27]  Dudley J Pennell,et al.  Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass , 2008, Nature Genetics.

[28]  G. Marano,et al.  Gender differences in cardiac hypertrophic remodeling. , 2016, Annali dell'Istituto superiore di sanita.

[29]  N. Dagres,et al.  Cellular Communications in the Heart. , 2015, Cardiac failure review.

[30]  Y-h. Taguchi,et al.  Comparative Gene Expression Analysis of Mouse and Human Cardiac Maturation , 2016, Genom. Proteom. Bioinform..

[31]  H. Aburatani,et al.  Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure , 2018, Nature Communications.

[32]  R. Gamelli,et al.  Genomic responses in mouse models poorly mimic human inflammatory diseases , 2013, Proceedings of the National Academy of Sciences.

[33]  J. Rice.  Animal models: Not close enough , 2012, Nature.

[34]  Eugene Berezikov,et al.  Modeling Human Cardiac Hypertrophy in Stem Cell-Derived Cardiomyocytes , 2018, Stem cell reports.

[35]  Hans Clevers,et al.  Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes , 2011, Nucleic acids research.

[36]  E. Dworatzek,et al.  Effects of aging on cardiac extracellular matrix in men and women , 2016, Proteomics. Clinical applications.

[37]  Eugene Berezikov,et al.  Rodent heart failure models do not reflect the human circulating microRNA signature in heart failure , 2017, PloS one.

[38]  A. Stark,et al.  Transcriptional enhancers: from properties to genome-wide predictions , 2014, Nature Reviews Genetics.

[39]  M. Molcanyi,et al.  Cardiomyocytes facing fibrotic conditions re-express extracellular matrix transcripts. , 2019, Acta biomaterialia.

[40]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[41]  M. Snyder,et al.  ChIP‐Seq: A Method for Global Identification of Regulatory Elements in the Genome , 2010, Current protocols in molecular biology.

[42]  Transforming growth factor-β: governing the transition from inflammation to fibrosis in heart failure with preserved left ventricular function. , 2011, Circulation. Heart failure.

[43]  B. O’Malley,et al.  Histone Marks in the 'Driver's Seat': Functional Roles in Steering the Transcription Cycle. , 2017, Trends in biochemical sciences.

[44]  Jason H. Moore,et al.  Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer , 2012, Science.

[45]  T. Miyakawa,et al.  Genomic responses in mouse models poorly mimic human inflammatory diseases , 2013 .

[46]  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.

[47]  H. S. Rho,et al.  An oviduct-on-a-chip provides an enhanced in vitro environment for zygote genome reprogramming , 2018, Nature Communications.

[48]  D. Geschwind,et al.  Histone Acetylome-wide Association Study of Autism Spectrum Disorder , 2016, Cell.

[49]  P. Elliott,et al.  Progressive left ventricular remodeling in patients with hypertrophic cardiomyopathy and severe left ventricular hypertrophy. , 2004, Journal of the American College of Cardiology.

[50]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[51]  Jin-hua Li,et al.  RNA‑seq profiling of mRNA associated with hypertrophic cardiomyopathy. , 2016, Molecular medicine reports.

[52]  Eileen E M Furlong,et al.  The role of transcription in shaping the spatial organization of the genome , 2019, Nature Reviews Molecular Cell Biology.

[53]  Sang Hoon Lee,et al.  Biomedical Engineering: Frontier Research and Converging Technologies , 2016 .

[54]  Andrew J. Bannister,et al.  Regulation of chromatin by histone modifications , 2011, Cell Research.

[55]  C. Tyler-Smith,et al.  Ancient DNA and the rewriting of human history: be sparing with Occam’s razor , 2016, Genome Biology.

[56]  S. Mundlos,et al.  Breaking TADs: How Alterations of Chromatin Domains Result in Disease. , 2016, Trends in genetics : TIG.

[57]  V. Regitz-Zagrosek,et al.  Sex‐dependent regulation of fibrosis and inflammation in human left ventricular remodelling under pressure overload , 2014, European journal of heart failure.

[58]  J. Molkentin,et al.  Molecular pathways underlying cardiac remodeling during pathophysiological stimulation. , 2010, Circulation.

[59]  F. Mackenzie,et al.  Dysfunctional Mechanotransduction through the YAP/TAZ/Hippo Pathway as a Feature of Chronic Disease , 2020, Cells.

[60]  Brian J. Bleakley,et al.  Integrated omics dissection of proteome dynamics during cardiac remodeling , 2018, Nature Communications.

[61]  Susmita Sahoo,et al.  Physiologic, Pathologic, and Therapeutic Paracrine Modulation of Cardiac Excitation-Contraction Coupling , 2018, Circulation research.

[62]  Jing Chen,et al.  ToppGene Suite for gene list enrichment analysis and candidate gene prioritization , 2009, Nucleic Acids Res..

[63]  R. Backofen,et al.  Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo , 2017, Nature Communications.

[64]  Alan J Tackett,et al.  Disruption of BRD4 at H3K27Ac-enriched enhancer region correlates with decreased c-Myc expression in Merkel cell carcinoma , 2015, Epigenetics.

[65]  C. Tribouilloy,et al.  Prognostic significance of left ventricular concentric remodelling in patients with aortic stenosis. , 2017, Archives of cardiovascular diseases.

[66]  Matteo Pellegrini,et al.  High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure , 2017, Circulation.

[67]  P. Kellman,et al.  Reverse Myocardial Remodeling Following Valve Replacement in Patients With Aortic Stenosis , 2018, Journal of the American College of Cardiology.

[68]  Daniel A. Skelly,et al.  Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart. , 2018, Cell reports.

[69]  T. Yokoyama,et al.  Endothelial PAS domain protein 1 (EPAS1) induces adrenomedullin gene expression in cardiac myocytes: role of EPAS1 in an inflammatory response in cardiac myocytes. , 2002, Journal of molecular and cellular cardiology.

[70]  Laura J. Scott,et al.  Genetic regulatory signatures underlying islet gene expression and type 2 diabetes , 2017, Proceedings of the National Academy of Sciences.

[71]  S. V. Heesch,et al.  IL-11 is a crucial determinant of cardiovascular fibrosis , 2017, Nature.

[72]  Z. Kassiri,et al.  Cardiac fibroblasts, fibrosis and extracellular matrix remodeling in heart disease , 2012, Fibrogenesis & tissue repair.

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

[74]  J. de Magalhães,et al.  A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels , 2015, BMC Evolutionary Biology.

[75]  K. Soo,et al.  Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity , 2016, Nature Communications.

[76]  Joseph A. Hill,et al.  Pathological Ventricular Remodeling: Mechanisms Part 1 of 2 , 2013, Circulation.

[77]  Shuqiang Li,et al.  CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq , 2016, Genome Biology.