Stressing out over long noncoding RNA

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1859, Issue 1, 2016, Pages 184-191

  Audas, Timothy E ^a,b   Lee, Stephen ^a,b  

^a UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF MIAMI   (United States)

Author keywords

Cancer; Long noncoding RNA; Stress response

Indexed keywords

ANTINEOPLASTIC AGENT; HEAT SHOCK PROTEIN; LONG UNTRANSLATED RNA; PROTEIN P53; TRANSCRIPTION FACTOR; TUMOR SUPPRESSOR PROTEIN;

CELL FUNCTION; CELL PROLIFERATION; DNA DAMAGE; EPIGENETICS; GENE EXPRESSION; GROWTH DISORDER; HEAT SHOCK RESPONSE; HUMAN; HYPOXIA; MALIGNANT NEOPLASTIC DISEASE; METABOLITE; NONHUMAN; PRIORITY JOURNAL; REVIEW; STARVATION; STRESS; ANIMAL; CLASSIFICATION; GENETICS; ONCOGENE; PHYSIOLOGICAL STRESS; PROTEOMICS;

ANIMALS; CELL PROLIFERATION; HUMANS; ONCOGENES; PROTEOMICS; RNA, LONG NONCODING; STRESS, PHYSIOLOGICAL; TUMOR SUPPRESSOR PROTEINS;

EID: 84953390884     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2015.06.010     Document Type: Review

References (156)

1. Crick F.H. On protein synthesis. Symp. Soc. Exp. Biol. 1958, 12:138-163.
2. Holley R.W., et al. Structure of a ribonucleic acid. Science 1965, 147(3664):1462-1465.
3. Busch H., Reddy R., Rothblum L., Choi Y.C. SnRNAs, SnRNPs, and RNA processing. Annu. Rev. Biochem. 1982, 51:617-654.
4. Jacob F., Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 1961, 3:318-356.
5. Consortium EP, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447(7146):799-816.
6. Mattick J.S. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep. 2001, 2(11):986-991.
7. Aparicio S., et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 2002, 297(5585):1301-1310.
8. Goodstadt L., Ponting C.P. Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput. Biol. 2006, 2(9):e133.
9. International Chicken Genome Sequencing C Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 2004, 432(7018):695-716.
10. Stein L.D., et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 2003, 1(2):E45.
11. Pennisi E. Genetics. Working the (gene count) numbers: finally, a firm answer?. Science 2007, 316(5828):1113.
12. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860-921.
13. Taft R.J., Pheasant M., Mattick J.S. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 2007, 29(3):288-299.
14. Bird A.P. Gene number, noise reduction and biological complexity. Trends Genet. 1995, 11(3):94-100.
15. Djebali S., et al. Landscape of transcription in human cells. Nature 2012, 489(7414):101-108.
16. Derrien T., et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012, 22(9):1775-1789.
17. Kultz D. Molecular and evolutionary basis of the cellular stress response. Annu. Rev. Physiol. 2005, 67:225-257.
18. Ritossa F. New puffing pattern induced by temperature shock and DNP in drosophila. Experientia 1962, 18(12). (571-&).
19. Jolly C., Morimoto R.I. Role of the heat shock response and molecular chaperones in oncogenesis and cell death. J. Natl. Cancer Inst. 2000, 92(19):1564-1572.
20. Richter K., Haslbeck M., Buchner J. The heat shock response: life on the verge of death. Mol. Cell 2010, 40(2):253-266.
21. Vabulas R.M., Raychaudhuri S., Hayer-Hartl M., Hartl F.U. Protein folding in the cytoplasm and the heat shock response. Cold Spring Harb. Perspect. Biol. 2010, 2(12):a004390.
22. Shamovsky I., Ivannikov M., Kandel E.S., Gershon D., Nudler E. RNA-mediated response to heat shock in mammalian cells. Nature 2006, 440(7083):556-560.
23. Kim D.S., Lee Y., Hahn Y. Evidence for bacterial origin of heat shock RNA-1. RNA 2010, 16(2):274-279.
24. Kortmann J., Sczodrok S., Rinnenthal J., Schwalbe H., Narberhaus F. Translation on demand by a simple RNA-based thermosensor. Nucleic Acids Res. 2011, 39(7):2855-2868.
25. Morita M.T., et al. Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor. Genes Dev. 1999, 13(6):655-665.
26. Nocker A., et al. A mRNA-based thermosensor controls expression of rhizobial heat shock genes. Nucleic Acids Res. 2001, 29(23):4800-4807.
27. Schumann W. Thermosensor systems in eubacteria. Adv. Exp. Med. Biol. 2012, 739:1-16.
28. Waldminghaus T., Heidrich N., Brantl S., Narberhaus F. FourU: a novel type of RNA thermometer in Salmonella. Mol. Microbiol. 2007, 65(2):413-424.
29. Giuliodori A.M., et al. The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA. Mol. Cell 2010, 37(1):21-33.
30. Ahmed R., Duncan R.F. Translational regulation of Hsp90 mRNA. AUG-proximal 5'-untranslated region elements essential for preferential heat shock translation. J. Biol. Chem. 2004, 279(48):49919-49930.
31. Johansson J., et al. An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell 2002, 110(5):551-561.
32. Schmid C.W. Alu: a parasite's parasite?. Nat. Genet. 2003, 35(1):15-16.
33. Schmid C.W., Jelinek W.R. The Alu family of dispersed repetitive sequences. Science 1982, 216(4550):1065-1070.
34. Fornace A.J., Mitchell J.B. Induction of B2 RNA polymerase III transcription by heat shock: enrichment for heat shock induced sequences in rodent cells by hybridization subtraction. Nucleic Acids Res. 1986, 14(14):5793-5811.
35. Li T., Spearow J., Rubin C.M., Schmid C.W. Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo. Gene 1999, 239(2):367-372.
36. Liu W.M., Chu W.M., Choudary P.V., Schmid C.W. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res. 1995, 23(10):1758-1765.
37. Kramerov D.A., Tillib S.V., Lekakh I.V., Ryskov A.P., Georgiev G.P. Biosynthesis and cytoplasmic distribution of small poly(A)-containing B2 RNA. Biochim. Biophys. Acta 1985, 824(2):85-98.
38. Espinoza C.A., Allen T.A., Hieb A.R., Kugel J.F., Goodrich J.A. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat. Struct. Mol. Biol. 2004, 11(9):822-829.
39. Mariner P.D., et al. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol. Cell 2008, 29(4):499-509.
40. Yakovchuk P., Goodrich J.A., Kugel J.F. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc. Natl. Acad. Sci. U. S. A. 2009, 106(14):5569-5574.
41. Misteli T. The concept of self-organization in cellular architecture. J. Cell Biol. 2001, 155(2):181-185.
42. Misteli T. Protein dynamics: implications for nuclear architecture and gene expression. Science 2001, 291(5505):843-847.
43. Hager G.L., McNally J.G., Misteli T. Transcription dynamics. Mol. Cell 2009, 35(6):741-753.
44. Bendena W.G., Garbe J.C., Traverse K.L., Lakhotia S.C., Pardue M.L. Multiple inducers of the Drosophila heat shock locus 93D (hsr omega): inducer-specific patterns of the three transcripts. J. Cell Biol. 1989, 108(6):2017-2028.
45. Lengyel J.A., Ransom L.J., Graham M.L., Pardue M.L. Transcription and metabolism of RNA from the Drosophila melanogaster heat shock puff site 93D. Chromosoma 1980, 80(3):237-252.
46. Mallik M., Lakhotia S.C. Pleiotropic consequences of misexpression of the developmentally active and stress-inducible non-coding hsromega gene in Drosophila. J. Biosci. 2011, 36(2):265-280.
47. Prasanth K.V., Rajendra T.K., Lal A.K., Lakhotia S.C. Omega speckles - a novel class of nuclear speckles containing hnRNPs associated with noncoding hsr-omega RNA in Drosophila. J. Cell Sci. 2000, 113(Pt 19):3485-3497.
48. Lakhotia S.C., Mallik M., Singh A.K., Ray M. The large noncoding hsromega-n transcripts are essential for thermotolerance and remobilization of hnRNPs, HP1 and RNA polymerase II during recovery from heat shock in Drosophila. Chromosoma 2012, 121(1):49-70.
49. Jolly C., Lakhotia S.C. Human sat III and Drosophila hsr omega transcripts: a common paradigm for regulation of nuclear RNA processing in stressed cells. Nucleic Acids Res. 2006, 34(19):5508-5514.
50. Valgardsdottir R., et al. Structural and functional characterization of noncoding repetitive RNAs transcribed in stressed human cells. Mol. Biol. Cell 2005, 16(6):2597-2604.
51. Jolly C., et al. Stress-induced transcription of satellite III repeats. J. Cell Biol. 2004, 164(1):25-33.
52. Denegri M., et al. Human chromosomes 9, 12, and 15 contain the nucleation sites of stress-induced nuclear bodies. Mol. Biol. Cell 2002, 13(6):2069-2079.
53. Rizzi N., et al. Transcriptional activation of a constitutive heterochromatic domain of the human genome in response to heat shock. Mol. Biol. Cell 2004, 15(2):543-551.
54. Valgardsdottir R., et al. Transcription of satellite III non-coding RNAs is a general stress response in human cells. Nucleic Acids Res. 2008, 36(2):423-434.
55. Eymery A., Souchier C., Vourc'h C., Jolly C. Heat shock factor 1 binds to and transcribes satellite II and III sequences at several pericentromeric regions in heat-shocked cells. Exp. Cell Res. 2010, 316(11):1845-1855.
56. Chiodi I., et al. RNA recognition motif 2 directs the recruitment of SF2/ASF to nuclear stress bodies. Nucleic Acids Res. 2004, 32(14):4127-4136.
57. Denegri M., et al. Stress-induced nuclear bodies are sites of accumulation of pre-mRNA processing factors. Mol. Biol. Cell 2001, 12(11):3502-3514.
58. Metz A., Soret J., Vourc'h C., Tazi J., Jolly C. A key role for stress-induced satellite III transcripts in the relocalization of splicing factors into nuclear stress granules. J. Cell Sci. 2004, 117(Pt 19):4551-4558.
59. Bond U. Heat shock but not other stress inducers leads to the disruption of a sub-set of snRNPs and inhibition of in vitro splicing in HeLa cells. EMBO J. 1988, 7(11):3509-3518.
60. Yost H.J., Lindquist S. RNA splicing is interrupted by heat shock and is rescued by heat shock protein synthesis. Cell 1986, 45(2):185-193.
61. Welch W.J., Feramisco J.R. Nuclear and nucleolar localization of the 72,000-dalton heat shock protein in heat-shocked mammalian cells. J. Biol. Chem. 1984, 259(7):4501-4513.
62. Audas T.E., Jacob M.D., Lee S. Immobilization of proteins in the nucleolus by ribosomal intergenic spacer noncoding RNA. Mol. Cell 2012, 45(2):147-157.
63. Jacob M.D., Audas T.E., Uniacke J., Trinkle-Mulcahy L., Lee S. Environmental cues induce a long noncoding RNA-dependent remodeling of the nucleolus. Mol. Biol. Cell 2013, 24(18):2943-2953.
64. Audas T.E., Jacob M.D., Lee S. The nucleolar detention pathway: a cellular strategy for regulating molecular networks. Cell Cycle 2012, 11(11):2059-2062.
65. Mekhail K., Gunaratnam L., Bonicalzi M.E., Lee S. HIF activation by pH-dependent nucleolar sequestration of VHL. Nat. Cell Biol. 2004, 6(7):642-647.
66. Jacob M.D., Audas T.E., Mullineux S.T., Lee S. Where no RNA polymerase has gone before: novel functional transcripts derived from the ribosomal intergenic spacer. Nucleus 2012, 3(4):315-319.
67. Mekhail K., et al. Regulation of ubiquitin ligase dynamics by the nucleolus. J. Cell Biol. 2005, 170(5):733-744.
68. Andersen J.S., et al. Nucleolar proteome dynamics. Nature 2005, 433(7021):77-83.
69. Phair R.D., Misteli T. High mobility of proteins in the mammalian cell nucleus. Nature 2000, 404(6778):604-609.
70. Jolly C., Usson Y., Morimoto R.I. Rapid and reversible relocalization of heat shock factor 1 within seconds to nuclear stress granules. Proc. Natl. Acad. Sci. U. S. A. 1999, 96(12):6769-6774.
71. Mourtada-Maarabouni M., Hedge V.L., Kirkham L., Farzaneh F., Williams G.T. Growth arrest in human T-cells is controlled by the non-coding RNA growth-arrest-specific transcript 5 (GAS5). J. Cell Sci. 2008, 121(Pt 7):939-946.
72. Schneider C., King R.M., Philipson L. Genes specifically expressed at growth arrest of mammalian cells. Cell 1988, 54(6):787-793.
73. Ciccarelli C., Philipson L., Sorrentino V. Regulation of expression of growth arrest-specific genes in mouse fibroblasts. Mol. Cell. Biol. 1990, 10(4):1525-1529.
74. Coccia E.M., et al. Regulation and expression of a growth arrest-specific gene (gas5) during growth, differentiation, and development. Mol. Cell. Biol. 1992, 12(8):3514-3521.
75. Smith C.M., Steitz J.A. Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5'-terminal oligopyrimidine gene family reveals common features of snoRNA host genes. Mol. Cell. Biol. 1998, 18(12):6897-6909.
76. Tani H., Torimura M., Akimitsu N. The RNA degradation pathway regulates the function of GAS5 a non-coding RNA in mammalian cells. PLoS One 2013, 8(1):e55684.
77. Tani H., et al. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res. 2012, 22(5):947-956.
78. Kino T., Hurt D.E., Ichijo T., Nader N., Chrousos G.P. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal. 2010, 3(107):ra8.
79. Boulon S., Westman B.J., Hutten S., Boisvert F.M., Lamond A.I. The nucleolus under stress. Mol. Cell 2010, 40(2):216-227.
80. Mayer C., Schmitz K.M., Li J., Grummt I., Santoro R. Intergenic transcripts regulate the epigenetic state of rRNA genes. Mol. Cell 2006, 22(3):351-361.
81. Bierhoff H., et al. Quiescence-induced LncRNAs trigger H4K20 trimethylation and transcriptional silencing. Mol. Cell 2014, 54(4):675-682.
82. Bierhoff H., Schmitz K., Maass F., Ye J., Grummt I. Noncoding transcripts in sense and antisense orientation regulate the epigenetic state of ribosomal RNA genes. Cold Spring Harb. Symp. Quant. Biol. 2010, 75:357-364.
83. Schmitz K.M., Mayer C., Postepska A., Grummt I. Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev. 2010, 24(20):2264-2269.
84. Zhou Y., et al. Reversible acetylation of the chromatin remodelling complex NoRC is required for non-coding RNA-dependent silencing. Nat. Cell Biol. 2009, 11(8):1010-1016.
85. Raval R.R., et al. Contrasting properties of hypoxia-inducible factor 1 (HIF-1) and HIF-2 in von Hippel-Lindau-associated renal cell carcinoma. Mol. Cell. Biol. 2005, 25(13):5675-5686.
86. Semenza G.L. Hypoxia-inducible factor 1 (HIF-1) pathway. Sci. STKE 2007, (407):cm8.
87. Uniacke J., et al. An oxygen-regulated switch in the protein synthesis machinery. Nature 2012, 486(7401):126-129.
88. Yang F., et al. Repression of the long noncoding RNA-LET by histone deacetylase 3 contributes to hypoxia-mediated metastasis. Mol. Cell 2013, 49(6):1083-1096.
89. Takahashi K., Yan I.K., Haga H., Patel T. Modulation of hypoxia-signaling pathways by extracellular linc-RoR. J. Cell Sci. 2014, 127(Pt 7):1585-1594.
90. Choudhry H., et al. Tumor hypoxia induces nuclear paraspeckle formation through HIF-2alpha dependent transcriptional activation of NEAT1 leading to cancer cell survival. Oncogene 2014, 1-9.
91. Gomez-Maldonado L., et al. EFNA3 long noncoding RNAs induced by hypoxia promote metastatic dissemination. Oncogene 2015, 34:2609-2620.
92. Yang F., Zhang H., Mei Y., Wu M. Reciprocal regulation of HIF-1alpha and lincRNA-p21 modulates the Warburg effect. Mol. Cell 2014, 53(1):88-100.
93. Sasaki Y.T., Ideue T., Sano M., Mituyama T., Hirose T. MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc. Natl. Acad. Sci. U. S. A. 2009, 106(8):2525-2530.
94. Ciccia A., Elledge S.J. The DNA damage response: making it safe to play with knives. Mol. Cell 2010, 40(2):179-204.
95. Liu Q., et al. Altered expression of long non-coding RNAs during genotoxic stress-induced cell death in human glioma cells. J. Neuro-Oncol. 2015, 122:283-292.
96. Ozgur E., et al. Differential expression of long non-coding RNAs during genotoxic stress-induced apoptosis in HeLa and MCF-7 cells. Clin. Exp. Med. 2013, 13(2):119-126.
97. Halaby M.J., Yang D.Q. p53 translational control: a new facet of p53 regulation and its implication for tumorigenesis and cancer therapeutics. Gene 2007, 395(1-2):1-7.
98. Meek D.W., Anderson C.W. Posttranslational modification of p53: cooperative integrators of function. Cold Spring Harb. Perspect. Biol. 2009, 1(6):a000950.
99. Loewer S., et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat. Genet. 2010, 42(12):1113-1117.
100. Zhang A., et al. The human long non-coding RNA-RoR is a p53 repressor in response to DNA damage. Cell Res. 2013, 23(3):340-350.
101. Huarte M., et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010, 142(3):409-419.
102. Hung T., et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat. Genet. 2011, 43(7):621-629.
103. Morachis J.M., Murawsky C.M., Emerson B.M. Regulation of the p53 transcriptional response by structurally diverse core promoters. Genes Dev. 2010, 24(2):135-147.
104. Peterlin B.M., Price D.H. Controlling the elongation phase of transcription with P-TEFb. Mol. Cell 2006, 23(3):297-305.
105. Nguyen V.T., Kiss T., Michels A.A., Bensaude O. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 2001, 414(6861):322-325.
106. Yang Z., Zhu Q., Luo K., Zhou Q. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 2001, 414(6861):317-322.
107. Barrandon C., Bonnet F., Nguyen V.T., Labas V., Bensaude O. The transcription-dependent dissociation of P-TEFb-HEXIM1-7SK RNA relies upon formation of hnRNP-7SK RNA complexes. Mol. Cell. Biol. 2007, 27(20):6996-7006.
108. 2+ signaling. Genes Dev. 2008, 22(10):1356-1368.
109. Wang X., et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 2008, 454(7200):126-130.
110. Khalil A.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.
111. Rinn J.L., et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007, 129(7):1311-1323.
112. Nagano T., et al. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 2008, 322(5908):1717-1720.
113. Pandey R.R., et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 2008, 32(2):232-246.
114. Zhao J., Sun B.K., Erwin J.A., Song J.J., Lee J.T. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008, 322(5902):750-756.
115. Guttman M., et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458(7235):223-227.
116. Negishi M., et al. A new lncRNA, APTR, associates with and represses the CDKN1A/p21 promoter by recruiting polycomb proteins. PLoS One 2014, 9(4):e95216.
117. Marin-Bejar O., et al. Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2. Genome Biol. 2013, 14(9):R104.
118. Hanahan D., Weinberg R.A. Hallmarks of cancer: the next generation. Cell 2011, 144(5):646-674.
119. Xu Y., et al. Upregulation of the long noncoding RNA TUG1 promotes proliferation and migration of esophageal squamous cell carcinoma. Tumour Biol. 2015, 36:1643-1651.
120. Mourtada-Maarabouni M., Pickard M.R., Hedge V.L., Farzaneh F., Williams G.T. GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene 2009, 28(2):195-208.
121. Brown C.J., et al. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 1991, 349(6304):38-44.
122. Bartolomei M.S., Zemel S., Tilghman S.M. Parental imprinting of the mouse H19 gene. Nature 1991, 351(6322):153-155.
123. Gupta R.A., et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010, 464(7291):1071-1076.
124. Yu W., et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 2008, 451(7175):202-206.
125. Tano K., et al. MALAT-1 enhances cell motility of lung adenocarcinoma cells by influencing the expression of motility-related genes. FEBS Lett. 2010, 584(22):4575-4580.
126. Prensner J.R., et al. The long non-coding RNA PCAT-1 promotes prostate cancer cell proliferation through cMyc. Neoplasia 2014, 16(11):900-908.
127. Prensner J.R., et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat. Biotechnol. 2011, 29(8):742-749.
128. Fu X., Ravindranath L., Tran N., Petrovics G., Srivastava S. Regulation of apoptosis by a prostate-specific and prostate cancer-associated noncoding gene, PCGEM1. DNA Cell Biol. 2006, 25(3):135-141.
129. Srikantan V., et al. PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer. Proc. Natl. Acad. Sci. U. S. A. 2000, 97(22):12216-12221.
130. Cheetham S.W., Gruhl F., Mattick J.S., Dinger M.E. Long noncoding RNAs and the genetics of cancer. Br. J. Cancer 2013, 108(12):2419-2425.
131. Gibb E.A., Brown C.J., Lam W.L. The functional role of long non-coding RNA in human carcinomas. Mol. Cancer 2011, 10:38.
132. Gutschner T., Diederichs S. The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol. 2012, 9(6):703-719.
133. Prensner J.R., Chinnaiyan A.M. The emergence of lncRNAs in cancer biology. Cancer Discov. 2011, 1(5):391-407.
134. Iyer M.K., et al. The landscape of long noncoding RNAs in the human transcriptome. Nat. Genet. 2015, 47(3):199-208.
135. Zhao W., Luo J., Jiao S. Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implications. Sci. Rep. 2014, 4:6591.
136. Trimarchi T., et al. Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia. Cell 2014, 158(3):593-606.
137. Dong R., et al. Genome-wide analysis of long noncoding RNA (lncRNA) expression in hepatoblastoma tissues. PLoS One 2014, 9(1):e85599.
138. Du Z., et al. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat. Struct. Mol. Biol. 2013, 20(7):908-913.
139. Maruyama R., et al. Altered antisense-to-sense transcript ratios in breast cancer. Proc. Natl. Acad. Sci. U. S. A. 2012, 109(8):2820-2824.
140. Ting D.T., et al. Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 2011, 331(6017):593-596.
141. Ma K.X., et al. Long noncoding RNA MALAT1 associates with the malignant status and poor prognosis in glioma. Tumour Biol. 2015, 36:3355-3359.
142. Pandey G.K., et al. The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma progression by regulating cell proliferation and neuronal differentiation. Cancer Cell 2014, 26(5):722-737.
143. Prensner J.R., et al. The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat. Genet. 2013, 45(11):1392-1398.
144. Hu Y., et al. Long noncoding RNA GAPLINC regulates CD44-dependent cell invasiveness and associates with poor prognosis of gastric cancer. Cancer Res. 2014, 74(23):6890-6902.
145. Hu X., et al. A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in cancer. Cancer Cell 2014, 26(3):344-357.
146. Yuan J.H., et al. A long noncoding RNA activated by TGF-beta promotes the invasion-metastasis cascade in hepatocellular carcinoma. Cancer Cell 2014, 25(5):666-681.
147. Liu B., et al. A cytoplasmic NF-kappaB interacting long noncoding RNA blocks IkappaB phosphorylation and suppresses breast cancer metastasis. Cancer Cell 2015, 27(3):370-381.
148. Prensner J.R., et al. RNA biomarkers associated with metastatic progression in prostate cancer: a multi-institutional high-throughput analysis of SChLAP1. Lancet Oncol. 2014, 15(13):1469-1480.
149. Tong Y.S., et al. Identification of the long non-coding RNA POU3F3 in plasma as a novel biomarker for diagnosis of esophageal squamous cell carcinoma. Mol. Cancer 2015, 14(1):3.
150. Zhang W., et al. A novel urinary long non-coding RNA transcript improves diagnostic accuracy in patients undergoing prostate biopsy. Prostate 2015, 75:653-661.
151. Yang Y., et al. The noncoding RNA expression profile and the effect of lncRNA AK126698 on cisplatin resistance in non-small-cell lung cancer cell. PLoS One 2013, 8(5):e65309.
152. Hou Z., et al. Long noncoding RNAs expression patterns associated with chemo response to cisplatin based chemotherapy in lung squamous cell carcinoma patients. PLoS One 2014, 9(9):e108133.
153. Thiebaut F., et al. Cellular localization of the multidrug-resistance gene product P-glycoprotein in normal human tissues. Proc. Natl. Acad. Sci. U. S. A. 1987, 84(21):7735-7738.
154. Wang Y., et al. Long noncoding RNA MRUL promotes ABCB1 expression in multidrug-resistant gastric cancer cell sublines. Mol. Cell. Biol. 2014, 34(17):3182-3193.
155. Liu Z., et al. The long noncoding RNA HOTAIR contributes to cisplatin resistance of human lung adenocarcinoma cells via downregulation of p21(WAF1/CIP1) expression. PLoS One 2013, 8(10):e77293.
156. Fan Y., et al. Long non-coding RNA UCA1 increases chemoresistance of bladder cancer cells by regulating Wnt signaling. FEBS J. 2014, 281(7):1750-1758.