Non-CpG Methylation is Prevalent in Embryonic Stem Cells and May Be Mediated by DNA Methyltransferase 3a

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2000 May 11

PMID 10805783

Citations 408

Authors

B H Ramsahoye

D Biniszkiewicz

F Lyko

V Clark

A P Bird

R Jaenisch

Affiliations

Soon will be listed here.

Abstract

Current evidence indicates that methylation of cytosine in mammalian DNA is restricted to both strands of the symmetrical sequence CpG, although there have been sporadic reports that sequences other than CpG may also be methylated. We have used a dual-labeling nearest neighbor technique and bisulphite genomic sequencing methods to investigate the nearest neighbors of 5-methylcytosine residues in mammalian DNA. We find that embryonic stem cells, but not somatic tissues, have significant cytosine-5 methylation at CpA and, to a lesser extent, at CpT. As the expression of the de novo methyltransferase Dnmt3a correlates well with the presence of non-CpG methylation, we asked whether Dnmt3a might be responsible for this modification. Analysis of genomic methylation in transgenic Drosophila expressing Dnmt3a reveals that Dnmt3a is predominantly a CpG methylase but also is able to induce methylation at CpA and at CpT.

Citing Articles

The Role of the DNA Methyltransferase Family and the Therapeutic Potential of DNMT Inhibitors in Tumor Treatment.

Kim D Curr Oncol. 2025; 32(2).

PMID: 39996888 PMC: 11854558. DOI: 10.3390/curroncol32020088.

Tissue-specific roles of de novo DNA methyltransferases.

Toth D, Szeri F, Ashaber M, Muazu M, Szekvolgyi L, Aranyi T Epigenetics Chromatin. 2025; 18(1):5.

PMID: 39819598 PMC: 11740433. DOI: 10.1186/s13072-024-00566-2.

Whole-genome methylation reveals tissue-specific differences in non-CG methylation in bovine.

Wang J, Yuan W, Liu F, Liu G, Geng X, Li C Zool Res. 2024; 45(6):1371-1384.

PMID: 39572019 PMC: 11668945. DOI: 10.24272/j.issn.2095-8137.2024.221.

Epigenetic regulation of cardiovascular diseases induced by behavioral and environmental risk factors: Mechanistic, diagnostic, and therapeutic insights.

Bi F, Gao C, Guo H FASEB Bioadv. 2024; 6(11):477-502.

PMID: 39512842 PMC: 11539034. DOI: 10.1096/fba.2024-00080.

Using human disease mutations to understand de novo DNA methyltransferase function.

Rolls W, Wilson M, Sproul D Biochem Soc Trans. 2024; 52(5):2059-2075.

PMID: 39446312 PMC: 11555716. DOI: 10.1042/BST20231017.

References

Lyko F, Ramsahoye B, Kashevsky H, TUDOR M, Mastrangelo M, Jaenisch R . Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in Drosophila. Nat Genet. 1999; 23(3):363-6. DOI: 10.1038/15551. View

SINSHEIMER R . The action of pancreatic deoxyribonuclease. II. Isomeric dinucleotides. J Biol Chem. 1955; 215(2):579-83. View

Salomon R, Kaye A . Methylation of mouse DNA in vivo: di- and tripyrimidine sequences containing 5-methylcytosine. Biochim Biophys Acta. 1970; 204(2):340-51. View

Gruenbaum Y, Stein R, Cedar H, Razin A . Methylation of CpG sequences in eukaryotic DNA. FEBS Lett. 1981; 124(1):67-71. DOI: 10.1016/0014-5793(81)80055-5. View

Grafstrom R, Yuan R, Hamilton D . The characteristics of DNA methylation in an in vitro DNA synthesizing system from mouse fibroblasts. Nucleic Acids Res. 1985; 13(8):2827-42. PMC: 341197. DOI: 10.1093/nar/13.8.2827. View

Nyce J, Liu L, Jones P . Variable effects of DNA-synthesis inhibitors upon DNA methylation in mammalian cells. Nucleic Acids Res. 1986; 14(10):4353-67. PMC: 339866. DOI: 10.1093/nar/14.10.4353. View

Woodcock D, Crowther P, Diver W . The majority of methylated deoxycytidines in human DNA are not in the CpG dinucleotide. Biochem Biophys Res Commun. 1987; 145(2):888-94. DOI: 10.1016/0006-291x(87)91048-5. View

Monk M, Boubelik M, Lehnert S . Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development. 1987; 99(3):371-82. DOI: 10.1242/dev.99.3.371. View

Tindall K, Kunkel T . Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry. 1988; 27(16):6008-13. DOI: 10.1021/bi00416a027. View

10.

Toth M, Muller U, DOERFLER W . Establishment of de novo DNA methylation patterns. Transcription factor binding and deoxycytidine methylation at CpG and non-CpG sequences in an integrated adenovirus promoter. J Mol Biol. 1990; 214(3):673-83. DOI: 10.1016/0022-2836(90)90285-T. View

11.

Laird P, Zijderveld A, Linders K, Rudnicki M, Jaenisch R, Berns A . Simplified mammalian DNA isolation procedure. Nucleic Acids Res. 1991; 19(15):4293. PMC: 328579. DOI: 10.1093/nar/19.15.4293. View

12.

Shemer R, Kafri T, OConnell A, Eisenberg S, Breslow J, Razin A . Methylation changes in the apolipoprotein AI gene during embryonic development of the mouse. Proc Natl Acad Sci U S A. 1991; 88(24):11300-4. PMC: 53122. DOI: 10.1073/pnas.88.24.11300. View

13.

Li E, Bestor T, Jaenisch R . Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell. 1992; 69(6):915-26. DOI: 10.1016/0092-8674(92)90611-f. View

14.

Carlson L, Page A, Bestor T . Properties and localization of DNA methyltransferase in preimplantation mouse embryos: implications for genomic imprinting. Genes Dev. 1992; 6(12B):2536-41. DOI: 10.1101/gad.6.12b.2536. View

15.

Tasheva E, Roufa D . Densely methylated DNA islands in mammalian chromosomal replication origins. Mol Cell Biol. 1994; 14(9):5636-44. PMC: 359088. DOI: 10.1128/mcb.14.9.5636-5644.1994. View

16.

Clark S, Harrison J, Frommer M . CpNpG methylation in mammalian cells. Nat Genet. 1995; 10(1):20-7. DOI: 10.1038/ng0595-20. View

17.

Tasheva E, Roufa D . A densely methylated DNA island is associated with a chromosomal replication origin in the human RPS14 locus. Somat Cell Mol Genet. 1995; 21(6):369-83. DOI: 10.1007/BF02310205. View

18.

Tucker K, Beard C, Dausmann J, Laird P, Lei H, Li E . Germ-line passage is required for establishment of methylation and expression patterns of imprinted but not of nonimprinted genes. Genes Dev. 1996; 10(8):1008-20. DOI: 10.1101/gad.10.8.1008. View

19.

Lei H, P Oh S, Okano M, Juttermann R, Goss K, Jaenisch R . De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells. Development. 1996; 122(10):3195-205. DOI: 10.1242/dev.122.10.3195. View

20.

Tucker K, Talbot D, Lee M, Leonhardt H, Jaenisch R . Complementation of methylation deficiency in embryonic stem cells by a DNA methyltransferase minigene. Proc Natl Acad Sci U S A. 1996; 93(23):12920-5. PMC: 24021. DOI: 10.1073/pnas.93.23.12920. View