CpG-MPs: Identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data

Nucleic Acids Research

Volumn 41, Issue 1, 2013, Pages

  Su, Jianzhong ^a   Yan, Haidan ^a   Wei, Yanjun ^a   Liu, Hongbo ^a   Liu, Hui ^a   Wang, Fang ^a   Lv, Jie ^b   Wu, Qiong ^b   Zhang, Yan ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

^b HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE;

ARTICLE; CELL DIFFERENTIATION; CELL SPECIFICITY; COMPUTER PROGRAM; CPG ISLAND; DNA DETERMINATION; DNA METHYLATION; DNA STRUCTURE; ENTROPY; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ALGORITHM; HIGH THROUGHPUT BISULFITE SEQUENCING; HIGH THROUGHPUT SEQUENCING; HOTSPOT EXTENSION ALGORITHM; HUMAN; HUMAN GENOME; PRIORITY JOURNAL; SHANNON ENTROPY;

CPG ISLANDS; DNA METHYLATION; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA; SOFTWARE; SULFITES;

EUKARYOTA;

EID: 84871799766     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks829     Document Type: Article

References (69)

1. Bird, A., Taggart, M., Frommer, M., Miller, O.J. and Macleod, D. (1985) A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell, 40, 91-99.
2. Suzuki, M.M. and Bird, A. (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet., 9, 465-476.
3. Cedar, H. and Bergman, Y. (2009) Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet., 10, 295-304.
4. Irizarry, R.A., Ladd-Acosta, C., Wen, B., Wu, Z., Montano, C., Onyango, P., Cui, H., Gabo, K., Rongione, M., Webster, M. et al. (2009) The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet., 41, 178-186.
5. Issa, J.P. (2000) CpG-island methylation in aging and cancer. Curr. Top. Microbiol. Immunol., 249, 101-118.
6. Fuke, C., Shimabukuro, M., Petronis, A., Sugimoto, J., Oda, T., Miura, K., Miyazaki, T., Ogura, C., Okazaki, Y. and Jinno, Y. (2004) Age related changes in 5-methylcytosine content in human peripheral leukocytes and placentas: an HPLC-based study. Ann. Hum. Genet., 68, 196-204.
7. Lister, R., Pelizzola, M., Dowen, R.H., Hawkins, R.D., Hon, G., Tonti-Filippini, J., Nery, J.R., Lee, L., Ye, Z., Ngo, Q.M. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462, 315-322.
8. Baylin, S.B., Esteller, M., Rountree, M.R., Bachman, K.E., Schuebel, K. and Herman, J.G. (2001) Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum. Mol. Genet., 10, 687-692.
9. Esteller, M., Fraga, M.F., Guo, M., Garcia-Foncillas, J., Hedenfalk, I., Godwin, A.K., Trojan, J., Vaurs-Barriere, C., Bignon, Y.J., Ramus, S. et al. (2001) DNA methylation patterns in hereditary human cancers mimic sporadic tumorigenesis. Hum. Mol. Genet., 10, 3001-3007.
10. Liu, H., Su, J., Li, J., Lv, J., Li, B., Qiao, H. and Zhang, Y. (2011) Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network. BMC Syst. Biol., 5, 158.
11. Laurent, L., Wong, E., Li, G., Huynh, T., Tsirigos, A., Ong, C.T., Low, H.M., Kin Sung, K.W., Rigoutsos, I., Loring, J. et al. (2010) Dynamic changes in the human methylome during differentiation. Genome Res., 20, 320-331.
12. Ball, M.P., Li, J.B., Gao, Y., Lee, J.H., LeProust, E.M., Park, I.H., Xie, B., Daley, G.Q. and Church, G.M. (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nature Biotechnol., 27, 361-368.
13. Laird, P.W. (2010) Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet., 11, 191-203.
14. Lister, R., O'Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H. and Ecker, J.R. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 133, 523-536.
15. Xiang, H., Zhu, J., Chen, Q., Dai, F., Li, X., Li, M., Zhang, H., Zhang, G., Li, D., Dong, Y. et al. (2010) Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nature Biotechnol., 28, 516-520.
16. Meissner, A., Mikkelsen, T.S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B.E., Nusbaum, C., Jaffe, D.B. et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature, 454, 766-770.
17. Zemach, A., McDaniel, I.E., Silva, P. and Zilberman, D. (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science, 328, 916-919.
18. Popp, C., Dean, W., Feng, S., Cokus, S.J., Andrews, S., Pellegrini, M., Jacobsen, S.E. and Reik, W. (2010) Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature, 463, 1101-1105.
19. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
20. Li, H., Ruan, J. and Durbin, R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
21. Li, R., Li, Y., Kristiansen, K. and Wang, J. (2008) SOAP: short oligonucleotide alignment program. Bioinformatics, 24, 713-714.
22. Li, R., Yu, C., Li, Y., Lam, T.W., Yiu, S.M., Kristiansen, K. and Wang, J. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
23. Krueger, F. and Andrews, S.R. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-1572.
24. Chen, P.Y., Cokus, S.J. and Pellegrini, M. (2010) BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics, 11, 203.
25. Xi, Y. and Li, W. (2009) BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics, 10, 232.
26. Grunau, C., Schattevoy, R., Mache, N. and Rosenthal, A. (2000) MethTools-a toolbox to visualize and analyze DNA methylation data. Nucleic Acids Res., 28, 1053-1058.
27. Kumaki, Y., Oda, M. and Okano, M. (2008) QUMA: quantification tool for methylation analysis. Nucleic Acids Res., 36, W170-W175.
28. Rohde, C., Zhang, Y., Reinhardt, R. and Jeltsch, A. (2010) BISMA-fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. BMC Bioinformatics, 11, 230.
29. Lutsik, P., Feuerbach, L., Arand, J., Lengauer, T., Walter, J. and Bock, C. (2011) BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res., 39, W551-W556.
30. Hackenberg, M., Barturen, G. and Oliver, J.L. (2011) NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data. Nucleic Acids Res., 39, D75-D79.
31. Law, J.A. and Jacobsen, S.E. (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet., 11, 204-220.
32. Bird, A. (2002) DNA methylation patterns and epigenetic memory. Genes Dev., 16, 6-21.
33. Reik, W., Dean, W. and Walter, J. (2001) Epigenetic reprogramming in mammalian development. Science, 293, 1089-1093.
34. Lister, R., Pelizzola, M., Kida, Y.S., Hawkins, R.D., Nery, J.R., Hon, G., Antosiewicz-Bourget, J., O'Malley, R., Castanon, R., Klugman, S. et al. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature, 471, 68-73.
35. Bock, C., Halachev, K., Buch, J. and Lengauer, T. (2009) EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biol., 10, R14.
36. Ponger, L. and Mouchiroud, D. (2002) CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics, 18, 631-633.
37. Su, J., Zhang, Y., Lv, J., Liu, H., Tang, X., Wang, F., Qi, Y., Feng, Y. and Li, X. (2010) CpG-MI: a novel approach for identifying functional CpG islands in mammalian genomes. Nucleic Acids Res., 38, e6.
38. Hackenberg, M., Previti, C., Luque-Escamilla, P.L., Carpena, P., Martinez-Aroza, J. and Oliver, J.L. (2006) CpGcluster: a distance-based algorithm for CpG-island detection. BMC Bioinformatics, 7, 446.
39. Sujuan, Y., Asaithambi, A. and Liu, Y. (2008) CpGIF: an algorithm for the identification of CpG islands. Bioinformation, 2, 335-338.
40. Heisler, L.E., Torti, D., Boutros, P.C., Watson, J., Chan, C., Winegarden, N., Takahashi, M., Yau, P., Huang, T.H., Farnham, P.J. et al. (2005) CpG island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res., 33, 2952-2961.
41. Illingworth, R., Kerr, A., Desousa, D., Jorgensen, H., Ellis, P., Stalker, J., Jackson, D., Clee, C., Plumb, R., Rogers, J. et al. (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS biology, 6, e22.
42. Bock, C., Tomazou, E.M., Brinkman, A.B., Muller, F., Simmer, F., Gu, H., Jager, N., Gnirke, A., Stunnenberg, H.G. and Meissner, A. (2010) Quantitative comparison of genome-wide DNA methylation mapping technologies. Nature Biotechnol., 28, 1106-1114.
43. Harris, R.A., Wang, T., Coarfa, C., Nagarajan, R.P., Hong, C., Downey, S.L., Johnson, B.E., Fouse, S.D., Delaney, A., Zhao, Y. et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnol., 28, 1097-1105.
44. Esteller, M. (2008) Epigenetics in cancer. N. Eng. J. Med., 358, 1148-1159.
45. Ooi, S.K., Wolf, D., Hartung, O., Agarwal, S., Daley, G.Q., Goff, S.P. and Bestor, T.H. (2010) Dynamic instability of genomic methylation patterns in pluripotent stem cells. Epigenet. Chromatin, 3, 17.
46. Doi, A., Park, I.H., Wen, B., Murakami, P., Aryee, M.J., Irizarry, R., Herb, B., Ladd-Acosta, C., Rho, J., Loewer, S. et al. (2009) Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat. Genet., 41, 1350-1353.
47. Su, J., Shao, X., Liu, H., Liu, S., Wu, Q. and Zhang, Y. (2012) Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts. Genomics, 99, 10-17.
48. Bibikova, M., Chudin, E., Wu, B., Zhou, L., Garcia, E.W., Liu, Y., Shin, S., Plaia, T.W., Auerbach, J.M., Arking, D.E. et al. (2006) Human embryonic stem cells have a unique epigenetic signature. Genome Res., 16, 1075-1083.
49. Byun, H.M., Siegmund, K.D., Pan, F., Weisenberger, D.J., Kanel, G., Laird, P.W. and Yang, A.S. (2009) Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue-and individual-specific DNA methylation patterns. Hum. Mol. Genet., 18, 4808-4817.
50. Eckhardt, F., Lewin, J., Cortese, R., Rakyan, V.K., Attwood, J., Burger, M., Burton, J., Cox, T.V., Davies, R., Down, T.A. et al. (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet., 38, 1378-1385.
51. Bock, C., Walter, J., Paulsen, M. and Lengauer, T. (2008) Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res., 36, e55.
52. Zhang, Y., Liu, H., Lv, J., Xiao, X., Zhu, J., Liu, X., Su, J., Li, X., Wu, Q., Wang, F. et al. (2011) QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res., 39, e58.
53. Fujita, P.A., Rhead, B., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Cline, M.S., Goldman, M., Barber, G.P., Clawson, H., Coelho, A. et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res., 39, D876-D882.
54. Huang da, W., Sherman, B.T. and Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protocols, 4, 44-57.
55. Hermann, A., Goyal, R. and Jeltsch, A. (2004) The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J. Biol. Chem., 279, 48350-48359.
56. Bock, C. and Lengauer, T. (2008) Computational epigenetics. Bioinformatics, 24, 1-10.
57. 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.
58. Luo, S. and Preuss, D. (2003) Strand-biased DNA methylation associated with centromeric regions in Arabidopsis. Proc. Natl Acad. Sci. USA, 100, 11133-11138.
59. Shoemaker, R., Deng, J., Wang, W. and Zhang, K. (2010) Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res., 20, 883-889.
60. Nautiyal, S., Carlton, V.E., Lu, Y., Ireland, J.S., Flaucher, D., Moorhead, M., Gray, J.W., Spellman, P., Mindrinos, M., Berg, P. et al. (2010) High-throughput method for analyzing methylation of CpGs in targeted genomic regions. Proc. Natl Acad. Sci. USA, 107, 12587-12592.
61. Feng, S., Cokus, S.J., Zhang, X., Chen, P.Y., Bostick, M., Goll, M.G., Hetzel, J., Jain, J., Strauss, S.H., Halpern, M.E. et al. (2010) Conservation and divergence of methylation patterning in plants and animals. Proc. Natl Acad. Sci. USA, 107, 8689-8694.
62. Brunlid, G., Pruszak, J., Holmes, B., Isacson, O. and Sonntag, K.C. (2007) Immature and neurally differentiated mouse embryonic stem cells do not express a functional Fas/Fas ligand system. Stem Cells, 25, 2551-2558.
63. Liu, Y., Wen, Q.J., Yin, Y., Lu, X.T., Pu, S.H., Tian, H.P., Lou, Y.F., Tang, Y.N., Jiang, X., Lu, G.S. et al. (2009) FASLG polymorphism is associated with cancer risk. Eur. J. Cancer, 45, 2574-2578.
64. Fernandez, A.F., Assenov, Y., Martin-Subero, J.I., Balint, B., Siebert, R., Taniguchi, H., Yamamoto, H., Hidalgo, M., Tan, A.C., Galm, O. et al. (2012) A DNA methylation fingerprint of 1628 human samples. Genome Res., 22, 407-419.
65. Brunner, A.L., Johnson, D.S., Kim, S.W., Valouev, A., Reddy, T.E., Neff, N.F., Anton, E., Medina, C., Nguyen, L., Chiao, E. et al. (2009) Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res., 19, 1044-1056.
66. Bird, A.P. (1986) CpG-rich islands and the function of DNA methylation. Nature, 321, 209-213.
67. Edwards, J.R., O'Donnell, A.H., Rollins, R.A., Peckham, H.E., Lee, C., Milekic, M.H., Chanrion, B., Fu, Y., Su, T., Hibshoosh, H. et al. (2010) Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns. Genome Res., 20, 972-980.
68. He, X., Chang, S., Zhang, J., Zhao, Q., Xiang, H., Kusonmano, K., Yang, L., Sun, Z.S., Yang, H. and Wang, J. (2008) MethyCancer: the database of human DNA methylation and cancer. Nucleic Acids Res., 36, D836-D841.
69. Zhang, Y., Lv, J., Liu, H., Zhu, J., Su, J., Wu, Q., Qi, Y., Wang, F. and Li, X. (2010) HHMD: the human histone modification database. Nucleic Acids Res., 38, D149-D154.