Distinct patterns of epigenetic marks and transcription factor binding sites across promoters of sense-intronic long noncoding RNAs

Journal of Genetics

Volumn 94, Issue 1, 2015, Pages 17-25

  Ghosh, Sourav ^a,b   Sati, Satish ^a   Sengupta, Shantanu ^a,b   Scaria, Vinod ^a,b  

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

^b ACADEMY OF SCIENTIFIC AND INNOVATIVE RESEARCH ACSIR   (India)

Author keywords

epigenetics; histone modifications; lncRNA; sense intronic

Indexed keywords

HISTONE; LONG UNTRANSLATED RNA; TRANSCRIPTION FACTOR;

BINDING SITE; CELL CULTURE; GENETIC EPIGENESIS; GENETICS; HUMAN; INTRON; METHYLATION; OPEN READING FRAME; PHYSIOLOGY; PROMOTER REGION; PROTEIN PROCESSING; TRANSCRIPTION INITIATION SITE;

BINDING SITES; CELLS, CULTURED; EPIGENESIS, GENETIC; HISTONES; HUMANS; INTRONS; METHYLATION; OPEN READING FRAMES; PROMOTER REGIONS, GENETIC; PROTEIN PROCESSING, POST-TRANSLATIONAL; RNA, LONG NONCODING; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE;

EID: 84939994791     PISSN: 00221333     EISSN: 09737731     Source Type: Journal    
DOI: 10.1007/s12041-015-0484-2     Document Type: Article

References (33)

1. Bernstein B. E., Birney E., Dunham I., Green E. D., Gunter C. and Snyder M. 2012 An integrated encyclopedia of DNA elements in the human genome. Nature489, 57–74.
2. Bhartiya D., Kapoor S., Jalali S., Sati S., Kaushik K. et al. 2012 Conceptual approaches for lncRNA drug discovery and future strategies. Expert. Opin. Drug Discov.7, 503–513.
3. Cedar H. and Bergman Y. 2009 Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet.10, 295–304.
4. Clark M. B. and Mattick J. S. 2011 Long non-coding RNAs in cell biology. Semin. Cell. Dev. Biol.22, 366–376.
5. Dhami P., Saffrey P., Bruce A. W., Dillon S. C., Chiang K. et al. 2010 Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution. PLoS One5, e12339.
6. Dieci G., Fiorino G., Castelnuovo M., Teichmann M. and Pagano A. 2007 The expanding RNA polymerase III transcriptome. Trends Genet.23, 614–622.
7. Dinger M. E., Amaral P. P., Mercer T. R., Pang K. C., Bruce S. J. et al. 2008 Long non-coding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res.18, 1433–1445.
8. Fasanaro P., D’Alessandra Y., Magenta A., Pompilio G. and Capogrossi M. C. 2013 MicroRNAs: promising biomarkers and therapeutic targets of acute myocardial ischemia. Curr. Vas. Pharmacol. (in press).
9. Guttman M. and Rinn J. L. 2012 Modular regulatory principles of large non-coding RNAs. Nature482, 339–346.
10. 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 One6, e18844.
11. He L. and Hannon G. J. 2004 MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet.5, 522–531.
12. Hurd P. J. and Nelson C. J. 2009 Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct. Genomic Proteomic8, 174–183.
13. Ji P., Diederichs S., Wang W., Boing S., Metzger R. et al. 2003 MALAT-1, a novel non-coding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene22, 8031–8041.
14. Kaushik K., Leonard V. E., Kv S., Lalwani M. K., Jalali S. et al. 2013 Dynamic expression of long non-coding RNAs (lncRNAs) in adult zebrafish. PLoS One8, e83616.
15. Kolasinska-Zwierz P., Down T., Latorre I., Liu T., Liu X. S. and Ahringer J. 2009 Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet.41, 376–381.
16. Liao Q., Liu C., Yuan X., Kang S., Miao R. et al. 2011 Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res.39, 3864–3878.
17. Mattick J. S., Amaral P. P., Dinger M. E., Mercer T. R. and Mehler M. F. 2009 RNA regulation of epigenetic processes. BioEssays31, 51–59.
18. Mercer T. R., Dinger M. E. and Mattick J. S. 2009 Long non-coding RNAs: insights into functions. Nat. Rev. Genet.10, 155–159.
19. Mercer T. R., Dinger M. E., Sunkin S. M., Mehler M. F. and Mattick J. S. 2008 Specific expression of long non-coding RNAs in the mouse brain. Proc. Natl. Acad. Sci. USA105, 716–721.
20. Morozova O., Hirst M. and Marra M. A. 2009 Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics Hum. Genet.10, 135–151.
21. Nagano T. and Fraser P. 2011 No-nonsense functions for long non-coding RNAs. Cell145, 178–181.
22. Pasmant E., Sabbagh A., Vidaud M. and Bieche I. 2011 ANRIL, a long, non-coding RNA, is an unexpected major hotspot in GWAS. FASEB J.25, 444–448.
23. Ponting C. P., Oliver P. L. and Reik W. 2009 Evolution and functions of long non-coding RNAs. Cell136, 629–641.
24. Rajpathak S. N., Vellarikkal S. K., Patowary A., Scaria V., Sivasubbu S. and Deobagkar D. D. 2014 Human 45,X fibroblast transcriptome reveals distinct differentially expressed genes including long non-coding RNAs potentially associated with the pathophysiology of turner syndrome. PLoS One9, e100076.
25. Rinn J. L., Kertesz M., Wang J. K., Squazzo S. L., Xu X. et al. 2007 Functional demarcation of active and silent chromatin domains in human HOX loci by non-coding RNAs. Cell129, 1311–1323.
26. Sati S., Ghosh S., Jain V., Scaria V. and Sengupta S. 2012a Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci. Nucleic Acids Res.40, 10018–10031.
27. Sati S., Tanwar V. S., Kumar K. A., Patowary A., Jain V. et al. 2012b High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region. PLoS One7, e31621.
28. Saxena A. and Carninci P. 2011 Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. BioEssays33, 830–839.
29. Tsai M. C., Manor O., Wan Y., Mosammaparast N., Wang J. K. et al. 2010 Long non-coding RNA as modular scaffold of histone modification complexes. Science329, 689–693.
30. Wang K. C. and Chang H. Y. 2011 Molecular mechanisms of long non-coding RNAs. Mol. Cell.43, 904–914.
31. Wapinski O. and Chang H. Y. 2011 Long non-coding RNAs and human disease. Trends Cell Biol.21, 354–361.
32. Yap K. L., Li S., Munoz-Cabello A. M., Raguz S., Zeng L. et al. 2010 Molecular interplay of the non-coding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol. Cell38, 662–674.
33. Zhang Z., Pang A. W., and Gerstein M. 2007 Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human. BMC Evol. Biol.7, suppl 1, S14.