Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci

Nucleic Acids Research

Volumn 40, Issue 20, 2012, Pages 10018-10031

  Sati, Satish ^a   Ghosh, Sourav ^a   Jain, Vaibhav ^a   Scaria, Vinod ^a   Sengupta, Shantanu ^a  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; LYSINE; UNTRANSLATED RNA;

ARTICLE; CELL DENSITY; CELL TYPE; CYTOLOGY; DNA METHYLATION; EPIGENETICS; GENE EXPRESSION; GENE LOCUS; GENETIC REGULATION; GENOME ANALYSIS; HISTONE MODIFICATION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; TISSUES; TRANSCRIPTION INITIATION SITE;

CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; GENETIC LOCI; GENOME, HUMAN; HISTONES; HUMANS; PROTEINS; RNA, LONG UNTRANSLATED; TRANSCRIPTION INITIATION SITE;

EID: 84869015900     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks776     Document Type: Article

References (59)

1. Zhou, H., Hu, H. and Lai, M. (2010) Non-coding RNAs and their epigenetic regulatory mechanisms. Biol. Cell Under Auspices Eur Cell Biol. Organizat., 102, 645-655.
2. Huttenhofer, A. and Vogel, J. (2006) Experimental approaches to identify non-coding RNAs. Nucleic Acids Res., 34, 635-646.
3. Lee, T.L., Pang, A.L., Rennert, O.M. and Chan, W.Y. (2009) Genomic landscape of developing male germ cells. Birth Defects Res. C Embryo Today Rev., 87, 43-63.
4. Amaral, P.P. and Mattick, J.S. (2008) Noncoding RNA in development. Mamm. Genome Off. J. Int. Mamm. Genome Soc., 19, 454-492.
5. Dinger, M.E., Amaral, P.P., Mercer, T.R., Pang, K.C., Bruce, S.J., Gardiner, B.B., Askarian-Amiri, M.E., Ru, K., Solda, G., Simons, C. et al. (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res., 18, 1433-1445.
6. Mercer, T.R., Dinger, M.E., Sunkin, S.M., Mehler, M.F. and Mattick, J.S. (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl Acad. Sci. USA, 105, 716-721.
7. Bhartiya, D., Kapoor, S., Jalali, S., Sati, S., Kaushik, K., Sachidanandan, C., Sivasubbu, S. and Scaria, V. (2012) Conceptual approaches for lncRNA drug discovery and future strategies. Exp. Opin. Drug Discov., 7, 503-513.
8. Taft, R.J., Pheasant, M. and Mattick, J.S. (2007) The relationship between non-protein-coding DNA and eukaryotic complexity. BioEssays News Rev. Mol. Cell. Dev. Biol., 29, 288-299.
9. Costa, F.F. (2008) Non-coding RNAs, epigenetics and complexity. Gene, 410, 9-17.
10. Prasanth, K.V. and Spector, D.L. (2007) Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev., 21, 11-42.
11. Sanchez-Elsner, T., Gou, D., Kremmer, E. and Sauer, F. (2006) Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science, 311, 1118-1123.
12. Rinn, J.L., Kertesz, M., Wang, J.K., Squazzo, S.L., Xu, X., Brugmann, S.A., Goodnough, L.H., Helms, J.A., Farnham, P.J., Segal, E. et al. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 129, 1311-1323.
13. Chen, X., Xu, H., Yuan, P., Fang, F., Huss, M., Vega, V.B., Wong, E., Orlov, Y.L., Zhang, W., Jiang, J. et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell, 133, 1106-1117.
14. Zhao, J., Sun, B.K., Erwin, J.A., Song, J.J. and Lee, J.T. (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science, 322, 750-756.
15. Khalil, A.M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B.E., van Oudenaarden, A. et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl Acad. Sci. USA, 106, 11667-11672.
16. Mehler, M.F. and Mattick, J.S. (2007) Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol. Rev., 87, 799-823.
17. Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.
18. Kim, E.D. and Sung, S. (2012) Long noncoding RNA: unveiling hidden layer of gene regulatory networks. Trends Plant Sci., 17, 16-21.
19. Brannan, C.I., Dees, E.C., Ingram, R.S. and Tilghman, S.M. (1990) The product of the H19 gene may function as an RNA. Mol. Cell. Biol., 10, 28-36.
20. Brown, C.J., Ballabio, A., Rupert, J.L., Lafreniere, R.G., Grompe, M., Tonlorenzi, R. and Willard, H.F. (1991) A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature, 349, 38-44.
21. Lee, J.T., Davidow, L.S. and Warshawsky, D. (1999) Tsix, a gene antisense to Xist at the X-inactivation centre. Nat. Genet., 21, 400-404.
22. Sotomaru, Y., Katsuzawa, Y., Hatada, I., Obata, Y., Sasaki, H. and Kono, T. (2002) Unregulated expression of the imprinted genes H19 and Igf2r in mouse uniparental fetuses. J. Biol. Chem., 277, 12 474-12478.
23. Beisel, C. and Paro, R. (2011) Silencing chromatin: comparing modes and mechanisms. Nat. Rev. Genet., 12, 123-135.
24. Wang, X.Q., Crutchley, J.L. and Dostie, J. (2011) Shaping the genome with non-coding RNAs. Curr. Genomics, 12, 307-321.
25. Gibb, E.A., Brown, C.J. and Lam, W.L. (2011) The functional role of long non-coding RNA in human carcinomas. Mol. Cancer, 10, 38.
26. Zaidi, S.K., Young, D.W., Montecino, M., Lian, J.B., Stein, J.L., van Wijnen, A.J. and Stein, G.S. (2010) Architectural epigenetics: mitotic retention of mammalian transcriptional regulatory information. Mol. Cell. Biol., 30, 4758-4766.
27. Rapicavoli, N.A., Poth, E.M., Zhu, H. and Blackshaw, S. (2011) The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Neural Dev., 6, 32.
28. Navarro, P., Page, D.R., Avner, P. and Rougeulle, C. (2006) Tsix-mediated epigenetic switch of a CTCF-flanked region of the Xist promoter determines the Xist transcription program. Genes Dev., 20, 2787-2792.
29. Wu, S.C., Kallin, E.M. and Zhang, Y. (2010) Role of H3K27 methylation in the regulation of lncRNA expression. Cell Res., 20, 1109-1116.
30. 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.
31. Bernstein, B.E., Stamatoyannopoulos, J.A., Costello, J.F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M.A., Beaudet, A.L., Ecker, J.R. et al. (2010) The NIH roadmap epigenomics mapping consortium. Nat. Biotechnol., 28, 1045-1048.
32. Harrow, J., Denoeud, F., Frankish, A., Reymond, A., Chen, C.K., Chrast, J., Lagarde, J., Gilbert, J.G., Storey, R., Swarbreck, D. et al. (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biol., 7(Suppl 1), S4 1-9.
33. Hubbard, T., Barker, D., Birney, E., Cameron, G., Chen, Y., Clark, L., Cox, T., Cuff, J., Curwen, V., Down, T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
34. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
35. Trapnell, C., Pachter, L. and Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
36. Roberts, A., Pimentel, H., Trapnell, C. and Pachter, L. (2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics, 27, 2325-2329.
37. Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
38. Gibney, E.R. and Nolan, C.M. (2010) Epigenetics and gene expression. Heredity, 105, 4-13.
39. 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.
40. Sati, S., Tanwar, V.S., Kumar, K.A., Patowary, A., Jain, V., Ghosh, S., Ahmad, S., Singh, M., Reddy, S.U., Chandak, G.R. et al. (2012) High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region. PloS One, 7, e31621.
41. Choi, J.K. (2010) Contrasting chromatin organization of CpG islands and exons in the human genome. Genome Biol., 11, R70.
42. Du, Z., Zhao, D., Zhao, Y., Wang, S., Gao, Y. and Li, N. (2007) Identification and characterization of bovine regulator of telomere length elongation helicase gene (RTEL): molecular cloning, expression distribution, splice variants and DNA methylation profile. BMC Mol. Biol., 8, 18.
43. Deaton, A.M. and Bird, A. (2011) CpG islands and the regulation of transcription. Genes Dev., 25, 1010-1022.
44. Maunakea, A.K., Nagarajan, R.P., Bilenky, M., Ballinger, T.J., D'Souza, C., Fouse, S.D., Johnson, B.E., Hong, C., Nielsen, C., Zhao, Y. et al. (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature, 466, 253-257.
45. Mattick, J.S. (2001) Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep., 2, 986-991.
46. Wapinski, O. and Chang, H.Y. (2011) Long noncoding RNAs and human disease. Trends Cell Biol., 21, 354-361.
47. Taft, R.J., Pang, K.C., Mercer, T.R., Dinger, M. and Mattick, J.S. (2010) Non-coding RNAs: regulators of disease. J. Pathol., 220, 126-139.
48. Saferali, A., Grundberg, E., Berlivet, S., Beauchemin, H., Morcos, L., Polychronakos, C., Pastinen, T., Graham, J., McNeney, B. and Naumova, A.K. (2010) Cell culture-induced aberrant methylation of the imprinted IG DMR in human lymphoblastoid cell lines. Epigenet. Off. J. DNA Methylation Soc., 5, 50-60.
49. Zemach, A., McDaniel, I.E., Silva, P. and Zilberman, D. (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science, 328, 916-919.
50. Brenet, F., Moh, M., Funk, P., Feierstein, E., Viale, A.J., Socci, N.D. and Scandura, J.M. (2011) DNA methylation of the first exon is tightly linked to transcriptional silencing. PLoS One, 6, e14524.
51. Illingworth, RS., Gruenewald-Schneider, U., Webb, S., Kerr, A.R., James, K.D., Turner, D.J., Smith, C., Harrison, D.J., Andrews, R. and Bird, A.P. (2010) Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet., 6.
52. Sleutels, F., Zwart, R. and Barlow, D.P. (2002) The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature, 415, 810-813.
53. Mancini-DiNardo, D., Steele, S.J., Ingram, R.S. and Tilghman, S.M. (2003) A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer. Hum. Mol. Genet., 12, 283-294.
54. Mancini-Dinardo, D., Steele, S.J., Levorse, J.M., Ingram, R.S. and Tilghman, S.M. (2006) Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev., 20, 1268-1282.
55. Guenther, M.G., Levine, S.S., Boyer, L.A., Jaenisch, R. and Young, R.A. (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell, 130, 77-88.
56. Mikkelsen, T.S., Ku, M., Jaffe, D.B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.K., Koche, R.P. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448, 553-560.
57. Cedar, H. and Bergman, Y. (2009) Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet., 10, 295-304.
58. Hahn, M.A., Wu, X., Li, A.X., Hahn, T. and Pfeifer, G.P. (2011) Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks. PLoS One, 6, e18844.
59. De Gobbi, M., Garrick, D., Lynch, M., Vernimmen, D., Hughes, J.R., Goardon, N., Luc, S., Lower, K.M., Sloane- Stanley, J.A., Pina, C. et al. (2011) Generation of bivalent chromatin domains during cell fate decisions. Epigenet. Chromatin, 4, 9.