Erratum: Genome-wide quantitative assessment of variation in DNA methylation patterns (Nucleic Acids Research (2011) 39 (4099-4108) DOI: 10.1093/nar/gkr017);Genome-wide quantitative assessment of variation in DNA methylation patterns

Nucleic Acids Research

Volumn 39, Issue 10, 2011, Pages 4099-4108

  Xie, Hehuang ^a,b   Wang, Min ^a,b   De Andrade, Alexandre ^a   Bonaldo, Maria De F ^a,b   Galat, Vasil ^c   Arndt, Kelly ^a   Rajaram, Veena ^a,d   Goldman, Stewart ^a,e   Tomita, Tadanori ^a,f   Soares, Marcelo B ^a,b  

^a Cancer Biology and Epigenomics Program   (China)

^b Department of Pediatrics ^*  (United States)

^c CHILDREN S MEMORIAL RESEARCH CENTER   (United States)

^d Division of Anatomic Pathology   (United States)

^e Division of Hematology Oncology Transplantation and   (United States)

^f NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ALU SEQUENCE; ARTICLE; CELL POPULATION; CONTROLLED STUDY; CPG ISLAND; DEPLETION; DNA METHYLATION; ENTROPY; EPIGENETICS; GC RICH SEQUENCE; GENE IDENTIFICATION; GENE LOCUS; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; HUMAN CELL; INHERITANCE; INTRON; LUNG FIBROBLAST; MOLECULAR CLONING; PRIORITY JOURNAL; PROMOTER REGION; QUANTITATIVE ANALYSIS; SEQUENCE ALIGNMENT; ALLELE; CELL LINE; CHROMOSOME 21; GENETIC EPIGENESIS; GENETICS; HUMAN GENOME; NEOPLASM; STATISTICAL ANALYSIS;

MAMMALIA;

ALLELES; ALU ELEMENTS; CELL LINE; CHROMOSOMES, HUMAN, PAIR 21; CPG ISLANDS; DATA INTERPRETATION, STATISTICAL; DNA METHYLATION; ENTROPY; EPIGENESIS, GENETIC; GENOME, HUMAN; HUMANS; NEOPLASMS; PROMOTER REGIONS, GENETIC;

EID: 79961177841     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt209     Document Type: Erratum

References (37)

1. Bird, A. (2002) DNA methylation patterns and epigenetic memory. Genes. Dev., 16, 6-21. (Pubitemid 34049633)
2. Mohn, F. and Schubeler, D. (2009) Genetics and epigenetics: stability and plasticity during cellular differentiation. Trends Genet., 25, 129-136.
3. Ooi, S.K., O'Donnell, A.H. and Bestor, T.H. (2009) Mammalian cytosine methylation at a glance. J. Cell Sci., 122, 2787-2791.
4. Okano, M., Bell, D.W., Haber, D.A. and Li, E. (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell, 99, 247-257. (Pubitemid 29519904)
5. Zhu, H., Geiman, T.M., Xi, S., Jiang, Q., Schmidtmann, A., Chen, T., Li, E. and Muegge, K. (2006) Lsh is involved in de novo methylation of DNA. EMBO J., 25, 335-345. (Pubitemid 43152854)
6. Arita, K., Ariyoshi, M., Tochio, H., Nakamura, Y. and Shirakawa, M. (2008) Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. Nature, 455, 818-821.
7. Bostick, M., Kim, J.K., Esteve, P.O., Clark, A., Pradhan, S. and Jacobsen, S.E. (2007) UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science, 317, 1760-1764. (Pubitemid 47461842)
8. Goyal, R., Reinhardt, R. and Jeltsch, A. (2006) Accuracy of DNA methylation pattern preservation by the Dnmt1 methyltransferase. Nucleic Acids Res., 34, 1182-1188.
9. Vilkaitis, G., Suetake, I., Klimasauskas, S. and Tajima, S. (2005) Processive methylation of hemimethylated CpG sites by mouse Dnmt1 DNA methyltransferase. J. Biol. Chem., 280, 64-72. (Pubitemid 40164965)
10. Ooi, S.K. and Bestor, T.H. (2008) Cytosine methylation: remaining faithful. Curr. Biol., 18, R174-176. (Pubitemid 351258345)
11. Ushijima, T., Watanabe, N., Okochi, E., Kaneda, A., Sugimura, T. and Miyamoto, K. (2003) Fidelity of the methylation pattern and its variation in the genome. Genome Res., 13, 868-874. (Pubitemid 36621747)
12. Watanabe, N., Okochi-Takada, E., Yagi, Y., Furuta, J.I. and Ushijima, T. (2006) Decreased fidelity in replicating DNA methylation patterns in cancer cells leads to dense methylation of a CpG island. Curr. Top. Microbiol. Immunol., 310, 199-210. (Pubitemid 47400291)
13. Ushijima, T., Watanabe, N., Shimizu, K., Miyamoto, K., Sugimura, T. and Kaneda, A. (2005) Decreased fidelity in replicating CpG methylation patterns in cancer cells. Cancer Res., 65, 11-17. (Pubitemid 40070790)
14. Chen, Z.X. and Riggs, A.D. (2005) Maintenance and regulation of DNA methylation patterns in mammals. Biochem. Cell. Biol., 83, 438-448. (Pubitemid 41626762)
15. Jones, P.A. and Liang, G. (2009) Rethinking how DNA methylation patterns are maintained. Nat. Rev. Genet., 10, 805-811.
16. Wigler, M., Levy, D. and Perucho, M. (1981) The somatic replication of DNA methylation. Cell, 24, 33-40. (Pubitemid 11157127)
17. Riggs, A.D. and Xiong, Z. (2004) Methylation and epigenetic fidelity. Proc. Natl Acad. Sci. USA, 101, 4-5. (Pubitemid 38084192)
18. Laird, C.D., Pleasant, N.D., Clark, A.D., Sneeden, J.L., Hassan, K.M., Manley, N.C., Vary, J.C. Jr, Morgan, T., Hansen, R.S. and Stoger, R. (2004) Hairpin-bisulfite PCR: assessing epigenetic methylation patterns on complementary strands of individual DNA molecules. Proc. Natl Acad. Sci. USA, 101, 204-209. (Pubitemid 38084228)
19. Riggs, A.D., Xiong, Z., Wang, L. and LeBon, J.M. (1998) Methylation dynamics, epigenetic fidelity and X chromosome structure. Novartis Found. Symp., 214, 214-225, discussion 225-232.
20. Pfeifer, G.P., Steigerwald, S.D., Hansen, R.S., Gartler, S.M. and Riggs, A.D. (1990) Polymerase chain reaction-aided genomic sequencing of an X chromosome-linked CpG island: methylation patterns suggest clonal inheritance, CpG site autonomy, and an explanation of activity state stability. Proc. Natl Acad. Sci. USA, 87, 8252-8256.
21. Xie, H., Wang, M., Bonaldo, M.D., Smith, C., Rajaram, V., Goldman, S., Tomita, T. and Soares, M.B. (2009) High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res., 37, 4331-4340.
22. Xie, H., Wang, M., Bonaldo Mde, F., Rajaram, V., Stellpflug, W., Smith, C., Arndt, K., Goldman, S., Tomita, T. and Soares, M.B. (2010) Epigenomic analysis of Alu repeats in human ependymomas. Proc. Natl Acad. Sci. USA, 107, 6952-6957.
23. Zhang, Y., Rohde, C., Tierling, S., Jurkowski, T.P., Bock, C., Santacruz, D., Ragozin, S., Reinhardt, R., Groth, M., Walter, J. et al. (2009) DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution. PLoS Genet., 5, e1000438.
24. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680. (Pubitemid 24354800)
25. Kuhn, R.M., Karolchik, D., Zweig, A.S., Wang, T., Smith, K.E., Rosenbloom, K.R., Rhead, B., Raney, B.J., Pohl, A., Pheasant, M. et al. (2009) The UCSC Genome Browser Database: update 2009. Nucleic Acids Res., 37, D755-D761.
26. Shannon, C.E. (1997) The mathematical theory of communication. 1963. MD Comput., 14, 306-317.
27. Louis, N., Evelegh, C. and Graham, F.L. (1997) Cloning and sequencing of the cellular-viral junctions from the human adenovirus type 5 transformed 293 cell line. Virology, 233, 423-429. (Pubitemid 27314828)
28. Shaw, G., Morse, S., Ararat, M. and Graham, F.L. (2002) Preferential transformation of human neuronal cells by human adenoviruses and the origin of HEK 293 cells. FASEB J., 16, 869-871.
29. Sandovici, I., Kassovska-Bratinova, S., Loredo-Osti, J.C., Leppert, M., Suarez, A., Stewart, R., Bautista, F.D., Schiraldi, M. and Sapienza, C. (2005) Interindividual variability and parent of origin DNA methylation differences at specific human Alu elements. Hum. Mol. Genet., 14, 2135-2143. (Pubitemid 41418013)
30. Zhang, Y., Rohde, C., Reinhardt, R., Voelcker-Rehage, C. and Jeltsch, A. (2009) Non-imprinted allele-specific DNA methylation on human autosomes. Genome Biol., 10, R138.
31. Liang, G., Chan, M.F., Tomigahara, Y., Tsai, Y.C., Gonzales, F.A., Li, E., Laird, P.W. and Jones, P.A. (2002) Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements. Mol. Cell. Biol., 22, 480-491. (Pubitemid 34027493)
32. Wang, M., Xie, H., Stellpflug, W., Rajaram, V., Bonaldo Mde, F., Goldman, S., Tomita, T. and Soares, M.B. (2011) BTECH: a platform to integrate genomic, transcriptomic and epigenomic alterations in brain tumors. Neuroinformatics, doi:10.1007/s12021-12010-19091-12029 [Epub ahead of print, 6 January 2011].
33. Talens, R.P., Boomsma, D.I., Tobi, E.W., Kremer, D., Jukema, J.W., Willemsen, G., Putter, H., Slagboom, P.E. and Heijmans, B.T. (2010) Variation, patterns, and temporal stability of DNA methylation: considerations for epigenetic epidemiology. FASEB J., 24, 3135-3144.
34. Flanagan, J.M., Popendikyte, V., Pozdniakovaite, N., Sobolev, M., Assadzadeh, A., Schumacher, A., Zangeneh, M., Lau, L., Virtanen, C., Wang, S.C. et al. (2006) Intra-and interindividual epigenetic variation in human germ cells. Am. J. Hum. Genet., 79, 67-84. (Pubitemid 43927378)
35. Schneider, E., Pliushch, G., El Hajj, N., Galetzka, D., Puhl, A., Schorsch, M., Frauenknecht, K., Riepert, T., Tresch, A., Muller, A.M. et al. (2010) Spatial, temporal and interindividual epigenetic variation of functionally important DNA methylation patterns. Nucleic Acids Res., 38, 3880-3890.
36. Probst, A.V., Dunleavy, E. and Almouzni, G. (2009) Epigenetic inheritance during the cell cycle. Nat. Rev. Mol. Cell Biol., 10, 192-206.
37. Riggs, A.D. (2002) X chromosome inactivation, differentiation, and DNA methylation revisited, with a tribute to Susumu Ohno. Cytogenet. Genome Res., 99, 17-24. (Pubitemid 37467819)