title: Genetic analysis of the cardiac methylome at single nucleotide resolution in a model of human cardiovascular disease.
abstract: Epigenetic marks such as cytosine methylation are important determinants of cellular and whole-body phenotypes. However, the extent of, and reasons for inter-individual differences in cytosine methylation, and their association with phenotypic variation are poorly characterised. Here we present the first genome-wide study of cytosine methylation at single-nucleotide resolution in an animal model of human disease. We used whole-genome bisulfite sequencing in the spontaneously hypertensive rat (SHR), a model of cardiovascular disease, and the Brown Norway (BN) control strain, to define the genetic architecture of cytosine methylation in the mammalian heart and to test for association between methylation and pathophysiological phenotypes. Analysis of 10.6 million CpG dinucleotides identified 77,088 CpGs that were differentially methylated between the strains. In F1 hybrids we found 38,152 CpGs showing allele-specific methylation and 145 regions with parent-of-origin effects on methylation. Cis-linkage explained almost 60% of inter-strain variation in methylation at a subset of loci tested for linkage in a panel of recombinant inbred (RI) strains. Methylation analysis in isolated cardiomyocytes showed that in the majority of cases methylation differences in cardiomyocytes and non-cardiomyocytes were strain-dependent, confirming a strong genetic component for cytosine methylation. We observed preferential nucleotide usage associated with increased and decreased methylation that is remarkably conserved across species, suggesting a common mechanism for germline control of inter-individual variation in CpG methylation. In the RI strain panel, we found significant correlation of CpG methylation and levels of serum chromogranin B (CgB), a proposed biomarker of heart failure, which is evidence for a link between germline DNA sequence variation, CpG methylation differences and pathophysiological phenotypes in the SHR strain. Together, these results will stimulate further investigation of the molecular basis of locally regulated variation in CpG methylation and provide a starting point for understanding the relationship between the genetic control of CpG methylation and disease phenotypes.
authors.affiliation: Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom; National Heart and Lung Institute, Imperial College, London, United Kingdom.
authors.forename: Michelle D
authors.initials: MD
authors.lastname: Johnson
authors.affiliation: Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom; National Heart and Lung Institute, Imperial College, London, United Kingdom.
authors.forename: Michael
authors.initials: M
authors.lastname: Mueller
authors.affiliation: Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom; National Heart and Lung Institute, Imperial College, London, United Kingdom.
authors.forename: Martyna
authors.initials: M
authors.lastname: Adamowicz-Brice
authors.affiliation: Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom; National Heart and Lung Institute, Imperial College, London, United Kingdom.
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Collins
authors.affiliation: Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom; Institute of Clinical Sciences, Imperial College, London, United Kingdom.
authors.forename: Pascal
authors.initials: P
authors.lastname: Gellert
authors.affiliation: Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom; Institute of Clinical Sciences, Imperial College, London, United Kingdom.
authors.forename: Klio
authors.initials: K
authors.lastname: Maratou
authors.affiliation: Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom.
authors.forename: Prashant K
authors.initials: PK
authors.lastname: Srivastava
authors.affiliation: Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom.
authors.forename: Maxime
authors.initials: M
authors.lastname: Rotival
authors.affiliation: Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom.
authors.forename: Shahena
authors.initials: S
authors.lastname: Butt
authors.affiliation: Genomics Core Laboratory, MRC Clinical Sciences Centre, London, United Kingdom.
authors.forename: Laurence
authors.initials: L
authors.lastname: Game
authors.affiliation: Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom; National Heart and Lung Institute, Imperial College, London, United Kingdom.
authors.forename: Santosh S
authors.initials: SS
authors.lastname: Atanur
authors.affiliation: Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom; National Heart and Lung Institute, Imperial College, London, United Kingdom.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Silver
authors.affiliation: Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom.
authors.forename: Penny J
authors.initials: PJ
authors.lastname: Norsworthy
authors.affiliation: Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom.
authors.forename: Sarah R
authors.initials: SR
authors.lastname: Langley
authors.affiliation: Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom.
authors.forename: Enrico
authors.initials: E
authors.lastname: Petretto
authors.affiliation: Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic.
authors.forename: Michal
authors.initials: M
authors.lastname: Pravenec
authors.affiliation: Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom; Institute of Clinical Sciences, Imperial College, London, United Kingdom.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Aitman
mesh_terms: D000818:Animals; D001483:Base Sequence; D002318:Cardiovascular Diseases / Q000235:genetics* / Q000473:pathology; D002478:Cells, Cultured; D019175:DNA Methylation; D004195:Disease Models, Animal; D016678:Genome; D006801:Humans; D008297:Male; D009206:Myocardium / Q000378:metabolism* / Q000473:pathology; D032383:Myocytes, Cardiac / Q000378:metabolism / Q000473:pathology; D020641:Polymorphism, Single Nucleotide; D051381:Rats; D011914:Rats, Inbred BN; D011918:Rats, Inbred SHR; D017422:Sequence Analysis, DNA / Q000379:methods