Discovering cooperative relationships of chromatin modifications in human T cells based on a proposed closeness measure

PLoS ONE

Volumn 5, Issue 12, 2010, Pages

  Lv, Jie ^a   Qiao, Hong ^a   Liu, Hongbo ^a   Wu, Xueting ^a   Zhu, Jiang ^a   Su, Jianzhong ^a   Wang, Fang ^a   Cui, Ying ^a   Zhang, Yan ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE;

ARTICLE; BAYES THEOREM; CD4+ T LYMPHOCYTE; CHROMATIN MODIFICATION; CHROMOSOMES AND CHROMOSOMAL PHENOMENA; CLUSTER ANALYSIS; COMPUTER MODEL; CONTROLLED STUDY; CORRELATION ANALYSIS; CPG ISLAND; DNA METHYLATION; DNA MODIFICATION; EPIGENETICS; GENE EXPRESSION; GENE INTERACTION; GENE LOCUS; GENE REGULATORY NETWORK; PROTEIN MODIFICATION; STRUCTURE ANALYSIS; T LYMPHOCYTE; T LYMPHOCYTE SUBPOPULATION; TRANSCRIPTION REGULATION; ALGORITHM; BIOLOGY; CELL COMMUNICATION; CHROMATIN; COMPUTER PROGRAM; GENETIC EPIGENESIS; HUMAN; METABOLISM; METHODOLOGY; STATISTICAL MODEL;

EUKARYOTA;

ALGORITHMS; BAYES THEOREM; CELL COMMUNICATION; CHROMATIN; COMPUTATIONAL BIOLOGY; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; HISTONES; HUMANS; MODELS, STATISTICAL; SOFTWARE; T-LYMPHOCYTES;

EID: 78649956430     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0014219     Document Type: Article

References (67)

1. Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A (2009) An operational definition of epigenetics. Genes Dev 23: 781-783.
2. Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128: 669-681.
3. Bock C, Lengauer T (2008) Computational epigenetics. Bioinformatics 24: 1-10.
4. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112.
5. Hsieh TF, Fischer RL (2005) Biology of chromatin dynamics. Annu Rev Plant Biol 56: 327-351.
6. Berger SL (2007) The complex language of chromatin regulation during transcription. Nature 447: 407-412.
7. Feng Y, Wang X, Xu L, Pan H, Zhu S, et al. (2009) The transcription factor ZBP-89 suppresses p16 expression through a histone modification mechanism to affect cell senescence. FEBS J 276: 4197-4206.
8. Illingworth RS, Bird AP (2009) CpG islands-'a rough guide'. FEBS Lett 583: 1713-1720.
9. Lv J, Su J, Wang F, Qi Y, Liu H, et al. (2010) Detecting novel hypermethylated genes in Breast cancer benefiting from feature selection. Comput Biol Med 40: 159-167.
10. Su J, Zhang Y, Lv J, Liu H, Tang X, et al. (2010) CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes. Nucleic Acids Res 38: e6.
11. Miranda TB, Jones PA (2007) DNA methylation: the nuts and bolts of repression. J Cell Physiol 213: 384-390.
12. Gebhard C, Benner C, Ehrich M, Schwarzfischer L, Schilling E, et al. (2010) General transcription factor binding at CpG islands in normal cells correlates with resistance to de novo DNA methylation in cancer cells. Cancer Res 70: 1398-1407.
13. Lennartsson A, Ekwall K (2009) Histone modification patterns and epigenetic codes. Biochim Biophys Acta 1790: 863-868.
14. Shilatifard A (2006) Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu Rev Biochem 75: 243-269.
15. Wang Z, Schones DE, Zhao K (2009) Characterization of human epigenomes. Curr Opin Genet Dev 19: 127-134.
16. Margueron R, Trojer P, Reinberg D (2005) The key to development: interpreting the histone code? Curr Opin Genet Dev 15: 163-176.
17. Mellor J (2006) It takes a PHD to read the histone code. Cell 126: 22-24.
18. Cedar H, Bergman Y (2009) Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 10: 295-304.
19. Allen ML, Koch CM, Clelland GK, Dunham I, Antoniou M (2009) DNA methylation-histone modification relationships across the desmin locus in human primary cells. BMC Mol Biol 10: 51.
20. Herranz M, Esteller M (2007) DNA methylation and histone modifications in patients with cancer: potential prognostic and therapeutic targets. Methods Mol Biol 361: 25-62.
21. Hebbar PB, Archer TK (2007) Chromatin-dependent cooperativity between site-specific transcription factors in vivo. J Biol Chem 282: 8284-8291.
22. Aslam A, Logie C (2010) Histone H3 serine 57 and lysine 56 interplay in transcription elongation and recovery from S-phase stress. PLoS ONE 5: e10851.
23. Jones B, Su H, Bhat A, Lei H, Bajko J, et al. (2008) The histone H3K79 methyltransferase Dot1L is essential for mammalian development and heterochromatin structure. PLoS Genet 4: e1000190.
24. Meneghini MD, Wu M, Madhani HD (2003) Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112: 725-736.
25. Hellman A, Chess A (2007) Gene body-specific methylation on the active X chromosome. Science 315: 1141-1143.
26. Bormann Chung CA, Boyd VL, McKernan KJ, Fu Y, Monighetti C, et al. (2010) Whole methylome analysis by ultra-deep sequencing using two-base encoding. PLoS ONE 5: e9320.
27. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) Highresolution profiling of histone methylations in the human genome. Cell 129: 823-837.
28. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903.
29. Choi JH, Li Y, Guo J, Pei L, Rauch TA, et al. (2010) Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylationenriched bisulfite sequencing. PLoS ONE 5: e13020.
30. Ke XS, Qu Y, Rostad K, Li WC, Lin B, et al. (2009) Genome-wide profiling of histone h3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis. PLoS ONE 4: e4687.
31. Tan J, Lu J, Huang W, Dong Z, Kong C, et al. (2009) Genome-wide analysis of histone H3 lysine9 modifications in human mesenchymal stem cell osteogenic differentiation. PLoS ONE 4: e6792.
32. Bhandare R, Schug J, Le Lay J, Fox A, Smirnova O, et al. (2010) Genome-wide analysis of histone modifications in human pancreatic islets. Genome Res 20: 428-433.
33. Jung I, Kim D (2009) Regulatory Patterns of Histone Modifications to Control the DNA Methylation Status at CpG Islands. Interdisciplinary Bio Central 1: 1-7.
34. Yu H, Zhu S, Zhou B, Xue H, Han JD (2008) Inferring causal relationships among different histone modifications and gene expression. Genome Res 18: 1314-1324.
35. Zhang Y, Liu T,Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
36. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, et al. (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38: 1378-1385.
37. Goecks J, Nekrutenko A, Taylor J, Galaxy Team T (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11: R86.
38. Hackenberg M, Previti C, Luque-Escamilla PL, Carpena P, Martinez-Aroza J, et al. (2006) CpGcluster: a distance-based algorithm for CpG-island detection. BMC Bioinformatics 7: 446.
39. Lindahl Allen M, Antoniou M (2007) Correlation of DNA methylation with histone modifications across the HNRPA2B1-CBX3 ubiquitously-acting chromatin open element (UCOE). Epigenetics 2: 227-236.
40. Kondo Y (2009) Epigenetic cross-talk between DNA methylation and histone modifications in human cancers. Yonsei Med J 50: 455-463.
41. Vaissiere T, Sawan C, Herceg Z (2008) Epigenetic interplay between histone modifications and DNA methylation in gene silencing. Mutat Res 659: 40-48.
42. Sharan R, Maron-Katz A, Shamir R (2003) CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinformatics 19: 1787-1799.
43. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, et al. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898.
44. Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
45. Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF (2007) A new method to measure the semantic similarity of GO terms. Bioinformatics 23: 1274-1281.
46. Yu G, Li F, Qin Y, Bo X, Wu Y, et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 26: 976-978.
47. Ji H, Jiang H, Ma W, Johnson DS, Myers RM, et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26: 1293-1300.
48. Calvanese V, Horrillo A, Hmadcha A, Suarez-Alvarez B, Fernandez AF, et al. (2008) Cancer genes hypermethylated in human embryonic stem cells. PLoS ONE 3: e3294.
49. Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, et al. (2008) An integrated resource for genome-wide identification and analysis of human tissuespecific differentially methylated regions (tDMRs). Genome Res 18: 1518-1529.
50. Hon G, Wang W, Ren B (2009) Discovery and annotation of functional chromatin signatures in the human genome. PLoS Comput Biol 5: e1000566.
51. Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, et al. (2010) CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464: 1082-1086.
52. Ng HH, Robert F, Young RA, Struhl K (2003) Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell 11: 709-719.
53. Takeshima H, Yamashita S, Shimazu T, Niwa T, Ushijima T (2009) The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands. Genome Res 19: 1974-1982.
54. Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S (2008) Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature 456: 125-129.
55. Ooi SK, Qiu C, Bernstein E, Li K, Jia D, et al. (2007) DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448: 714-717.
56. Ayton PM, Chen EH, Cleary ML (2004) Binding to nonmethylated CpG DNA is essential for target recognition, transactivation, and myeloid transformation by an MLL oncoprotein. Mol Cell Biol 24: 10470-10478.
57. Chernukhin I, Shamsuddin S, Kang SY, Bergstrom R, Kwon YW, et al. (2007) CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. Mol Cell Biol 27: 1631-1648.
58. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130: 77-88.
59. Lee JH, Skalnik DG (2005) CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex. J Biol Chem 280: 41725-41731.
60. Ruthenburg AJ, Allis CD, Wysocka J (2007) Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol Cell 25: 15-30.
61. Voo KS, Carlone DL, Jacobsen BM, Flodin A, Skalnik DG (2000) Cloning of a mammalian transcriptional activator that binds unmethylated CpG motifs and shares a CXXC domain with DNA methyltransferase, human trithorax, and methyl-CpG binding domain protein 1. Mol Cell Biol 20: 2108-2121.
62. Hon G, Ren B, Wang W (2008) ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol 4: e1000201.
63. Zhang Y, Lv J, Liu H, Zhu J, Su J, et al. (2010) HHMD: the human histone modification database. Nucleic Acids Res 38: D149-D154.
64. Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, et al. (2009) A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics 10: 618.
65. Robyr D, Suka Y, Xenarios I, Kurdistani SK, Wang A, et al. (2002) Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109: 437-446.
66. Suka N, Suka Y, Carmen AA, Wu J, Grunstein M (2001) Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol Cell 8: 473-479.
67. Garfinkel MD, Sollars VE, Lu X, Ruden DM (2004) Multigenerational selection and detection of altered histone acetylation and methylation patterns: toward a quantitative epigenetics in Drosophila. Methods Mol Biol 287: 151-168.