Home LiteratureArticle Details
PMID: 18952162 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

Tissue specific differentially methylated regions (TDMR): Changes in DNA methylation during development.

Genomics ·Vol. 93 ·No. 2 ·2009-02-00 ·Pages 130-9

Song F, Mahmood S, Ghosh S, Liang P, Smiraglia DJ, Nagase H, Held WA

Abstract

Tissue specific differentially methylated regions (TDMRs) were identified and localized in the mouse genome using second generation virtual RLGS (vRLGS). Sequenom MassARRAY quantitative methylation analysis was used to confirm and determine the fine structure of tissue specific differences in DNA methylation. TDMRs have a broad distribution of locations to intragenic and intergenic regions including both CpG islands, and non-CpG islands regions. Somewhat surprising, there is a strong bias for TDMR location in non-promoter intragenic regions. Although some TDMRs are within or close to repeat sequences, overall they are less frequently associated with repetitive elements than expected from a random distribution. Many TDMRs are methylated at early developmental stages, but unmethylated later, suggesting active or passive demethylation, or expansions of populations of cells with unmethylated TDMRs. This is notable during postnatal testis differentiation where many testis specific TDMRs become progressively "demethylated". These results suggest that methylation changes during development are dynamic, involve demethylation and methylation, and may occur at late stages of embryonic development or even postnatally.

MeSH Terms
Animals Computational Biology/methods CpG Islands DNA Methylation Embryo, Mammalian Epigenesis, Genetic Gene Expression Profiling/methods Gene Expression Regulation, Developmental Gene Silencing Genome Male Mice Mice, Inbred C57BL Oligonucleotide Array Sequence Analysis Software Testis/metabolism Tissue Distribution
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Song Fei
Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA.
Mahmood Saleh
Ghosh Srimoyee
Liang Ping
Smiraglia Domminic J
Nagase Hiroki
Held William A
References (44)
44 references, click to expand
  1. Genome-scale DNA methylation maps of pluripotent and differentiated cells.
    Nature. 2008 Aug 7;454(7205):766-70 PMID: 18600261
  2. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation.
    Cell Stem Cell. 2008 Feb 7;2(2):160-9 PMID: 18371437
  3. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene.
    Nature. 2000 May 25;405(6785):482-5 PMID: 10839546
  4. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus.
    Nature. 2000 May 25;405(6785):486-9 PMID: 10839547
  5. Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer.
    Hum Mol Genet. 2001 Apr;10(7):687-92 PMID: 11257100
  6. Virtual genome scan: a tool for restriction landmark-based scanning of the human genome.
    Genome Res. 2001 Aug;11(8):1453-9 PMID: 11483587
  7. Large-scale analysis of the human and mouse transcriptomes.
    Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4465-70 PMID: 11904358
  8. Restriction landmark genome scanning.
    Methods. 2002 Jun;27(2):144-9 PMID: 12095273
  9. Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice.
    Genes Cells. 2002 Sep;7(9):961-9 PMID: 12296826
  10. MethPrimer: designing primers for methylation PCRs.
    Bioinformatics. 2002 Nov;18(11):1427-31 PMID: 12424112
  11. Expression of various genes is controlled by DNA methylation during mammalian development.
    J Cell Biochem. 2003 Apr 1;88(5):899-910 PMID: 12616529
  12. DAVID: Database for Annotation, Visualization, and Integrated Discovery.
    Genome Biol. 2003;4(5):P3 PMID: 12734009
  13. Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS).
    Nucleic Acids Res. 2003 Aug 1;31(15):4490-6 PMID: 12888509
  14. Expression profiling of the developing testis in wild-type and Dazl knockout mice.
    Mol Reprod Dev. 2004 Jan;67(1):26-54 PMID: 14648873
  15. DNA methylation profiles of CpG islands for cellular differentiation and development in mammals.
    Cytogenet Genome Res. 2004;105(2-4):325-34 PMID: 15237220
  16. A genomic scanning method for higher organisms using restriction sites as landmarks.
    Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9523-7 PMID: 1946366
  17. A reagent for the single-step simultaneous isolation of RNA, DNA and proteins from cell and tissue samples.
    Biotechniques. 1993 Sep;15(3):532-4, 536-7 PMID: 7692896
  18. Methylation profiles of genomic DNA of mouse developmental brain detected by restriction landmark genomic scanning (RLGS) method.
    Nucleic Acids Res. 1993 Dec 11;21(24):5604-8 PMID: 8284204
  19. Accessibility to tissue-specific genes from methylation profiles of mouse brain genomic DNA.
    Electrophoresis. 1995 Feb;16(2):218-26 PMID: 7774562
  20. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands.
    Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9821-6 PMID: 8790415
  21. Cytosine methylation and the ecology of intragenomic parasites.
    Trends Genet. 1997 Aug;13(8):335-40 PMID: 9260521
  22. DNA methylation is the primary silencing mechanism for a set of germ line- and tumor-specific genes with a CpG-rich promoter.
    Mol Cell Biol. 1999 Nov;19(11):7327-35 PMID: 10523621
  23. Calendar of gametogenic development in the prepuberal male mouse.
    Science. 1961 Sep 22;134(3482):832-3 PMID: 13728067
  24. Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression.
    Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3336-41 PMID: 15728362
  25. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3.
    Nat Genet. 2005 Jun;37(6):645-51 PMID: 15895082
  26. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells.
    Nat Genet. 2005 Aug;37(8):853-62 PMID: 16007088
  27. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry.
    Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15785-90 PMID: 16243968
  28. Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band.
    Nat Genet. 2006 May;38(5):540-9 PMID: 16642018
  29. The orphan nuclear receptor GCNF recruits DNA methyltransferase for Oct-3/4 silencing.
    Biochem Biophys Res Commun. 2006 Jun 9;344(3):845-51 PMID: 16631596
  30. CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure.
    PLoS Genet. 2006 Mar;2(3):e26 PMID: 16520826
  31. DNA methylation profiling of human chromosomes 6, 20 and 22.
    Nat Genet. 2006 Dec;38(12):1378-85 PMID: 17072317
  32. Differential recruitment of methylated CpG binding domains by the orphan receptor GCNF initiates the repression and silencing of Oct4 expression.
    Mol Cell Biol. 2006 Dec;26(24):9471-83 PMID: 17030610
  33. DNA methylation regulates long-range gene silencing of an X-linked homeobox gene cluster in a lineage-specific manner.
    Genes Dev. 2006 Dec 15;20(24):3382-94 PMID: 17182866
  34. A unique configuration of genome-wide DNA methylation patterns in the testis.
    Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):228-33 PMID: 17190809
  35. Using GOstats to test gene lists for GO term association.
    Bioinformatics. 2007 Jan 15;23(2):257-8 PMID: 17098774
  36. Analysis of tissue-specific differentially methylated regions (TDMs) in humans.
    Genomics. 2007 Mar;89(3):326-37 PMID: 17188838
  37. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome.
    Nat Genet. 2007 Apr;39(4):457-66 PMID: 17334365
  38. Developmental acquisition of genome-wide DNA methylation occurs prior to meiosis in male germ cells.
    Dev Biol. 2007 Jul 15;307(2):368-79 PMID: 17559830
  39. Global, comparative analysis of tissue-specific promoter CpG methylation.
    Genomics. 2007 Sep;90(3):314-23 PMID: 17582736
  40. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters.
    PLoS Genet. 2007 Oct;3(10):2023-36 PMID: 17967063
  41. A novel CpG island set identifies tissue-specific methylation at developmental gene loci.
    PLoS Biol. 2008 Jan;6(1):e22 PMID: 18232738
  42. Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.
    BMC Genomics. 2007;8:446 PMID: 18053125
  43. Unraveling epigenetic regulation in embryonic stem cells.
    Cell Stem Cell. 2008 Feb 7;2(2):123-34 PMID: 18371433
  44. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).
    Genome Res. 2008 Sep;18(9):1518-29 PMID: 18577705
Article Info
Journal
Genomics
Abbr.
Genomics
ISSN
1089-8646
DOI
10.1016/j.ygeno.2008.09.003
Published
2009-02-00
Epub
2008-00-13
Pages
130-9
Language
English
Region
United States
NLM ID
8800135
PMCID
PMC2658018
Subset
IM
Grants
NCI NIH HHS · P30 CA016056 · United States
NCI NIH HHS · CA16056 · United States
NCI NIH HHS · R01 CA102423 · United States
NCI NIH HHS · R01 CA102423-04 · United States
NCI NIH HHS · CA102423 · United States
External Links
PubMed source DOI: 10.1016/j.ygeno.2008.09.003 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2