A tag-based approach for high-throughput analysis of CCWGG methylation

Analytical Biochemistry

Volumn 369, Issue 2, 2007, Pages 154-160

  Denisova, Oksana V ^a   Chernov, Andrei V ^a   Koledachkina, Tatyana Y ^a   Matvienko, Nicholas I ^a  

^a INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

CCWGG methylation; DNA methylation; Epigenome; Non CpG methylation

Indexed keywords

DNA; MAMMALS; METHYLATION;

DNA METHYLATION; EPIGENOMES; FLANKING REGIONS; HIGH-THROUGHPUT ANALYSIS; HIGH-THROUGHPUT SEQUENCING; NON-CPG METHYLATION; RESTRICTION ENDONUCLEASES; WHOLE-GENOME APPROACHES;

ALKYLATION;

AJNI PROTEIN; CCWGG PROTEIN; DNA; ECORII C PROTEIN; ENDONUCLEASE; GENE PRODUCT; GENOMIC DNA; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; DNA METHYLATION; GENE LOCATION; GENETIC ANALYSIS; GENOME; METHYLATION; MOLECULAR BIOLOGY; NONHUMAN; PRIORITY JOURNAL;

ANIMALIA; MAMMALIA;

EID: 34548385743     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2007.06.048     Document Type: Article

References (20)

1. Bird A.P. DNA methylation patterns and epigenetic memory. Genes Dev. 16 (2002) 6-21
2. Goll M.G., and Bestor T.H. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 74 (2005) 481-514
3. Bender J., and Fink G.R. Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 83 (1995) 725-734
4. Finnegan E.J., and Kovac K.A. Plant DNA methyltransferases. Plant Mol. Biol. 43 (2000) 189-201
5. Chan S.W.-L., Henderson I.R., and Jacobsen S.E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 6 (2005) 351-360
6. Malone C.S., Miner M.D., Doerr J.R., Jackson J.P., Jacobsen S.E., Wall R., and Teitell M. CmC(A/T)GG DNA methylation in mature B cell lymphoma gene silencing. Proc. Natl. Acad. Sci. USA 98 (2001) 10404-10409
7. Lorincz M.C., and Groudine M. CmC(a/t)GG methylation: a new epigenetic mark in mammalian DNA?. Proc. Natl. Acad. Sci. USA 98 (2001) 10034-10036
8. Imamura T., Ohgane J., Ito S., Ogawa T., Hattori N., Tanaka S., and Shiota K. CpG island of rat sphingosine kinase-1 gene: tissue-dependent DNA methylation status and multiple alternative first exons. Genomics 76 (2001) 117-125
9. Ramsahoye B.H., Biniszkiewicz D., Lyko F., Clark V., Bird A.P., and Jaenisch R. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl. Acad. Sci. USA 97 (2000) 5237-5242
10. Meissner A., Gnirke A., Bell G.W., Ramsahoye B., Lander E.S., and Jaenisch R. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33 (2005) 5868-5877
11. Ching T.T., Maunakea A.K., Jun P., Hong C., Zardo G., Pinkel D., Albertson D.G., Fridlyand J., Mao J.H., Shchors K., Weiss W.A., and Costello J.F. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat. Genet. 37 (2005) 645-651
12. Hatada I., Fukasawa M., Kimura M., Morita S., Yamada K., Yoshikawa T., Yamanaka S., Endo C., Sakurada A., Sato M., Kondo T., Horii A., Ushijima T., and Sasaki H. Genome-wide profiling of promoter methylation in human. Oncogene 25 (2006) 3059-3064
13. Tran R.K., Henikoff J.G., Zilberman D., Ditt R.F., Jacobsen S.E., and Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr. Biol. 15 (2005) 154-159
14. Zhang X., Yazaki J., Sundaresan A., Cokus S., Chan S.W., Chen H., Henderson I.R., Shinn P., Pellegrini M., Jacobsen S.E., and Ecker J.R. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126 (2006) 1189-1201
15. Kruger D.H., and Reuter M. Reliable detection of DNA cytosine methylation at CpNpG sites using the engineered restriction enzyme EcoRII-C. BioTechniques 38 (2005) 855-856
16. Matvienko N.N., Zheleznaya L.A., Chernyshova E.E., Buryanov Y.I., and Matvienko N.I. Peculiarities of gene expression of the Eco RII modification-restriction system. Biochemistry (Moscow) 62 (1997) 1124-1127
17. Sambrook J., and Russell D. Molecular Cloning: A Laboratory Manual (2001), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
18. Mucke M., Grelle G., Behlke J., Kraft R., Kruger D.H., and Reuter M. EcoRII: a restriction enzyme evolving recombination functions?. EMBO J. 21 (2002) 5262-5268
19. Reuter M., Kupper D., Meisel A., Schroeder C., and Kruger D.H. Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J. Biol. Chem. 273 (1998) 8294-8300
20. Zheleznaya L.A., Perevyazova T.A., Alzhanova D.V., and Matvienko N.I. Site-specific nickase from Bacillus species strain D6. Biochemistry (Moscow) 66 (2001) 989-993