Liang et al. BMC Genomics 2011, 12:231 http://www.biomedcentral.com/1471-2164/12/231 R E S E A R C H A R T I C L E Open Access Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development Ping Liang1*†, Fei Song2,3†, Srimoyee Ghosh4,5, Evan Morien4,6, Maochun Qin4, Saleh Mahmood2,7, Kyoko Fujiwara4,8, Jun Igarashi8, Hiroki Nagase4,8,9* and William A Held2 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. Background DNA methylation in mammals occurs predominantly at CpG dinucleotides [1]. Early studies indicated that in normal cells, most CpGs in repeats, retroviral sequences, and within the coding region of genes are methylated, whereas most CpG island (CpGi) regions are maintained in an unmethylated state [2,3]. After fertilization there is * Correspondence: pliang@brocku.ca; hnagase@chiba-cc.jp † Contributed equally 1Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada 4Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, USA Full list of author information is available at the end of the article a period of genome-wide demethylation followed by per- iods of remethylation in somatic cells after implantation. Demethylation and reprogramming is also necessary in the germ cells to reset gamete-specific imprinting [4-7]. There is a long history and generally inverse correlation between gene promoter DNA methylation and gene expression [8-12]. Early studies proposed that regulated methylation and demethylation has a role regulating gene expression during development [10,13]. The critical function of DNA methylation during devel- opment is also apparent from the consequence of targeted knockouts of DNA methyltransferase genes. The knockout of Dnmt1, which has a strong preference for hemimethy- lated DNA and is thus considered to be a maintenance © 2011 Liang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.