CpG site-specific alteration of hydroxymethylcytosine to methylcytosine beyond DNA replication

Biochemical and Biophysical Research Communications

Volumn 426, Issue 1, 2012, Pages 141-147

  Kubosaki, Atsutaka ^a   Tomaru, Yasuhiro ^a   Furuhata, Erina ^a   Suzuki, Takahiro ^a   Shin, Jay W ^a   Simon, Christophe ^a   Ando, Yoshinari ^a   Hasegawa, Ryota ^a,b   Hayashizaki, Yoshihide ^a,b   Suzuki, Harukazu ^a  

^a RIKEN   (Japan)

^b YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

Bisulfite sequencing; DNA demethylation; DNA replication; Episomal vector; Hydroxymethylcytosine; Methylcytosine

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; CYTOSINE;

ARTICLE; CELL DIVISION; CPG ISLAND; DNA METHYLATION; DNA MODIFICATION; DNA REPLICATION; EMBRYO; HUMAN; HUMAN CELL; PRIORITY JOURNAL; SOMATIC CELL; SYSTEM ANALYSIS;

5-METHYLCYTOSINE; BASE SEQUENCE; CPG ISLANDS; CYTOSINE; DNA METHYLATION; DNA REPLICATION; GENETIC VECTORS; HEK293 CELLS; HUMANS; POLYMERASE CHAIN REACTION;

EID: 84866327032     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2012.08.053     Document Type: Article

References (30)

1. Sato S., Maeda C., Hattori N., Yagi S., Tanaka S., Shiota K. DNA methylation-dependent modulator of Gsg2/Haspin gene expression. J. Reprod. Dev. 2011, 57:526-533.
2. Nishino K., Toyoda M., Yamazaki-Inoue M., Fukawatase Y., Chikazawa E., Sakaguchi H., Akutsu H., Umezawa A. DNA methylation dynamics in human induced pluripotent stem cells over time. PLoS Genet. 2011, 7:e1002085.
3. Medvedeva Y.A., Fridman M.V., Oparina N.J., Malko D.B., Ermakova E.O., Kulakovskiy I.V., Heinzel A., Makeev V.J. Intergenic, gene terminal, and intragenic CpG islands in the human genome. BMC Genomics 2010, 11:48.
4. Schmidl C., Klug M., Boeld T.J., Andreesen R., Hoffmann P., Edinger M., Rehli M. Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity. Genome Res. 2009, 19:1165-1174.
5. Ushijima T., Asada K. Aberrant DNA methylation in contrast with mutations. Cancer Sci. 2010, 101:300-305.
6. Tomizawa S., Sasaki H. Genomic imprinting and its relevance to congenital disease, infertility, molar pregnancy and induced pluripotent stem cell. J. Hum. Genet. 2012, 57:84-91.
7. Kriaucionis S., Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009, 324:929-930.
8. Tahiliani M., Koh K.P., Shen Y., Pastor W.A., Bandukwala H., Brudno Y., Agarwal S., Iyer L.M., Liu D.R., Aravind L., Rao A. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009, 324:930-935.
9. Song C.X., Szulwach K.E., Fu Y., Dai Q., Yi C., Li X., Li Y., Chen C.H., Zhang W., Jian X., Wang J., Zhang L., Looney T.J., Zhang B., Godley L.A., Hicks L.M., Lahn B.T., Jin P., He C. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. 2011, 29:68-72.
10. Szulwach K.E., Li X., Li Y., Song C.X., Han J.W., Kim S., Namburi S., Hermetz K., Kim J.J., Rudd M.K., Yoon Y.S., Ren B., He C., Jin P. Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet. 2011, 7:e1002154.
11. Jin S.G., Kadam S. G.P. Pfeifer, Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. 2010, 38:e125.
12. Valinluck V., Tsai H.H., Rogstad D.K., Burdzy A., Bird A., Sowers L.C. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res. 2004, 32:4100-4108.
13. Robertson J., Robertson A.B., Klungland A. The presence of 5-hydroxymethylcytosine at the gene promoter and not in the gene body negatively regulates gene expression. Biochem. Biophys. Res. Commun. 2011, 411:40-43.
14. Ficz G., Branco M.R., Seisenberger M.R., Santos F., Krueger F., Hore T.A., Marques C.J., Andrews S., Reik W. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 2011, 473:398-402.
15. Inoue A., Zhang Y. Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science 2011, 334:194.
16. Okitsu C.Y., Hsieh C.L. DNA methylation dictates histone H3K4 methylation. Mol. Cell. Biol. 2007, 27:2746-2757.
17. Shibata M.A., Miwa Y., Morimoto J., Otsuki Y. Easy stable transfection of a human cancer cell line by electrogene transfer with an Epstein-Barr virus-based plasmid vector. Med. Mol. Morphol. 2007, 40:103-107.
18. Sleight S.C., Bartley B.A., Lieviant J.A., Sauro H.M. In-fusion BioBrick assembly and re-engineering. Nucleic Acids Res. 2010, 38:2624-2636.
19. Kumaki Y., Oda M., Okano M. QUMA: quantification tool for methylation analysis. Nucleic Acids Res. 2008, 36:W170-W175.
20. Huang Y., Pastor W.A., Shen Y., Tahiliani M., Liu D.R., Rao A. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 2010, 5:e8888.
21. Williams K., Christensen J., Helin K. DNA methylation: TET proteins-guardians of CpG islands?. EMBO Rep. 2011, 13:28-35.
22. Guo J.U., Su Y., Zhong C., Ming G.L., Song H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 2011, 145:423-434.
23. Valinluck V., Sowers L.C. Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res. 2007, 67:946-950.
24. Frauer C., Hoffmann T., Bultmann S., Casa V., Cardoso M.C., Antes I., Leonhardt H. Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain. PLoS One 2011, 6:e21306.
25. Hashimoto H., Liu Y., Upadhyay A.K., Chang Y., Howerton S.B., Vertino P.M., Zhang X., Cheng X. Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res. 2012, 40:4841-4849.
26. Scherf U., Ross D.T., Waltham M., Smith L.H., Lee J.K., Tanabe L., Kohn K.W., Reinhold W.C., Myers T.G., Andrews D.T., Scudiero D.A., Eisen M.B., Sausville E.A., Pommier Y., Botstein D., Brown P.O., Weinstein J.N. A gene expression database for the molecular pharmacology of cancer. Nat. Genet. 2000, 24:236-244.
27. Wu H., Zhang Y. Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev. 2011, 25:2436-2452.
28. Yu M., Hon G.C., Szulwach K.E., Song C.X., Zhang L., Kim A., Li X., Dai Q., Shen Y., Park B., Min J.H., Jin P., Ren B., He C. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 2012, 149:1368-1380.
29. Globisch D., Münzel M., Müller M., Michalakis S., Wagner M., Koch S., Brückl T., Biel M., Carell T. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 2010, 5:e15367.
30. Ito S., Shen L., Dai Q., Wu S.C., Collins L.B., Swenberg J.A., He C., Zhang Y. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011, 333:1300-1303.