tripartite paternally methylated region within the Gpr1-Zdbf2 imprinted domain on mouse chromosome 1 identified by meDIP-on-chip
The parent-of-origin specific expression of imprinted genes relies on DNA methylation of CpG-dinucleotides at differentially methylated regions (DMRs) during gametogenesis. To date, four paternally methylated DMRs have been identified in screens based on conventional approaches. These DMRs are linke...
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Published in | Nucleic acids research Vol. 38; no. 15; pp. 4929 - 4945 |
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Main Authors | , , , , , , , , , , , |
Format | Journal Article |
Language | English |
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England
Oxford University Press
01.08.2010
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Abstract | The parent-of-origin specific expression of imprinted genes relies on DNA methylation of CpG-dinucleotides at differentially methylated regions (DMRs) during gametogenesis. To date, four paternally methylated DMRs have been identified in screens based on conventional approaches. These DMRs are linked to the imprinted genes H19, Gtl2 (IG-DMR), Rasgrf1 and, most recently, Zdbf2 which encodes zinc finger, DBF-type containing 2. In this study, we applied a novel methylated-DNA immunoprecipitation-on-chip (meDIP-on-chip) method to genomic DNA from mouse parthenogenetic- and androgenetic-derived stem cells and sperm and identified 458 putative DMRs. This included the majority of known DMRs. We further characterized the paternally methylated Zdbf2/ZDBF2 DMR. In mice, this extensive germ line DMR spanned 16 kb and possessed an unusual tripartite structure. Methylation was dependent on DNA methyltransferase 3a (Dnmt3a), similar to H19 DMR and IG-DMR. In both humans and mice, the adjacent gene, Gpr1/GPR1, which encodes a G-protein-coupled receptor 1 protein with transmembrane domain, was also imprinted and paternally expressed. The Gpr1-Zdbf2 domain was most similar to the Rasgrf1 domain as both DNA methylation and the actively expressed allele were in cis on the paternal chromosome. This work demonstrates the effectiveness of meDIP-on-chip as a technique for identifying DMRs. |
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AbstractList | The parent-of-origin specific expression of imprinted genes relies on DNA methylation of CpG-dinucleotides at differentially methylated regions (DMRs) during gametogenesis. To date, four paternally methylated DMRs have been identified in screens based on conventional approaches. These DMRs are linked to the imprinted genes H19, Gtl2 (IG-DMR), Rasgrf1 and, most recently, Zdbf2 which encodes zinc finger, DBF-type containing 2. In this study, we applied a novel methylated-DNA immunoprecipitation-on-chip (meDIP-on-chip) method to genomic DNA from mouse parthenogenetic- and androgenetic-derived stem cells and sperm and identified 458 putative DMRs. This included the majority of known DMRs. We further characterized the paternally methylated Zdbf2/ZDBF2 DMR. In mice, this extensive germ line DMR spanned 16 kb and possessed an unusual tripartite structure. Methylation was dependent on DNA methyltransferase 3a (Dnmt3a), similar to H19 DMR and IG-DMR. In both humans and mice, the adjacent gene, Gpr1/GPR1, which encodes a G-protein-coupled receptor 1 protein with transmembrane domain, was also imprinted and paternally expressed. The Gpr1-Zdbf2 domain was most similar to the Rasgrf1 domain as both DNA methylation and the actively expressed allele were in cis on the paternal chromosome. This work demonstrates the effectiveness of meDIP-on-chip as a technique for identifying DMRs. The parent-of-origin specific expression of imprinted genes relies on DNA methylation of CpG-dinucleotides at differentially methylated regions (DMRs) during gametogenesis. To date, four paternally methylated DMRs have been identified in screens based on conventional approaches. These DMRs are linked to the imprinted genes H19 , Gtl2 (IG-DMR), Rasgrf1 and, most recently, Zdbf2 which encodes zinc finger, DBF-type containing 2. In this study, we applied a novel methylated-DNA immunoprecipitation-on-chip (meDIP-on-chip) method to genomic DNA from mouse parthenogenetic- and androgenetic-derived stem cells and sperm and identified 458 putative DMRs. This included the majority of known DMRs. We further characterized the paternally methylated Zdbf2/ZDBF2 DMR. In mice, this extensive germ line DMR spanned 16 kb and possessed an unusual tripartite structure. Methylation was dependent on DNA methyltransferase 3a (Dnmt3a), similar to H19 DMR and IG-DMR. In both humans and mice, the adjacent gene, Gpr1 / GPR1 , which encodes a G-protein-coupled receptor 1 protein with transmembrane domain, was also imprinted and paternally expressed. The Gpr1-Zdbf2 domain was most similar to the Rasgrf1 domain as both DNA methylation and the actively expressed allele were in cis on the paternal chromosome. This work demonstrates the effectiveness of meDIP-on-chip as a technique for identifying DMRs. |
Author | Miyanari, Yusuke John, Rosalind M Hiura, Hitoshi Miyauchi, Naoko Sasaki, Hiroyuki Ogawa, Hidehiko Horiike, Tokumasa Sugawara, Atsushi Yaegashi, Nobuo Arima, Takahiro Kono, Tomohiro Li, Yufeng |
AuthorAffiliation | 1 Innovation of New Biomedical Engineering Center, University of Tohoku, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575, 2 Departments of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, 3 Department of BioScience, Tokyo University of Agriculture, Tokyo, Japan 4 Cardiff School of Biosciences, Museum Avenue, Cardiff, UK, 5 Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, 6 Department of Genetics, The Graduate University for Advanced Studies (Sokendai), Mishima and 7 Division of Global Research Leaders, Shizuoka University, Shizuoka, Japan |
AuthorAffiliation_xml | – name: 1 Innovation of New Biomedical Engineering Center, University of Tohoku, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575, 2 Departments of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, 3 Department of BioScience, Tokyo University of Agriculture, Tokyo, Japan 4 Cardiff School of Biosciences, Museum Avenue, Cardiff, UK, 5 Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, 6 Department of Genetics, The Graduate University for Advanced Studies (Sokendai), Mishima and 7 Division of Global Research Leaders, Shizuoka University, Shizuoka, Japan |
Author_xml | – sequence: 1 fullname: Hiura, Hitoshi – sequence: 2 fullname: Sugawara, Atsushi – sequence: 3 fullname: Ogawa, Hidehiko – sequence: 4 fullname: John, Rosalind M – sequence: 5 fullname: Miyauchi, Naoko – sequence: 6 fullname: Miyanari, Yusuke – sequence: 7 fullname: Horiike, Tokumasa – sequence: 8 fullname: Li, Yufeng – sequence: 9 fullname: Yaegashi, Nobuo – sequence: 10 fullname: Sasaki, Hiroyuki – sequence: 11 fullname: Kono, Tomohiro – sequence: 12 fullname: Arima, Takahiro |
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SubjectTerms | Animals Chromatin Immunoprecipitation Chromosomes, Mammalian DNA (Cytosine-5-)-Methyltransferases - metabolism DNA Methylation Female Gene Regulation, Chromatin and Epigenetics Genomic Imprinting Humans Immunoprecipitation Male Mice Oligonucleotide Array Sequence Analysis Receptors, G-Protein-Coupled - genetics Receptors, G-Protein-Coupled - metabolism |
Title | tripartite paternally methylated region within the Gpr1-Zdbf2 imprinted domain on mouse chromosome 1 identified by meDIP-on-chip |
URI | https://www.ncbi.nlm.nih.gov/pubmed/20385583 https://search.proquest.com/docview/753994128 https://search.proquest.com/docview/755139994 https://search.proquest.com/docview/853485979 https://search.proquest.com/docview/856764489 https://pubmed.ncbi.nlm.nih.gov/PMC2926594 |
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