Role of long non-coding RNAs in gene regulation and oncogenesis

Chinese Medical Journal

Volumn 124, Issue 15, 2011, Pages 2378-2383

  Pan, Yan Feng ^a   Feng, Lei ^a   Zhang, Xian Qiang ^a   Song, Li Jie ^a   Liang, Hong Xia ^a   Li, Zhi Qin ^a   Tao, Feng Bao ^a  

^a ZHENGZHOU UNIVERSITY   (China)

Author keywords

Cancer; Gene regulation; Long non coding RNA

Indexed keywords

LONG NON CODING RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ANRIL GENE; BIOLOGICAL ACTIVITY; CARCINOGENESIS; CELL TRANSFORMATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; DOWN REGULATION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE LOCATION; GENE OVEREXPRESSION; GENOME IMPRINTING; GROWTH ARREST SPECIFIC TRANSCRIPT 5 GENE; HOTAIR GENE; HUMAN; MALAT1 GENE; MATERNALLY EXPRESSED GENE 3; REVIEW; RNA PROCESSING; TRANSCRIPTION REGULATION; TUMOR PROMOTION; TUMOR SUPPRESSOR GENE; UPREGULATION;

ANIMALS; CELL TRANSFORMATION, NEOPLASTIC; GENE EXPRESSION REGULATION; HUMANS; NEOPLASMS; RNA, UNTRANSLATED;

EID: 79961067069     PISSN: 03666999     EISSN: None     Source Type: Journal    
DOI: 10.3760/cma.j.issn.0366-6999.2011.15.023     Document Type: Review

References (43)

1. Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447: 799-816.
2. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet 2009; 10: 155-159.
3. Struhl K. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol 2007; 14: 103-105.
4. Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009; 136: 629-641.
5. Brosnan CA, Voinnet O. The long and the short of noncoding RNAs. Curr Opin Cell Biol 2009; 21: 416-425.
6. Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 2011; 39: D146-D151.
7. Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS. NRED: a database of long noncoding RNA expression. Nucleic Acids Res 2009; 37 (Database issue): D122-D126.
8. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, et al. Analysis of the mouse transcriptome based on functional annotation of 60 770 full-length cDNAs. Nature 2002; 420: 563-573.
9. Migeon BR, Lee CH, Chowdhury AK, Carpenter H. Species differences in TSIX/Tsix reveal the roles of these genes in X-chromosome inactivation. Am J Hum Genet 2002; 71: 286-293.
10. Leeb M, Steffen PA, Wutz A. X chromosome inactivation sparked by non-coding RNAs. RNA Biol 2009; 6: 94-99.
11. Chen LL, Carmichael GG. Decoding the function of nuclear long non-coding RNAs. Curr Opin Cell Biol 2010; 22: 357-364.
12. Tian D, Sun S, Lee JT. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 143: 390-403.
13. Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level control. Mol Cell 2008; 32: 232-246.
14. Mohammad F, Mondal T, Guseva N, Pandey GK, Kanduri C. Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development 2010; 137: 2493-2499.
15. Sleutels F, Zwart R, Barlow DP. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 2002; 415: 810-813.
16. Sleutels F, Tjon G, Ludwig T, Barlow DP. Imprinted silencing of Slc22a2 and Slc22a3 does not need transcriptional overlap between Igf2r and Air. EMBO J 2003; 22: 3696-3704.
17. Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, et al. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 2008; 322: 1717-1720.
18. Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD. The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 2006; 20: 1470-1484.
19. Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010; 143: 46-58.
20. Wang X, Arai S, Song X, Reichart D, Du K, Pascual G, et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 2008; 454: 126-130.
21. Martianov I, Ramadass A, Serra BA, Chow N, Akoulitchev A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 2007; 445: 666-670.
22. He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW. The antisense transcriptomes of human cells. Science 2008; 322: 1855-1857.
23. Beltran M, Puig I, Peña C, García JM, Alvarez AB, Peña R, et al. A natural antisense transcript controls Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 2008; 22: 756-769.
24. Ogawa Y, Sun BK, Lee JT. Intersection of the RNA interference and X-inactivation pathways. Science 2008; 320: 1336-1341.
25. Wilusz JE, Freier SM, Spector DL. 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 2008; 135: 919-932.
26. Luo JH, Ren B, Keryanov S, Tseng GC, Rao UN, Monga SP, et al. Transcriptomic and genomic analysis of human hepatocellular carcinomas and hepatoblastomas. Hepatology 2007; 44: 1012-1024.
27. Lin R, Maeda S, Liu C, Karin M, Edgington TS. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene 2007; 26: 851-858.
28. Guffanti A, Iacono M, Pelucchi P, Kim N, Soldà G, Croft LJ, et al. A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics 2009; 10: 163.
29. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, et al. The nuclear-retained noncoding RNA MALAT1 controls alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 2010; 39: 925-938.
30. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007; 129: 1311-1323.
31. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464: 1071-1076.
32. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010; 329: 689-693.
33. Yap KL, Li S, Muñoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 2010; 38: 662-674.
34. Cunnington MS, Santibanez KM, Mayosi BM, Burn J, Keavney B. Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate with ANRIL Expression. PLoS Genet 2010; 6: e1000899.
35. Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, et al. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15 (INK4B) tumor suppressor gene. Oncogene 2011; 30: 1956-1962.
36. Panzitt K, Tschernatsch MM, Guelly C, Moustafa T, Stradner M, Strohmaier HM, et al. Characterization of HULC, a novel gene with striking up-control in hepatocellular carcinoma, as noncoding RNA. Gastroenterology 2007; 132: 330-342.
37. Wang J, Liu X, Wu H, Ni P, Gu Z, Qiao Y, et al. CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res 2010; 38: 5366-5383.
38. Huarte M, Rinn JL. Large non-coding RNAs: missing links in cancer. Hum Mol Genet 2010; 19: R152-R161.
39. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010; 142: 409-419.
40. Mourtada-Maarabouni M, Pickard MR, Hedge VL, Farzaneh F, Williams GT. GAS5, a non-protein-coding RNA, controls apoptosis and is downcontrold in breast cancer. Oncogene 2009; 28: 195-208.
41. Zhao J, Dahle D, Zhou Y, Zhang X, Klibanski A. Hypermethylation of the promoter region is associated with the loss of MEG3 ge ne expression in human pituitary tumors. J Clin Endocrinol Metab 2005; 90: 2179-2186.
42. Zhang X, Rice K, Wang Y, Chen W, Zhong Y, Nakayama Y, et al. Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform structure, expression, and functions. Endocrinology 2010; 151: 939-947.
43. Zhou Y, Zhong Y, Wang Y, Zhang X, Batista DL, Gejman R, et al. Activation of p53 by MEG3 non-coding RNA. J Biol Chem 2007; 282: 24731-24742.