Imprinted Genes and Imprinting Control Regions Show Predominant Intermediate Methylation in Adult Somatic Tissues

References

• McGrath J , SolterD . Completion of mouse embryogenesis requires both the maternal and paternal genomes . Cell37 ( 1 ), 179 – 183 ( 1984 ).
   PubMed Web of Science ®Google Scholar
• Surani MA , BartonSC . Development of gynogenetic eggs in the mouse: implications for parthenogenetic embryos . Science222 ( 4627 ), 1034 – 1036 ( 1983 ).
   PubMed Web of Science ®Google Scholar
• Renfree MB , SuzukiS , Kaneko-IshinoT . The origin and evolution of genomic imprinting and viviparity in mammals . Philos. Trans. R. Soc. Lond. B. Biol. Sci.368 ( 1609 ), 20120151 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Hoggart CJ , VenturiniG , ManginoMet al. Novel approach identifies SNPs in SLC2A10 and KCNK9 with evidence for parent-of-origin effect on body mass index . PLoS Genet.10 ( 7 ), e1004508 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Lindsay RS , KobesS , KnowlerWC , HansonRL . Genome-wide linkage analysis assessing parent-of-origin effects in the inheritance of birth weight . Hum. Genet.110 ( 5 ), 503 – 509 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Barlow DP . Genomic imprinting: a mammalian epigenetic discovery model . Annu. Rev. Genet.45 ( 1 ), 379 – 403 ( 2011 ).
   PubMedGoogle Scholar
• Edwards CA , Ferguson-SmithAC . Mechanisms regulating imprinted genes in clusters . Curr. Opin. Cell Biol.19 ( 3 ), 281 – 289 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• MouseBook . www.mousebook.org .
   Google Scholar
• Peters J , RobsonJE . Imprinted noncoding RNAs . Mamm. Genome.19 ( 7–8 ), 493 – 502 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Ideraabdullah FY , VigneauS , BartolomeiMS . Genomic imprinting mechanisms in mammals . Mutat. Res.647 ( 1–2 ), 77 – 85 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Lalande M . Parental imprinting and human disease . Annu. Rev. Genet ( 1997 ).
   Web of Science ®Google Scholar
• Smith ZD , MeissnerA . DNA methylation: roles in mammalian development . Nat. Rev. Genet.14 ( 3 ), 204 – 220 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Bourc’his D , XuGL , LinCS , BollmanB , BestorTH . Dnmt3L and the establishment of maternal genomic imprints . Science294 ( 5551 ), 2536 – 2539 ( 2001 ).
   PubMed Web of Science ®Google Scholar
• Hata K , OkanoM , LeiH , LiE . Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice . Development129 , 1983 – 1993 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Das R , LeeYK , StrogantsevRet al. DNMT1 and AIM1 Imprinting in human placenta revealed through a genome-wide screen for allele-specific DNA methylation . BMC Genomics14 ( 1 ), 685 ( 2013 ).
   PubMedGoogle Scholar
• Lopes S . Epigenetic modifications in an imprinting cluster are controlled by a hierarchy of DMRs suggesting long-range chromatin interactions . Hum. Mol. Genet.12 ( 3 ), 295 – 305 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Coombes C , ArnaudP , GordonEet al. Epigenetic properties and identification of an imprint mark in the Nesp-Gnasxl domain of the mouse Gnas imprinted locus . Mol. Cell. Biol.23 ( 16 ), 5475 – 5488 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Kagami M , MatsuokaK , NagaiTet al. Paternal uniparental disomy 14 and related disorders: placental gene expression analyses and histological examinations . Epigenetics7 ( 10 ), 1142 – 1150 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Court F , TayamaC , RomanelliVet al. Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of the human imprintome and suggests a germline methylation independent establishment of imprinting . Genome Res.24 ( 4 ), 554 – 569 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Kobayashi H , YamadaK , MoritaSet al. Identification of the mouse paternally expressed imprinted gene Zdbf2 on chromosome 1 and its imprinted human homolog ZDBF2 on chromosome 2 . Genomics93 ( 5 ), 461 – 472 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Woodfine K , HuddlestonJE , MurrellA . Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue . Epigenetics Chromatin4 ( 1 ), 1 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Bibikova M , BarnesB , TsanCet al. High density DNA methylation array with single CpG site resolution . Genomics98 ( 4 ), 288 – 295 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Lokk K , ModhukurV , RajashekarBet al. DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns . Genome Biol.15 ( 4 ), R54 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Franz H , UllmannC , BeckerAet al. Systematic analysis of gene expression in human brains before and after death . Genome Biol.6 ( 13 ), R112 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Sluimer JC , KistersN , CleutjensKBet al. Dead or alive: gene expression profiles of advanced atherosclerotic plaques from autopsy and surgery . Physiol. Genomics30 ( 3 ), 335 – 341 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Vaniushin BF . DNA methylation and epigenetics . Genetika42 ( 9 ), 1186 – 1199 ( 2006 ).
   PubMedGoogle Scholar
• Newell-Price J , ClarkAJ , KingP . DNA methylation and silencing of gene expression . Trends Endocrinol. Metab.11 ( 4 ), 142 – 148 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Ehrlich M . DNA methylation in cancer: too much, but also too little . Oncogene21 ( 35 ), 5400 – 5413 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Li Y , SasakiH . Genomic imprinting in mammals: its life cycle, molecular mechanisms and reprogramming . Cell Res.21 ( 3 ), 466 – 473 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Metsalu T , ViltropT , TiiratsAet al. Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta . Epigenetics9 ( 10 ), 1397 – 1409 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Li E , BeardC , JaenischR . Role for DNA methylation in genomic imprinting . Nature366 ( 6453 ), 362 – 365 ( 1993 ).
   PubMed Web of Science ®Google Scholar
• Barbaux S , Gascoin-LachambreG , BuffatCet al. A genome-wide approach reveals novel imprinted genes expressed in the human placenta . Epigenetics7 ( 9 ), 1079 – 1090 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Kobayashi H , YanagisawaE , SakashitaAet al. Epigenetic and transcriptional features of the novel human imprinted lncRNA GPR1AS suggest it is a functional ortholog to mouse Zdbf2linc . Epigenetics8 , 635 – 645 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Noguer-Dance M , Abu-AmeroS , Al-KhtibMet al. The primate-specific microRNA gene cluster (C19MC) is imprinted in the placenta . Hum. Mol. Genet.19 ( 18 ), 3566 – 3582 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Krjutškov K , KoltšinaM , GrandKet al. Tissue-specific mitochondrial heteroplasmy at position 16,093 within the same individual . Curr. Genet.60 ( 1 ), 11 – 16 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Žilina O , KoltšinaM , RaidR , KurgA , TõnissonN , SalumetsA . Somatic mosaicism for copy-neutral loss of heterozygosity and DNA copy number variations in the human genome . BMC Genomics16 ( 1 ), 703 ( 2015 ).
   PubMedGoogle Scholar
• Aryee MJ , JaffeAE , Corrada-BravoHet al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays . Bioinformatics30 ( 10 ), 1363 – 1369 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Makismovic J , GordonL , OshlackA . SWAN: subset-quantile within array normalization for Illumina Infinium HumanMethylation450 BeadChips . Genome Biol.13 ( 6 ), R44 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Catalogue of Parent of Origin Effects Imprinted Genes and Related Effects . http://igc.otago.ac.nz/Search.html .
   Google Scholar
• Geneimprint . www.geneimprint.com/ .
   Google Scholar