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Long Non-Coding RNAs And Their Relevance in Cancer


Authors: J. Šána 1,2;  P. Faltejsková 1,2;  M. Svoboda 1,2,3;  O. Slabý 1,2
Authors place of work: CEITEC – Středoevropský technologický institut, MU Brno 1;  Klinika komplexní onkologické péče, Masarykův onkologický ústav, Brno 2;  Oddělení epidemiologie a genetiky nádorů, Masarykův onkologický ústav, Brno 3
Published in the journal: Klin Onkol 2012; 25(4): 246-254
Category: Reviews

Summary

A major portion of the eukaryotic genome is occupied by DNA sequences; transcripts of these sequences do not code for proteins. This part of the eukaryotic genome is transcribed in a developmentally regulated manner or as a response to external stimuli to produce large numbers of long non-coding RNAs (lncRNAs). Genome-wide studies indicate the existence of more than 3,300 lncRNAs. Long non-coding RNAs are tentatively defined as molecules of ncRNAs that are more than two hundred nucleotides long. Due to the complexity and diversity of their sequences, progress in the field of lncRNAs has been very slow. Nonetheless, lncRNAs have emerged as key molecules involved in the control of transcriptional and posttranscriptional gene regulatory pathways. Although limited numbers of functional lncRNAs have been identified so far, the immense regulatory potential of lncRNAs is already evident, emphasizing that a genome-wide characterization of functional lncRNAs is needed. The fact that many lncRNAs are deregulated in various human cancers, together with their functional characteris­tics, implies their eminent role in carcinoge­nesis. In this review, we summarize novel classes of lncRNAs, describe their biological functions emphasizing their roles in tumor biology and translational oncology research.

Key words:
long non-coding RNAs – lincRNA – pseudogenes – T-UCR – cancer

This study was supported by grants of Internal Grant Agency of the Czech Ministry of Health No. NT11214-4/2010, NT13514-4/2012, NT/13549, NT/13860 and NT/13585 and by Institutional Resources for Supporting the Research Organization provided by the Czech Ministry of Health in 2012.

The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.

The Editorial Board declares that the manuscript met the ICMJE “uniform requirements” for biomedical papers.

Submitted:
30. 6. 2012

Accepted:
3. 8. 2012


Zdroje

1. Stein LD. Human genome: end of the beginning. Nature 2004; 431(7011): 915–916.

2. Taft RJ, Pang KC, Mercer TR et al. Non-coding RNAs: regulators of disease. J Pathol 2010; 220(2): 126–139.

3. Mattick JS. Non-coding RNAs: the architects of euka­ryotic complexity. EMBO Rep 2001; 2: 986–991.

4. Zhang R, Zhang L, Yu W. Genome-wide expression of non-coding RNA and global chromatin modification. Acta Biochim Biophys Sin (Shanghai) 2012; 44(1): 40–47.

5. Pagano A, Castelnuovo M, Tortelli F et al. New small nuclear RNA gene-like transcriptional units as sources of regulatory transcripts. PLoS Genet 2007; 3(2): e1.

6. Guttman M, Amit I, Garber M et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458(7235): 223–237.

7. Costa FF. Non-coding RNAs: Meet thy masters. Bioessays 2010; 32(7): 599–608.

8. Chen Y, Song Y, Wang Z et al. Altered expression of MiR-148a and MiR-152 in gastrointestinal cancers and its clinical significance. J Gastrointest Surg 2010; 14(7): 1170–1179.

9. Lipovich L, Johnson R, Lin CY. MacroRNA underdogs in a mikroRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA. Biochim Biophys Acta 2010; 1799(9): 597–615.

10. Tripathi V, Ellis JD, Shen Z et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 2010; 39(6): 925–938.

11. Gupta RA, Shah N, Wang KC et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464(7291): 1071–1076.

12. Orom UA, Derrien T, Beringer M et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010; 143(1): 46–58.

13. Iacoangeli A, Lin Y, Morley EJ et al. BC200 RNA in invasive and preinvasive breast cancer. Carcinogenesis 2004; 25(11): 2125–2133.

14. Mattick JS, Amaral PP, Dinger ME et al. RNA regulation of epigenetic processes. Bioessays 2009; 31(1): 51–59.

15. Ishii N, Ozaki K, Sato H et al. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet 2006; 51(12): 1087–1099.

16. Faghihi MA, Modarresi F, Khalil AM et al. Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med 2008; 14(7): 723–730.

17. Sana J, Faltejskova P, Svoboda M et al. Novel classes of non-coding RNAs and cancer. J Transl Med 2012; 10(1): 103.

18. Costa FF. Non-coding RNAs: new players in eukaryotic biology. Gene 2005; 357(2): 83–94.

19. Okamura K, Chung WJ, Ruby JG et al. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature 2008; 453(7196): 803–806.

20. Rinn JL, Kertesz M, Wang JK et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007; 129(7): 1311–1323.

21. Khalil AM, Guttman M, Huarte M et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 2009; 106(28): 11667–11672.

22. Brannan CI, Dees EC, Ingram RS et al. The product of the H19 gene may function as an RNA. Mol Cell Biol 1990; 10(1): 28–36.

23. Gabory A, Jammes H, Dandolo L. The H19 locus: role of an imprinted non-coding RNA in growth and development. Bioessays 2010; 32(6): 473–480.

24. Hibi K, Nakamura H, Hirai A et al. Loss of H19 imprinting in esophageal cancer. Cancer Res 1996; 56(3): 480–482.

25. Tsai MC, Manor O, Wan Y et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010; 329(5992): 689–693.

26. Yang Z, Zhou L, Wu LM et al. Overexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation. Ann Surg Oncol 2011; 18(5): 1243–1250.

27. Louro R, Smirnova AS, Verjovski-Almeida S. Long intronic noncoding RNA transcription: expression noise or expression choice? Genomics 2009; 93(4): 291–298.

28. Louro R, Nakaya HI, Amaral PP et al. Androgen responsive intronic non-coding RNAs. BMC Biol 2007; 5: 4.

29. Cawley S, Bekiranov S, Ng HH et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 2004; 116(4): 499–509.

30. Nakaya HI, Amaral PP, Louro R et al. Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol 2007; 8(3): R43.

31. Dinger ME, Amaral PP, Mercer TR et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 2008; 18(9): 1433–1445.

32. Kravchenko JE, Rogozin IB, Koonin EV et al. Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin. Nature 2005; 436(7051): 735–739.

33. Li SC, Tang P, Lin WC. Intronic mikroRNA: discovery and biological implications. DNA Cell Biol 2007; 26(4): 195–207.

34. Borchert GM, Lanier W, Davidson BL. RNA polymerase III transcribes human mikroRNAs. Nat Struct Mol Biol 2006; 13(12): 1097–1101.

35. Massone S, Vassallo I, Castelnuovo M et al. RNA polymerase III drives alternative splicing of the potassium channel-interacting protein contributing to brain complexity and neurodegeneration. J Cell Biol 2011; 193(5): 851–866.

36. Massone S, Vassallo I, Fiorino G et al. 17A, a novel non-coding RNA, regulates GABA B alternative splicing and signaling in response to inflammatory stimuli and in Alzheimer disease. Neurobiol Dis 2011; 41(2): 308–317.

37. Louro R, El-Jundi T, Nakaya HI et al. Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse loci. Genomics 2008; 92(1): 18–25.

38. Rearick D, Prakash A, McSweeny A et al. Critical asso­ciation of ncRNA with introns. Nucleic Acids Res 2011; 39(6): 2357–2366.

39. Mercer TR, Dinger ME, Sunkin SM et al. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 2008; 105(2): 716–721.

40. Katayama S, Tomaru Y, Kasukawa T et al. Antisense transcription in the mammalian transcriptome. Science 2005; 309(5740): 1564–1566.

41. Filipowicz W, Pogacic V. Biogenesis of small nucleolar ribonucleoproteins. Curr Opin Cell Biol 2002; 14(3): 319–327.

42. Hirose T, Ideue T, Nagai M et al. A spliceosomal intron binding protein, IBP160, links position-dependent assembly of intron-encoded box C/D snoRNP to pre-mRNA splicing. Mol Cell 2006; 23(5): 673–684.

43. Heo JB, Sung S. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 2011; 331(6013): 76–79.

44. Tahira AC, Kubrusly MS, Faria MF et al. Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer. Mol Cancer 2011; 10: 141.

45. Isken O, Maquat LE. Telomeric RNAs as a novel player in telomeric integrity. F1000 Biol Rep 2009; 1: 90.

46. Azzalin CM, Reichenbach P, Khoriauli L et al. Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science 2007; 318(5851): 798–801.

47. Schoeftner S, Blasco MA. Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II. Nat Cell Biol 2008; 10(2): 228–236.

48. Schoeftner S, Blasco MA. A ‚higher order‘ of telomere regulation: telomere heterochromatin and telomeric RNAs. EMBO J 2009; 28(16): 2323–2336.

49. Luke B, Panza A, Redon S et al. The Rat1p 5‘ to 3‘ exonuclease degrades telomeric repeat-containing RNA and promotes telomere elongation in Saccharomyces cerevisiae. Mol Cell 2008; 32(4): 465–477.

50. Sampl S, Pramhas S, Stern C et al. Expression of Telomeres in Astrocytoma WHO Grade 2 to 4: TERRA Level Correlates with Telomere Length, Telomerase Activity, and Advanced Clinical Grade. Transl Oncol 2012; 5(1): 56–65.

51. Schoeftner S, Blasco MA. Chromatin regulation and non-coding RNAs at mammalian telomeres. Semin Cell Dev Biol 2010; 21(2): 186–193.

52. Ulveling D, Francastel C, Hube F. When one is better than two: RNA with dual functions. Biochimie 2011; 93(4): 633–644.

53. Lanz RB, McKenna NJ, Onate SA et al. A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell 1999; 97(1): 17–27.

54. Kawashima H, Takano H, Sugita S et al. A novel steroid receptor co-activator protein (SRAP) as an alternative form of steroid receptor RNA-activator gene: expression in prostate cancer cells and enhancement of androgen receptor activity. Biochem J 2003; 369(Pt 1): 163–171.

55. Chooniedass-Kothari S, Emberley E, Hamedani MK, et al. The steroid receptor RNA activator is the first functional RNA encoding a protein. FEBS Lett 2004; 566 (1–3): 43–47.

56. Xu K, Liang X, Cui D et al. miR-1915 inhibits Bcl-2 to modulate multidrug resistance by increasing drug-sensitivity in human colorectal carcinoma cells. Mol Carcinog 2011. [Epub ahead of print].

57. Hussein-Fikret S, Fuller PJ. Expression of nuclear receptor coregulators in ovarian stromal and epithelial tumours. Mol Cell Endocrinol 2005; 229(1–2): 149–160.

58. Lanz RB, Chua SS, Barron N et al. Steroid receptor RNA activator stimulates proliferation as well as apoptosis in vivo. Mol Cell Biol 2003; 23(20): 7163–7176.

59. Leygue E, Dotzlaw H, Watson PH et al. Expression of the steroid receptor RNA activator in human breast tumors. Cancer Res 1999; 59(17): 4190–4193.

60. Harrison PM, Zheng D, Zhang Z et al. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res 2005; 33(8): 2374–2383.

61. Pink RC, Wicks K, Caley DP et al. Pseudogenes: pseudo-functional or key regulators in health and disease? RNA 2011; 17(5): 792–798.

62. Esnault C, Maestre J, Heidmann T. Human LINE retrotransposons generate processed pseudogenes. Nat Genet 2000; 24(4): 363–367.

63. Terai G, Yoshizawa A, Okida H et al. Discovery of short pseudogenes derived from messenger RNAs. Nucleic Acids Res 2010; 38(4): 1163–1171.

64. Devor EJ. Primate mikroRNAs miR-220 and miR-492 lie within processed pseudogenes. J Hered 2006; 97(2): 186–190.

65. Han YJ, Ma SF, Yourek G et al. A transcribed pseudogene of MYLK promotes cell proliferation. FASEB J 2011; 25(7): 2305–2312.

66. Lu W, Zhou D, Glusman G et al. KLK31P is a novel androgen regulated and transcribed pseudogene of kallikreins that is expressed at lower levels in prostate cancer cells than in normal prostate cells. Prostate 2006; 66(9): 936–944.

67. Bejerano G, Pheasant M, Makunin I et al. Ultraconserved elements in the human genome. Science 2004; 304(5675): 1321–1325.

68. Nobrega MA, Ovcharenko I, Afzal V et al. Scanning human gene deserts for long-range enhancers. Science 2003; 302(5 644): 413.

69. Lujambio A, Portela A, Liz J et al. CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer. Oncogene 2010; 29(48): 6390–63401.

70. Calin GA, Liu CG, Ferracin M et al. Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 2007; 12(3): 215–229.

71. Scaruffi P, Stigliani S, Moretti S et al. Transcribed-Ultra Conserved Region expression is associated with outcome in high-risk neuroblastoma. BMC Cancer 2009; 9: 441.

72. Sana J, Hankeova S, Svoboda M et al. Expression levels of transcribed ultraconserved regions uc.73 and uc.388 are altered in colorectal cancer. Oncology 2012; 82(2): 114–118.

73. Mestdagh P, Fredlund E, Pattyn F et al. An integrative genomics screen uncovers ncRNA T-UCR func­tions in neuroblastoma tumours. Oncogene 2010; 29(24): 3583–3592.

74. Catucci I, Verderio P, Pizzamiglio S et al. SNPs in ultraconserved elements and familial breast cancer risk. Carcinogenesis 2009; 30(3): 544–545; author reply 6.

75. Yang R, Frank B, Hemminki K et al. SNPs in ultraconserved elements and familial breast cancer risk. Carcinogenesis 2008; 29(2): 351–355.

76. Ji P, Diederichs S, Wang W et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 2003; 22(39): 8031–8041.

77. Lin R, Maeda S, Liu C et al. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene 2007; 26(6): 851–858.

78. Davis IJ, Hsi BL, Arroyo JD et al. Cloning of an Alpha-TFEB fusion in renal tumors harboring the t(6;11)(p21;q13) chromosome translocation. Proc Natl Acad Sci U S A 2003; 100(10): 6051–6056.

79. Guo F, Li Y, Liu Y et al. Inhibition of metastasis-asso­ciated lung adenocarcinoma transcript 1 in CaSki human cervical cancer cells suppresses cell proliferation and invasion. Acta Biochim Biophys Sin (Shanghai) 2010; 42(3): 224–229.

80. Fellenberg J, Bernd L, Delling G et al. Prognostic significance of drug-regulated genes in high-grade osteosarcoma. Mod Pathol 2007; 20(10): 1085–1094.

81. Koshimizu TA, Fujiwara Y, Sakai N et al. Oxytocin stimulates expression of a noncoding RNA tumor marker in a human neuroblastoma cell line. Life Sci 2010; 86 (11–12): 455–460.

82. Panzitt K, Tschernatsch MM, Guelly C et al. Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA. Gastroenterology 2007; 132(1): 330–342.

83. Matouk IJ, Abbasi I, Hochberg A et al. Highly upregulated in liver cancer noncoding RNA is overexpressed in hepatic colorectal metastasis. Eur J Gastroenterol Hepatol 2009; 21(6): 688–692.

84. Chen W, Bocker W, Brosius J et al. Expression of neural BC200 RNA in human tumours. J Pathol 1997; 183(3): 345–351.

85. Berteaux N, Lottin S, Adriaenssens E et al. Hormonal regulation of H19 gene expression in prostate epithelial cells. J Endocrinol 2004; 183(1): 69–78.

86. Eis PS, Tam W, Sun L et al. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc Natl Acad Sci U S A 2005; 102(10): 3627–3632.

87. Chung S, Nakagawa H, Uemura M et al. Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility. Cancer Sci 2011; 102(1): 245–252.

88. Pasic I, Shlien A, Durbin AD et al. Recurrent focal copy-number changes and loss of heterozygosity implicate two noncoding RNAs and one tumor suppressor gene at chromosome 3q13.31 in osteosarcoma. Cancer Res 2010; 70(1): 160–171.

89. Petrovics G, Zhang W, Makarem M et al. Elevated expression of PCGEM1, a prostate-specific gene with cell growth-promoting function, is associated with high-risk prostate cancer patients. Oncogene 2004; 23(2): 605–611.

90. Srikantan V, Zou Z, Petrovics G et al. PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer. Proc Natl Acad Sci U S A 2000; 97(22): 12216–12221.

91. Fu X, Ravindranath L, Tran N et al. Regulation of apoptosis by a prostate-specific and prostate cancer-associated noncoding gene, PCGEM1. DNA Cell Biol 2006; 25(3): 135–141.

92. Wang XS, Zhang Z, Wang HC et al. Rapid identification of UCA1 as a very sensitive and specific unique marker for human bladder carcinoma. Clin Cancer Res 2006; 12(16): 4851–4858.

93. Wang F, Li X, Xie X et al. UCA1, a non-protein-coding RNA up-regulated in bladder carcinoma and embryo, influencing cell growth and promoting invasion. FEBS Lett 2008; 582(13): 1919–1927.

94. Bussemakers MJ, van Bokhoven A, Verhaegh GW et al. DD3: a new prostate-specific gene, highly overexpressed in prostate cancer. Cancer Res 1999; 59(23): 5975–5979.

95. de Kok JB, Verhaegh GW, Roelofs RW et al. DD3(PCA3), a very sensitive and specific marker to detect prostate tumors. Cancer Res 2002; 62(9): 2695–2698.

96. Korneev SA, Korneeva EI, Lagarkova MA et al. Novel noncoding antisense RNA transcribed from human anti-NOS2A locus is differentially regulated during neuronal differentiation of embryonic stem cells. RNA 2008; 14(10): 2030–2037.

97. Braconi C, Valeri N, Kogure T et al. Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma. Proc Natl Acad Sci U S A 2011; 108(2): 786–791.

98. Yu W, Gius D, Onyango P et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 2008; 451(7175): 202–206.

99. Folkersen L, Kyriakou T, Goel A et al. Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. PLoS One 2009; 4(11): e7677.

100. Yap KL, Li S, Munoz-Cabello AM 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(5): 662–674.

101. Pasmant E, Laurendeau I, Heron D et al. Characterization of a germ-line deletion, including the entire INK4//ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Res 2007; 67(8): 3963–3969.

102. Miyoshi N, Wagatsuma H, Wakana S et al. Identification of an imprinted gene, Meg3/Gtl2 and its human homologue MEG3, first mapped on mouse distal chromosome 12 and human chromosome 14q. Genes Cells 2000; 5(3): 211–220.

103. Zhang X, Zhou Y, Mehta KR et al. A pituitary-derived MEG3 isoform functions as a growth suppressor in tumor cells. J Clin Endocrinol Metab 2003; 88(11): 5119–5126.

104. Zhang X, Rice K, Wang Y et al. Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform structure, expression, and functions. Endocrinology 2010; 151(3): 939–947.

105. Mourtada-Maarabouni M, Pickard MR, Hedge VL et al. GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene 2009; 28(2): 195–208.

106. Chooniedass-Kothari S, Hamedani MK, Troup S et al. The steroid receptor RNA activator protein is expressed in breast tumor tissues. Int J Cancer 2006; 118(4): 1054–1059.

107. Poliseno L, Salmena L, Zhang J et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 2010; 465(7301): 1033–1038.

108. Alimonti A, Carracedo A, Clohessy JG et al. Subtle variations in Pten dose determine cancer susceptibility. Nat Genet 2010; 42(5): 454–458.

109. Zhu Y, Yu M, Li Z et al. ncRAN, a newly identified long noncoding RNA, enhances human bladder tumor growth, invasion, and survival. Urology 2011; 77(2): 510e1–510e5.

110. Yu M, Ohira M, Li Y et al. High expression of ncRAN, a novel non-coding RNA mapped to chromosome 17q25.1, is associated with poor prognosis in neuroblastoma. Int J Oncol 2009; 34(4): 931–938.

111. Silva JM, Boczek NJ, Berres MW et al. LSINCT5 is over expressed in breast and ovarian cancer and affects cellular proliferation. RNA Biol 2011; 8(3): 496–505.

112. Gibb EA, Brown CJ, Lam WL. The functional role of long non-coding RNA in human carcinomas. Mol Cancer 2011; 10: 38.

Štítky
Paediatric clinical oncology Surgery Clinical oncology

Článok vyšiel v časopise

Clinical Oncology

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