title: Imprinted genes and imprinting control regions show predominant intermediate methylation in adult somatic tissues.
abstract: Genomic imprinting is an epigenetic feature characterized by parent-specific monoallelic gene expression. The aim of this study was to compare the DNA methylation status of imprinted genes and imprinting control regions (ICRs), harboring differentially methylated regions (DMRs) in a comprehensive panel of 18 somatic tissues. The germline DMRs analyzed were divided into ubiquitously imprinted and placenta-specific DMRs, which show identical and different methylation imprints in adult somatic and placental tissues, respectively. We showed that imprinted genes and ICR DMRs maintain methylation patterns characterized by intermediate methylation levels in somatic tissues, which are pronounced in a specific region of the promoter area, located 200-1500 bp from the transcription start site. This intermediate methylation is concordant with gene expression from a single unmethylated allele and silencing of a reciprocal parental allele through DNA methylation. The only exceptions were seen for ICR DMRs of placenta-specific imprinted genes, which showed low levels of methylation, suggesting that these genes escape parent-specific epigenetic regulation in somatic tissues.
authors.affiliation: Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia.|National Institute for Health & Welfare, University of Helsinki, Helsinki FI-00271, Finland.|Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Natalia
authors.initials: N
authors.lastname: Pervjakova
authors.affiliation: Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia.|Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Silva
authors.initials: S
authors.lastname: Kasela
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.|Department of Biostatistics, University of Liverpool, Liverpool, L69 3GA, UK.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Morris
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.|Institute of Mathematical Statistics, University of Tartu, Tartu 50409, Estonia.
authors.forename: Mart
authors.initials: M
authors.lastname: Kals
authors.affiliation: Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia.|Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Andres
authors.initials: A
authors.lastname: Metspalu
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.|The Big Data Institute, University of Oxford, Oxford, OX3 7BN, UK.|Broad Institute of the Massachusetts Institute of Technology & Harvard University, Cambridge, MA 02142, USA.
authors.forename: Cecilia M
authors.initials: CM
authors.lastname: Lindgren
authors.affiliation: Competence Centre on Health Technologies, Tartu 50410, Estonia.|Department of Obstetrics & Gynecology, University of Tartu, Tartu 51014, Estonia.|Institute of Bio- & Translational Medicine, University of Tartu, Tartu 50411, Estonia.
authors.forename: Andres
authors.initials: A
authors.lastname: Salumets
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Reedik
authors.initials: R
authors.lastname: Mägi
mesh_terms: D000328:Adult; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D015870:Gene Expression; D018392:Genomic Imprinting; D005854:Germ Cells / Q000378:metabolism; D006801:Humans; D008297:Male; D008875:Middle Aged; D009928:Organ Specificity; D010920:Placenta / Q000378:metabolism; D011247:Pregnancy; D011401:Promoter Regions, Genetic
keywords: ICR; Levene's test; genomic imprinting; methylation; somatic tissues