Prediction of CpG-island function: CpG clustering vs. sliding-window methods

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Hackenberg, Michael ^a,b   Barturen, Guillermo ^a,b   Carpena, Pedro ^c,d   Luque Escamilla, Pedro L ^e   Previti, Christopher ^f   Oliver, José L ^a,b  

^a UNIVERSITY OF GRANADA   (Spain)

^b PTS   (Spain)

^c UNIVERSITY OF MÁLAGA   (Spain)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

^e UNIVERSITY OF JAÉN   (Spain)

^f UNIVERSITY OF BERGEN   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CPG ISLAND; DNA METHYLATION; GENE CLUSTER; GENE FUNCTION; GENE LOCATION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC CONSERVATION; GENOMICS; PREDICTION; PROMOTER REGION; PROTEIN DOMAIN; RETROPOSON; TRANSCRIPTION INITIATION SITE; ALGORITHM; ALU SEQUENCE; CLUSTER ANALYSIS; COMPARATIVE STUDY; GENETICS; HUMAN; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE;

MAMMALIA;

ALGORITHMS; ALU ELEMENTS; CLUSTER ANALYSIS; CONSERVED SEQUENCE; CPG ISLANDS; DNA METHYLATION; EVOLUTION, MOLECULAR; HUMANS; PROMOTER REGIONS, GENETIC;

EID: 77952655502     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-327     Document Type: Article

References (46)

1. Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. Journal of molecular biology 1987, 196(2):261-282. 10.1016/0022-2836(87)90689-9, 3656447.
2. Larsen F, Gundersen G, Lopez R, Prydz H. CpG islands as gene markers in the human genome. Genomics 1992, 13(4):1095-1107. 10.1016/0888-7543(92)90024-M, 1505946.
3. Antequera F. Structure, function and evolution of CpG island promoters. Cell Mol Life Sci 2003, 60(8):1647-1658. 10.1007/s00018-003-3088-6, 14504655.
4. Bird A. DNA methylation patterns and epigenetic memory. Genes & development 2002, 16(1):6-21.
5. Bird AP. CpG-rich islands and the function of DNA methylation. Nature 1986, 321(6067):209-213. 10.1038/321209a0, 2423876.
6. Zhu J, He F, Hu S, Yu J. On the nature of human housekeeping genes. Trends Genet 2008, 24(10):481-484. 10.1016/j.tig.2008.08.004, 18786740.
7. Baylin SB, Esteller M, Rountree MR, Bachman KE, Schuebel K, Herman JG. Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Human molecular genetics 2001, 10(7):687-692. 10.1093/hmg/10.7.687, 11257100.
8. De Smet C, Lurquin C, Lethe B, Martelange V, Boon T. DNA methylation is the primary silencing mechanism for a set of germ line- and tumor-specific genes with a CpG-rich promoter. Molecular and cellular biology 1999, 19(11):7327-7335. 84726, 10523621.
9. Esteller M, Corn PG, Baylin SB, Herman JG. A gene hypermethylation profile of human cancer. Cancer research 2001, 61(8):3225-3229.
10. Issa JP. CpG island methylator phenotype in cancer. Nature reviews 2004, 4(12):988-993. 10.1038/nrc1507, 15573120.
11. Riazalhosseini Y, Hoheisel JD. Do we use the appropriate controls for the identification of informative methylation markers for early cancer detection?. Genome biology 2008, 9(11):405. 10.1186/gb-2008-9-11-405, 2614489, 19040775.
12. Song F, Smith JF, Kimura MT, Morrow AD, Matsuyama T, Nagase H, Held WA. Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(9):3336-3341. 10.1073/pnas.0408436102, 552919, 15728362.
13. Hsieh F, Chen SC, Pollard K. A Nearly Exhaustive Search for CpG Islands on Whole Chromosomes. The International Journal of Biostatistics 2009, 5:1-24. The Berkeley Electronic Press, 10.2202/1557-4679.1158, 2818740,2818740, 20148132.
14. Hackenberg M, Previti C, Luque-Escamilla PL, Carpena P, Martínez-Aroza J, Oliver JL. CpGcluster: A distance-based algorithm for CpG-island detection. BMC Bioinformatics 2006, 7(1):446. 10.1186/1471-2105-7-446, 1617122, 17038168.
15. Glass JL, Thompson RF, Khulan B, Figueroa ME, Olivier EN, Oakley EJ, Van Zant G, Bouhassira EE, Melnick A, Golden A, et al. CG dinucleotide clustering is a species-specific property of the genome. Nucleic acids research 2007, 35(20):6798-6807. 10.1093/nar/gkm489, 2175314, 17932072.
16. Sujuan Y, Asaithambi A, Liu Y. CpGIF: an algorithm for the identification of CpG islands. Bioinformation 2008, 2(8):335-338. 2478732, 18685720.
17. Irizarry RA, Wu H, Feinberg AP. A species-generalized probabilistic model-based definition of CpG islands. Mamm Genome 2009, 20(9-10):674-680. 10.1007/s00335-009-9222-5, 19777308.
18. Wu H, Caffo B, Jaffee HA, Irizarry RA, Feinberg AP. Redefining CpG islands using hidden Markov models. Biostatistics 2010,
19. Hughes A, Rando OJ. Chromatin 'programming' by sequence - is there more to the nucleosome code than %GC?. J Biol 2009, 8(11):96. 10.1186/jbiol207, 20067596.
20. Bock C, Walter J, Paulsen M, Lengauer T. CpG island mapping by epigenome prediction. PLoS Comput Biol 2007, 3(6):e110. 10.1371/journal.pcbi.0030110, 1892605,1892605, 17559301.
21. Takai D, Jones PA. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proceedings of the National Academy of Sciences of the United States of America 2002, 99(6):3740-3745. 10.1073/pnas.052410099, 122594, 11891299.
22. Han L, Zhao Z. CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?. BMC Bioinformatics 2009, 10:65. 10.1186/1471-2105-10-65, 2652441, 19232104.
23. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005, 15(8):1034-1050. 10.1101/gr.3715005, 1182216, 16024819.
24. Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proceedings of the National Academy of Sciences of the United States of America 2006, 103(5):1412-1417. 10.1073/pnas.0510310103, 1345710, 16432200.
25. Illingworth RS, Bird AP. CpG islands--'a rough guide'. FEBS letters 2009, 583(11):1713-1720. 10.1016/j.febslet.2009.04.012, 19376112.
26. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature genetics 2007, 39(4):457-466. 10.1038/ng1990, 17334365.
27. Burset M, Guigo R. Evaluation of gene structure prediction programs. Genomics 1996, 34(3):353-367. 10.1006/geno.1996.0298, 8786136.
28. Illingworth R, Kerr A, Desousa D, Jorgensen H, Ellis P, Stalker J, Jackson D, Clee C, Plumb R, Rogers J, et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS biology 2008, 6(1):e22. 10.1371/journal.pbio.0060022, 2214817, 18232738.
29. Previti C, Harari O, Zwir I, del Val C. Profile analysis and prediction of tissue-specific CpG island methylation classes. BMC Bioinformatics 2009, 10:116. 10.1186/1471-2105-10-116, 2683815, 19383127.
30. Tanay A, O'Donnell AH, Damelin M, Bestor TH. Hyperconserved CpG domains underlie Polycomb-binding sites. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(13):5521-5526. 10.1073/pnas.0609746104, 1838490, 17376869.
31. Yamashita R, Suzuki Y, Wakaguri H, Tsuritani K, Nakai K, Sugano S. DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic acids research 2006, (34 Database):D86-89. 10.1093/nar/gkj129, 1347491, 16381981.
32. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(16):6062-6067. 10.1073/pnas.0400782101, 395923, 15075390.
33. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462(7271):315-322. 10.1038/nature08514, 2857523, 19829295.
34. Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, et al. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res 2009, 19(9):1593-1605. 10.1101/gr.095190.109, 2752124, 19581485.
35. Wong NC, Wong LH, Quach JM, Canham P, Craig JM, Song JZ, Clark SJ, Choo KH. Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation. PLoS genetics 2006, 2(2):e17. 10.1371/journal.pgen.0020017, 1361766,1361766, 16477312.
36. Li W, Bernaola-Galván P, Haghighi F, Grosse I. Applications of recursive segmentation to the analysis of DNA sequences. Computers & chemistry 2002, 26(5):491-510.
37. Luque-Escamilla PL, Martínez-Aroza J, Oliver JL, Gómez-Lopera JF, Román-Roldán R. Compositional searching of CpG islands in the human genome. Phys Rev E 2005, 71:6.
38. Ponger L, Mouchiroud D. CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics (Oxford, England) 2002, 18(4):631-633. 10.1093/bioinformatics/18.4.631, 12016061.
39. Takai D, Jones PA. The CpG island searcher: a new WWW resource. silico biology 2003, 3(3):235-240.
40. Wang Y, Leung FC. An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics (Oxford, England) 2004, 20(7):1170-1177. 10.1093/bioinformatics/bth059, 14764558.
41. Human Epigenome Project. , http://www.epigenome.org/
42. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nature genetics 2006, 38(12):1378-1385. 10.1038/ng1909, 17072317.
43. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic acids research 2007, (35 Database):D61-65. 10.1093/nar/gkl842, 1716718, 17130148.
44. Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K. DBTSS: database of transcription start sites, progress report 2008. Nucleic acids research 2008, (36 Database):D97-101. 2238895, 17942421.
45. RepeatMasker. , http://www.repeatmasker.org/
46. Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, et al. The UCSC Genome Browser Database: 2008 update. Nucleic acids research 2008, (36 Database):D773-779. 2238835, 18086701.