title: Global DNA methylation analysis of human atherosclerotic plaques reveals extensive genomic hypomethylation and reactivation at imprinted locus 14q32 involving induction of a miRNA cluster.
abstract: OBJECTIVE
  We conducted a genome-wide analysis to identify differentially methylated genes in atherosclerotic lesions.
  
  
  METHODS
  DNA methylation at promoters, exons and introns was identified by massive parallel sequencing. Gene expression was analysed by microarrays, qPCR, immunohistochemistry and western blots.
  
  
  RESULTS
  Globally, hypomethylation of chromosomal DNA predominates in atherosclerotic plaques and two-thirds of genes showing over 2.5-fold differential in DNA methylation are up-regulated in comparison to healthy mammary arteries. The imprinted chromatin locus 14q32 was identified for the first time as an extensively hypomethylated area in atherosclerosis with highly induced expression of miR127, -136, -410, -431, -432, -433 and capillary formation-associated gene RTL1. The top 100 list of hypomethylated promoters exhibited over 1000-fold enrichment for miRNAs, many of which mapped to locus 14q32. Unexpectedly, also gene body hypermethylation was found to correlate with stimulated mRNA expression.
  
  
  CONCLUSIONS
  Significant changes in genomic methylation were identified in atherosclerotic lesions. The most prominent gene cluster activated via hypomethylation was detected at imprinted chromosomal locus 14q32 with several clustered miRNAs that were up-regulated. These results suggest that epigenetic changes are involved in atherogenesis and may offer new potential therapeutic targets for vascular diseases.
authors.affiliation: Department of Biotechnology and Molecular Medicine, A. I. Virtanen Institute, Kuopio, University of Eastern Finland, PO Box 1627 (Neulaniementie 2), Kuopio, FIN-70211, Finland.
authors.forename: Einari
authors.initials: E
authors.lastname: Aavik
authors.affiliation: Department of Biotechnology and Molecular Medicine, A. I. Virtanen Institute, Kuopio, University of Eastern Finland, PO Box 1627 (Neulaniementie 2), Kuopio, FIN-70211, Finland.
authors.forename: Henri
authors.initials: H
authors.lastname: Lumivuori
authors.affiliation: Centre for R&D, Uppsala University/County Council of Gävleborg, Gävle, Sweden.
authors.forename: Olli
authors.initials: O
authors.lastname: Leppänen
authors.affiliation: Department of Biotechnology and Molecular Medicine, A. I. Virtanen Institute, Kuopio, University of Eastern Finland, PO Box 1627 (Neulaniementie 2), Kuopio, FIN-70211, Finland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Wirth
authors.affiliation: Department of Biotechnology and Molecular Medicine, A. I. Virtanen Institute, Kuopio, University of Eastern Finland, PO Box 1627 (Neulaniementie 2), Kuopio, FIN-70211, Finland.
authors.forename: Sanna-Kaisa
authors.initials: SK
authors.lastname: Häkkinen
authors.affiliation: Institut für Pathologie, Medizinische Hochschule Hannover, Hannover, Germany.
authors.forename: Jan-Hinrich
authors.initials: JH
authors.lastname: Bräsen
authors.affiliation: Department of Angiology, Universitäts-Herzzentrum Freiburg Bad Krozingen, Bad Krozingen, Germany.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Beschorner
authors.affiliation: Department of Angiology, Universitäts-Herzzentrum Freiburg Bad Krozingen, Bad Krozingen, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Zeller
authors.affiliation: NXT-Dx, Ghent, Belgium.
authors.forename: Maarten
authors.initials: M
authors.lastname: Braspenning
authors.affiliation: Laboratory for Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium.
authors.forename: Wim
authors.initials: W
authors.lastname: van Criekinge
authors.affiliation: Vascular Surgery Unit, Kuopio University Hospital, Kuopio, Finland.
authors.forename: Kimmo
authors.initials: K
authors.lastname: Mäkinen
authors.affiliation: Department of Biotechnology and Molecular Medicine, A. I. Virtanen Institute, Kuopio, University of Eastern Finland, PO Box 1627 (Neulaniementie 2), Kuopio, FIN-70211, Finland Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland seppo.ylaherttuala@uef.fi.
authors.forename: Seppo
authors.initials: S
authors.lastname: Ylä-Herttuala
mesh_terms: D000368:Aged; D016022:Case-Control Studies; D002883:Chromosomes, Human, Pair 14 / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D015536:Down-Regulation / Q000235:genetics; D005091:Exons / Q000235:genetics; D005260:Female; D063990:Gene Ontology; D056426:Genetic Loci / Q000235:genetics; D055106:Genome-Wide Association Study; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058226:Plaque, Atherosclerotic / Q000235:genetics*; D011257:Pregnancy Proteins / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D012333:RNA, Messenger / Q000378:metabolism; D015854:Up-Regulation / Q000235:genetics
chemical_list: D035683:MicroRNAs; D011257:Pregnancy Proteins; D012333:RNA, Messenger; C579465:RTL1 protein, human
keywords: Atherosclerosis; DNA methylation; Epigenetics; Peripheral vascular disease