title: Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development.
abstract: BACKGROUND
  Changes in DNA methylation in the mammalian genome during development are frequent events and play major roles regulating gene expression and other developmental processes. It is necessary to identify these events so that we may understand how these changes affect normal development and how aberrant changes may impact disease.
  
  
  RESULTS
  In this study Methylated DNA ImmunoPrecipitation (MeDIP) was used in conjunction with a NimbleGen promoter plus CpG island (CpGi) array to identify Tissue and Developmental Stage specific Differentially Methylated DNA Regions (T-DMRs and DS-DMRs) on a genome-wide basis. Four tissues (brain, heart, liver, and testis) from C57BL/6J mice were analyzed at three developmental stages (15 day embryo, E15; new born, NB; 12 week adult, AD). Almost 5,000 adult T-DMRs and 10,000 DS-DMRs were identified. Surprisingly, almost all DS-DMRs were tissue specific (i.e. methylated in at least one tissue and unmethylated in one or more tissues). In addition our results indicate that many DS-DMRs are methylated at early development stages (E15 and NB) but are unmethylated in adult. There is a very strong bias for testis specific methylation in non-CpGi promoter regions (94%). Although the majority of T-DMRs and DS-DMRs tended to be in non-CpGi promoter regions, a relatively large number were also located in CpGi in promoter, intragenic and intergenic regions (>15% of the 15,979 CpGi on the array).
  
  
  CONCLUSIONS
  Our data suggests the vast majority of unique sequence DNA methylation has tissue specificity, that demethylation has a prominent role in tissue differentiation, and that DNA methylation has regulatory roles in alternative promoter selection and in non-promoter regions. Overall, our studies indicate changes in DNA methylation during development are a dynamic, widespread, and tissue-specific process involving both DNA methylation and demethylation.
authors.affiliation: Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada. pliang@brocku.ca
authors.forename: Ping
authors.initials: P
authors.lastname: Liang
authors.forename: Fei
authors.initials: F
authors.lastname: Song
authors.forename: Srimoyee
authors.initials: S
authors.lastname: Ghosh
authors.forename: Evan
authors.initials: E
authors.lastname: Morien
authors.forename: Maochun
authors.initials: M
authors.lastname: Qin
authors.forename: Saleh
authors.initials: S
authors.lastname: Mahmood
authors.forename: Kyoko
authors.initials: K
authors.lastname: Fujiwara
authors.forename: Jun
authors.initials: J
authors.lastname: Igarashi
authors.forename: Hiroki
authors.initials: H
authors.lastname: Nagase
authors.forename: William A
authors.initials: WA
authors.lastname: Held
mesh_terms: D000818:Animals; D000831:Animals, Newborn; D001921:Brain / Q000196:embryology / Q000254:growth & development* / Q000378:metabolism; D015820:Cadherins / Q000235:genetics; D002478:Cells, Cultured; D018899:CpG Islands; D019175:DNA Methylation; D004622:Embryo, Mammalian; D053595:Embryonic Stem Cells / Q000378:metabolism; D044127:Epigenesis, Genetic; D018507:Gene Expression Regulation, Developmental; D055106:Genome-Wide Association Study; D006321:Heart / Q000196:embryology / Q000254:growth & development*; D018398:Homeodomain Proteins / Q000235:genetics; D008099:Liver / Q000196:embryology / Q000254:growth & development* / Q000378:metabolism; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D005810:Multigene Family; D009206:Myocardium / Q000378:metabolism; D009928:Organ Specificity; D011401:Promoter Regions, Genetic; D013737:Testis / Q000196:embryology / Q000254:growth & development* / Q000378:metabolism
chemical_list: D015820:Cadherins; D018398:Homeodomain Proteins