title: Deciphering the Epigenetic Code of Cardiac Myocyte Transcription.
abstract: BACKGROUND
  Epigenetic mechanisms are crucial for cell identity and transcriptional control. The heart consists of different cell types, including cardiac myocytes, endothelial cells, fibroblasts, and others. Therefore, cell type-specific analysis is needed to gain mechanistic insight into the regulation of gene expression in cardiac myocytes. Although cytosolic mRNA represents steady-state levels, nuclear mRNA more closely reflects transcriptional activity. To unravel epigenetic mechanisms of transcriptional control, cell type-specific analysis of nuclear mRNA and epigenetic modifications is crucial.
  
  
  OBJECTIVE
  The aim was to purify cardiac myocyte nuclei from hearts of different species by magnetic- or fluorescent-assisted sorting and to determine the nuclear and cellular RNA expression profiles and epigenetic marks in a cardiac myocyte-specific manner.
  
  
  RESULTS
  Frozen cardiac tissue samples were used to isolate cardiac myocyte nuclei. High sorting purity was confirmed for cardiac myocyte nuclei isolated from mice, rats, and humans. Deep sequencing of nuclear RNA revealed a major fraction of nascent, unspliced RNA in contrast to results obtained from purified cardiac myocytes. Cardiac myocyte nuclear and cellular RNA expression profiles showed differences, especially for metabolic genes. Genome-wide maps of the transcriptional elongation mark H3K36me3 were generated by chromatin-immunoprecipitation. Transcriptome and epigenetic data confirmed the high degree of cardiac myocyte-specificity of our protocol. An integrative analysis of nuclear mRNA and histone mark occurrence indicated a major impact of the chromatin state on transcriptional activity in cardiac myocytes.
  
  
  CONCLUSIONS
  This study establishes cardiac myocyte-specific sorting of nuclei as a universal method to investigate epigenetic and transcriptional processes in cardiac myocytes of different origins. These data sets provide novel insight into cardiac myocyte transcription.
authors.affiliation: From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.).
authors.forename: Sebastian
authors.initials: S
authors.lastname: Preissl
authors.affiliation: From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.).
authors.forename: Martin
authors.initials: M
authors.lastname: Schwaderer
authors.affiliation: From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.).
authors.forename: Alexandra
authors.initials: A
authors.lastname: Raulf
authors.affiliation: From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.).
authors.forename: Michael
authors.initials: M
authors.lastname: Hesse
authors.affiliation: From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.).
authors.forename: Björn A
authors.initials: BA
authors.lastname: Grüning
authors.affiliation: From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.).
authors.forename: Claudia
authors.initials: C
authors.lastname: Köbele
authors.affiliation: From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.).
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
authors.affiliation: From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.).
authors.forename: Bernd K
authors.initials: BK
authors.lastname: Fleischmann
authors.affiliation: From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.). ralf.gilsbach@pharmakol.uni-freiburg.de lutz.hein@pharmakol.uni-freiburg.de.
authors.forename: Lutz
authors.initials: L
authors.lastname: Hein
authors.affiliation: From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.). ralf.gilsbach@pharmakol.uni-freiburg.de lutz.hein@pharmakol.uni-freiburg.de.
authors.forename: Ralf
authors.initials: R
authors.lastname: Gilsbach
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism; D002478:Cells, Cultured; D044127:Epigenesis, Genetic / Q000502:physiology*; D005260:Female; D006801:Humans; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D008822:Mice, Transgenic; D032383:Myocytes, Cardiac / Q000502:physiology*; D051381:Rats; D017208:Rats, Wistar; D013045:Species Specificity; D014158:Transcription, Genetic / Q000502:physiology*
keywords: cardiac myocyte; epigenetics; histone modifications; nuclear RNA; transcriptome