Characterizing Genes with Distinct Methylation Patterns in the Context of Protein-Protein Interaction Network: Application to Human Brain Tissues

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Li, Yongsheng ^a   Xu, Juan ^a   Chen, Hong ^a   Zhao, Zheng ^a   Li, Shengli ^a   Bai, Jing ^a   Wu, Aiwei ^a   Jiang, Chunjie ^a   Wang, Yuan ^a   Su, Bin ^a   Li, Xia ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; BINDING AFFINITY; BRAIN TISSUE; DNA METHYLATION; GENE; GENE EXPRESSION; GENE FUNCTION; GENETIC ANALYSIS; HIGH METHYLATED GENE; HUMAN; HUMAN GENOME; HUMAN TISSUE; LOW METHYLATED GENE; PROTEIN PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION NETWORK; TRANSCRIPTION REGULATION; TUMOR GENE;

BRAIN; COMPUTATIONAL BIOLOGY; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; GENES; HUMANS; MICRORNAS; PROTEIN INTERACTION MAPS; PROTEOMICS;

EID: 84878952113     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0065871     Document Type: Article

References (56)

1. Li E, Bestor TH, Jaenisch R, (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915-926.
2. Li E, Beard C, Jaenisch R, (1993) Role for DNA methylation in genomic imprinting. Nature 366: 362-365.
3. Heard E, Clerc P, Avner P, (1997) X-chromosome inactivation in mammals. Annu Rev Genet 31: 571-610.
4. Egger G, Liang G, Aparicio A, Jones PA, (2004) Epigenetics in human disease and prospects for epigenetic therapy. Nature 429: 457-463.
5. Saxonov S, Berg P, Brutlag DL, (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 103: 1412-1417.
6. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39: 457-466.
7. Jiang C, Han L, Su B, Li WH, Zhao Z, (2007) Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Mol Biol Evol 24: 1991-2000.
8. Su Z, Xia J, Zhao Z, (2011) Functional complementation between transcriptional methylation regulation and post-transcriptional microRNA regulation in the human genome. BMC Genomics 12Suppl 5: S15.
9. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322.
10. Fernandez AF, Rosales C, Lopez-Nieva P, Grana O, Ballestar E, et al. (2009) The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer. Genome Res 19: 438-451.
11. Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, et al. (2011) DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol 12: R10.
12. Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, et al. (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 6: e1000952.
13. Hernandez DG, Nalls MA, Gibbs JR, Arepalli S, van der Brug M, et al. (2011) Distinct DNA methylation changes highly correlated with chronological age in the human brain. Hum Mol Genet 20: 1164-1172.
14. Numata S, Ye T, Hyde TM, Guitart-Navarro X, Tao R, et al. (2012) DNA methylation signatures in development and aging of the human prefrontal cortex. Am J Hum Genet 90: 260-272.
15. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067.
16. Awan A, Bari H, Yan F, Moksong S, Yang S, et al. (2007) Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signalling network. IET Syst Biol 1: 292-297.
17. Kitano H, (2002) Systems biology: a brief overview. Science 295: 1662-1664.
18. Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, et al. (2008) A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol 4: 169.
19. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957-968.
20. Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, et al. (2009) Genome-wide DNA methylation profiling using Infinium(R) assay. Epigenomics 1: 177-200.
21. Gronniger E, Weber B, Heil O, Peters N, Stab F, et al. (2010) Aging and chronic sun exposure cause distinct epigenetic changes in human skin. PLoS Genet 6: e1000971.
22. Zeng J, Konopka G, Hunt BG, Preuss TM, Geschwind D, et al. (2012) Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. Am J Hum Genet 91: 455-465.
23. Yang X, Noushmehr H, Han H, Andreu-Vieyra C, Liang G, et al. (2012) Gene reactivation by 5-aza-2′-deoxycytidine-induced demethylation requires SRCAP-mediated H2A.Z insertion to establish nucleosome depleted regions. PLoS Genet 8: e1002604.
24. Attisano L, Wrana JL, (2000) Smads as transcriptional co-modulators. Curr Opin Cell Biol 12: 235-243.
25. Derynck R, Zhang Y, Feng XH, (1998) Smads: transcriptional activators of TGF-beta responses. Cell 95: 737-740.
26. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430: 88-93.
27. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, et al. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34: 166-176.
28. Hsu CW, Juan HF, Huang HC, (2008) Characterization of microRNA-regulated protein-protein interaction network. Proteomics 8: 1975-1979.
29. Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T, (2006) CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22: 1021-1023.
30. Kesavapany S, Amin N, Zheng YL, Nijhara R, Jaffe H, et al. (2004) p35/cyclin-dependent kinase 5 phosphorylation of ras guanine nucleotide releasing factor 2 (RasGRF2) mediates Rac-dependent Extracellular Signal-regulated kinase 1/2 activity, altering RasGRF2 and microtubule-associated protein 1b distribution in neurons. J Neurosci 24: 4421-4431.
31. Quilliam LA, Khosravi-Far R, Huff SY, Der CJ, (1995) Guanine nucleotide exchange factors: activators of the Ras superfamily of proteins. Bioessays 17: 395-404.
32. Jones PA, Baylin SB, (2002) The fundamental role of epigenetic events in cancer. Nat Rev Genet 3: 415-428.
33. Baylin SB, Herman JG, (2000) DNA hypermethylation in tumorigenesis: epigenetics joins genetics. Trends Genet 16: 168-174.
34. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, et al. (2004) A census of human cancer genes. Nat Rev Cancer 4: 177-183.
35. Horvath S, Zhang Y, Langfelder P, Kahn RS, Boks MP, et al. (2012) Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biol 13: R97.
36. Winnefeld M, Lyko F, (2012) The aging epigenome: DNA methylation from the cradle to the grave. Genome Biol 13: 165.
37. Wang J, Zhang S, Wang Y, Chen L, Zhang XS, (2009) Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Comput Biol 5: e1000521.
38. Xiao Y, Guan J, Ping Y, Xu C, Huang T, et al. (2012) Prioritizing cancer-related key miRNA-target interactions by integrative genomics. Nucleic Acids Res 40: 7653-7665.
39. Bossi A, Lehner B, (2009) Tissue specificity and the human protein interaction network. Mol Syst Biol 5: 260.
40. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, et al. (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490: 556-560.
41. Bundo M, Sunaga F, Ueda J, Kasai K, Kato T, et al. (2012) A systematic evaluation of whole genome amplification of bisulfite-modified DNA. Clin Epigenetics 4: 22.
42. Deneberg S, Guardiola P, Lennartsson A, Qu Y, Gaidzik V, et al. (2011) Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks. Blood 118: 5573-5582.
43. Campbell DB, Buie TM, Winter H, Bauman M, Sutcliffe JS, et al. (2009) Distinct genetic risk based on association of MET in families with co-occurring autism and gastrointestinal conditions. Pediatrics 123: 1018-1024.
44. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
45. Tang P, Steck PA, Yung WK, (1997) The autocrine loop of TGF-alpha/EGFR and brain tumors. J Neurooncol 35: 303-314.
46. Kefas B, Godlewski J, Comeau L, Li Y, Abounader R, et al. (2008) microRNA-7 inhibits the epidermal growth factor receptor and the Akt pathway and is down-regulated in glioblastoma. Cancer Res 68: 3566-3572.
47. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res 37: D767-772.
48. Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, et al. (2009) Genome-wide DNA methylation profiling using Infinium((R)) assay. Epigenomics 1: 177-200.
49. de Magalhaes JP, Toussaint O, (2004) GenAge: a genomic and proteomic network map of human ageing. FEBS Lett 571: 243-247.
50. Blake JA, Eppig JT, Richardson JE, Davisson MT, (2000) The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. The Mouse Genome Database Group. Nucleic Acids Res 28: 108-111.
51. Blake JA, Richardson JE, Bult CJ, Kadin JA, Eppig JT, (2003) MGD: the Mouse Genome Database. Nucleic Acids Res 31: 193-195.
52. Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, et al. (2012) TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res 40: D222-229.
53. Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, et al. (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 39: D163-169.
54. Xiao F, Zuo Z, Cai G, Kang S, Gao X, et al. (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37: D105-110.
55. Jiang Q, Wang Y, Hao Y, Juan L, Teng M, et al. (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37: D98-104.
56. Lewis BP, Burge CB, Bartel DP, (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.