RNA splicing control: Yet another gene regulatory role for long nuclear noncoding RNAs

RNA Biology

Volumn 8, Issue 6, 2011, Pages

  Zong, Xinying ^a   Tripathi, Vidisha ^a   Prasanth, Kannanganattu V ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Alternative splicing; MALAT 1; MALAT1; Non coding RNA; Nuclear domains; Nuclear RNA; Pre mRNA splicing

Indexed keywords

MESSENGER RNA PRECURSOR; NUCLEAR RNA; ONCOPROTEIN; PROTEIN MALAT1; UNCLASSIFIED DRUG;

CELL FUNCTION; CELL NUCLEUS; CHROMATIN; CHROMATIN STRUCTURE; GENE CONTROL; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENOME; GENOME IMPRINTING; HUMAN GENOME; MACROMOLECULE; MAMMAL CELL; NONHUMAN; NOTE; NUCLEOCYTOPLASMIC TRANSPORT; PROTEIN DOMAIN; REGULATORY MECHANISM; RNA PROCESSING; RNA SPLICING;

MAMMALIA;

EID: 81255211626     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: None     Document Type: Note

References (147)

1. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo 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. (Pubitemid 46920138)
2. Mattick JS. The genetic signatures of noncoding RNAs. PLoS genetics 2009; 5:1000459.
3. Mattick JS. The functional genomics of noncoding RNA. Science (New York, NY) 2005; 309:1527-8. (Pubitemid 41266470)
4. Mattick JS, Makunin IV. Non-coding RNA. Human molecular genetics 2006; 15:17-29.
5. Prasanth KV, Spector DL. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes & development 2007; 21:11-42. (Pubitemid 46089704)
6. Ponjavic J, Ponting CP, Lunter G. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome research 2007; 17:556-65. (Pubitemid 46715505)
7. Struhl K. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nature structural & molecular biology 2007; 14:103-5.
8. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458:223-7.
9. Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009; 136:629- 41.
10. Chen LL, Carmichael GG. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Molecular cell 2009; 35:467-78.
11. Chen LL, Carmichael GG. Decoding the function of nuclear long non-coding RNAs. Current opinion in cell biology 2010; 22:357-64.
12. Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A, et al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Molecular cell 2009; 33:717-26.
13. Cohen HR, Panning B. XIST RNA exhibits nuclear retention and exhibits reduced association with the export factor TAP/NXF1. Chromosoma 2007; 116:373-83. (Pubitemid 46995576)
14. Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC genomics 2007; 8:39.
15. Sasaki YT, Ideue T, Sano M, Mituyama T, Hirose T. MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proceedings of the National Academy of Sciences of the United States of America 2009; 106:2525-30.
16. Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. Journal of cell science 2007; 120:2498-506. (Pubitemid 47323859)
17. Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL. MEN varepsilon/beta nuclear- retained non-coding RNAs are upregulated upon muscle differentiation and are essential components of paraspeckles. Genome research 2009; 19:347-59.
18. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, et al. The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation. Molecular cell 2010; 39:925-38.
19. Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, et al. Genomic analysis of mouse retinal development. PLoS biology 2004; 2:247.
20. Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 2004; 116:499-509. (Pubitemid 38264428)
21. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome research 2008; 18:1433-45.
22. Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS. NRED: a database of long noncoding RNA expression. Nucleic acids research 2009; 37:122-6.
23. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. Specific expression of long noncoding RNAs in the mouse brain. Proceedings of the National Academy of Sciences of the United States of America 2008; 105:716-21. (Pubitemid 351171774)
24. Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M, Okunishi R, et al. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome research 2006; 16:11-9. (Pubitemid 43048929)
25. 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; 129:1311-23. (Pubitemid 46962090)
26. Costa FF. Non-coding RNAs: new players in eukaryotic biology. Gene 2005; 357:83-94. (Pubitemid 41297574)
27. Huarte M, Rinn JL. Large non-coding RNAs: missing links in cancer? Human molecular genetics 2010.
28. Perez DS, Hoage TR, Pritchett JR, Ducharme-Smith AL, Halling ML, Ganapathiraju SC, et al. Long, abundantly expressed non-coding transcripts are altered in cancer. Human molecular genetics 2008; 17:642-55. (Pubitemid 351292254)
29. Qureshi IA, Mattick JS, Mehler MF. Long non-coding RNAs in nervous system function and disease. Brain Res 2010; 1338:20-35.
30. Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J. A new frontier for molecular medicine: noncoding RNAs. Biochimica et biophysica acta 2005; 1756:65-75.
31. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nature reviews 2009; 10:155-9.
32. Mattick JS. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 2003; 25:930-9. (Pubitemid 37221517)
33. Lipovich L, Johnson R, Lin CY. MacroRNA underdogs in a microRNA world: evolutionary, regulatory and biomedical significance of mammalian long non-protein- coding RNA. Biochimica et biophysica acta 2010; 1799:597-615.
34. Nagano T, Fraser P. No-Nonsense Functions for Long Noncoding RNAs. Cell 2011; 145:178-81.
35. Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes & development 2009; 23:1494-504.
36. Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs. Nucleic acids research 2011; 39:146-51.
37. Orom UA, Shiekhattar R. Long non-coding RNAs and enhancers. Current opinion in genetics & development 2011; 21:194-8.
38. Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A. The expanding RNA polymerase III transcriptome. Trends in genetics: TIG 2007; 23:614-22. (Pubitemid 350180140)
39. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, et al. Many human large intergenic noncoding RNAs associate with chromatinmodifying complexes and affect gene expression. Proceedings of the National Academy of Sciences of the United States of America 2009; 106:11667-72.
40. Wang X, Song X, Glass CK, Rosenfeld MG. The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs. Cold Spring Harbor perspectives in biology 2011; 3:3756.
41. Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, et al. Distribution of NFkappaB-binding sites across human chromosome 22. Proceedings of the National Academy of Sciences of the United States of America 2003; 100:12247-52.
42. Clark MB, Mattick JS. Long noncoding RNAs in cell biology. Seminars in cell & developmental biology 2011.
43. Nagano T, Fraser P. Emerging similarities in epigenetic gene silencing by long noncoding RNAs. Mamm Genome 2009; 20:557-62.
44. Lee JT. The X as model for RNA's niche in epigenomic regulation. Cold Spring Harbor perspectives in biology 2010; 2:003749.
45. Lee JT. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes & development 2009; 23:1831-42.
46. Masui O, Heard E. RNA and protein actors in X-chromosome inactivation. Cold Spring Harb Symp Quant Biol 2006; 71:419-28.
47. Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science (New York, NY) 2008; 322:750-6.
48. Tian D, Sun S, Lee JT. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 2010; 143:390-403.
49. Ilik I, Akhtar A. roX RNAs: non-coding regulators of the male X chromosome in flies. RNA biology 2009; 6:113-21.
50. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular cell 2010; 40:939-53.
51. Hung T, Chang HY. Long noncoding RNA in genome regulation: prospects and mechanisms. RNA biology 2010; 7:582-5.
52. 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 (New York, NY) 2010; 329:689-93.
53. 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; 464:1071-6.
54. 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; 30:1956-62.
55. Yap KL, Li S, Munoz-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. Molecular cell 2010; 38:662-74.
56. Imamura T, Yamamoto S, Ohgane J, Hattori N, Tanaka S, Shiota K. Non-coding RNA directed DNA demethylation of Sphk1 CpG island. Biochem Biophys Res Commun 2004; 322:593-600. (Pubitemid 39490344)
57. Schmitz KM, Mayer C, Postepska A, Grummt I. Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes & development 2010; 24:2264-9.
58. Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 2008; 451:202-6.
59. Wang KC, Yang YW, Liu B, Sanyal A, Corces- Zimmerman R, Chen Y, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 2011; 472:120-4.
60. Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 2007; 445:666-70. (Pubitemid 46232888)
61. Allen TA, Von Kaenel S, Goodrich JA, Kugel JF. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nature structural & molecular biology 2004; 11:816-21. (Pubitemid 39136221)
62. Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nature structural & molecular biology 2004; 11:822-9. (Pubitemid 39128797)
63. Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, et al. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Molecular cell 2008; 29:499- 509.
64. Yakovchuk P, Goodrich JA, Kugel JF. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proceedings of the National Academy of Sciences of the United States of America 2009; 106:5569-74.
65. Hatchell EC, Colley SM, Beveridge DJ, Epis MR, Stuart LM, Giles KM, et al. SLIRP, a small SRA binding protein, is a nuclear receptor corepressor. Molecular cell 2006; 22:657-68. (Pubitemid 43817609)
66. Lanz RB, McKenna NJ, Onate SA, Albrecht U, Wong J, Tsai SY, et al. A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell 1999; 97:17-27. (Pubitemid 29165886)
67. Zhao X, Patton JR, Davis SL, Florence B, Ames SJ, Spanjaard RA. Regulation of nuclear receptor activity by a pseudouridine synthase through post-transcriptional modification of steroid receptor RNA activator. Molecular cell 2004; 15:549-58. (Pubitemid 39141782)
68. 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; 142:409-19.
69. 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; 454:126-30. (Pubitemid 351934270)
70. 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.
71. 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 & development 2006; 20:1470-84. (Pubitemid 43830654)
72. Ashe HL, Monks J, Wijgerde M, Fraser P, Proudfoot NJ. Intergenic transcription and transinduction of the human beta-globin locus. Genes & development 1997; 11:2494-509. (Pubitemid 27438831)
73. Kong S, Bohl D, Li C, Tuan D. Transcription of the HS2 enhancer toward a cis-linked gene is independent of the orientation, position and distance of the enhancer relative to the gene. Molecular and cellular biology 1997; 17:3955-65. (Pubitemid 27281871)
74. Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 2010; 465:182-7.
75. Hirota K, Miyoshi T, Kugou K, Hoffman CS, Shibata T, Ohta K. Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs. Nature 2008; 456:130-4.
76. Martens JA, Laprade L, Winston F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 2004; 429:571-4. (Pubitemid 38737662)
77. Martens JA, Wu PY, Winston F. Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes & development 2005; 19:2695-704. (Pubitemid 41627936)
78. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, et al. Alternative isoform regulation in human tissue transcriptomes. Nature 2008; 456:470- 6.
79. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature genetics 2008; 40:1413-5.
80. Blencowe BJ. Alternative splicing: new insights from global analyses. Cell 2006; 126:37-47. (Pubitemid 44040990)
81. Hallegger M, Llorian M, Smith CW. Alternative splicing: global insights. Febs J 2010; 277:856-66.
82. Licatalosi DD, Darnell RB. RNA processing and its regulation: global insights into biological networks. Nature reviews Genetics 2010; 11:75-87.
83. Hocine S, Singer RH, Grunwald D. RNA processing and export. Cold Spring Harbor perspectives in biology 2010; 2:000752.
84. Lin S, Fu XD. SR proteins and related factors in alternative splicing. Advances in experimental medicine and biology 2007; 623:107-22.
85. Long JC, Caceres JF. The SR protein family of splicing factors: master regulators of gene expression. The Biochemical journal 2009; 417:15-27.
86. Luco RF, Misteli T. More than a splicing code: integrating the role of RNA, chromatin and non-coding RNA in alternative splicing regulation. Current opinion in genetics & development 2011.
87. Krystal GW, Armstrong BC, Battey JF. N-myc mRNA forms an RNA-RNA duplex with endogenous antisense transcripts. Molecular and cellular biology 1990; 10:4180-91.
88. Hastings ML, Ingle HA, Lazar MA, Munroe SH. Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA. The Journal of biological chemistry 2000; 275:11507-13. (Pubitemid 30212807)
89. Munroe SH, Lazar MA. Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. The Journal of biological chemistry 1991; 266:22083-6. (Pubitemid 21908616)
90. Beltran M, Puig I, Pena C, Garcia JM, Alvarez AB, Pena R, et al. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes & development 2008; 22:756-69. (Pubitemid 351439107)
91. Biamonti G, Vourc'h C. Nuclear stress bodies. Cold Spring Harbor perspectives in biology 2010; 2:695.
92. Biamonti G, Caceres JF. Cellular stress and RNA splicing. Trends in biochemical sciences 2009; 34:146-53.
93. Jolly C, Lakhotia SC. Human sat III and Drosophila hsr omega transcripts: a common paradigm for regulation of nuclear RNA processing in stressed cells. Nucleic acids research 2006; 34:5508-14. (Pubitemid 44742439)
94. Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan Z, et al. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. The EMBO journal 2010; 29:3082-93.
95. Lin R, Roychowdhury-Saha M, Black C, Watt AT, Marcusson EG, Freier SM, et al. Control of RNA processing by a large non-coding RNA overexpressed in carcinomas. FEBS letters 2011; 585:671-6.
96. Tano K, Mizuno R, Okada T, Rakwal R, Shibato J, Masuo Y, et al. MALAT-1 enhances cell motility of lung adenocarcinoma cells by influencing the expression of motility-related genes. FEBS letters 2010; 584:4575-80.
97. Ji P, Diederichs S, Wang W, Boing S, Metzger R, Schneider PM, 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; 22:8031-41. (Pubitemid 37175867)
98. 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 2006.
99. Fellenberg J, Bernd L, Delling G, Witte D, Zahlten- Hinguranage A. Prognostic significance of drug-regulated genes in high-grade osteosarcoma. Mod Pathol 2007; 20:1085-94. (Pubitemid 47429197)
100. Guffanti A, Iacono M, Pelucchi P, Kim N, Solda G, Croft LJ, et al. A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC genomics 2009; 10:163.
101. 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 (Baltimore, Md) 2006; 44:1012-24. (Pubitemid 46489565)
102. Yamada K, Kano J, Tsunoda H, Yoshikawa H, Okubo C, Ishiyama T, et al. Phenotypic characterization of endometrial stromal sarcoma of the uterus. Cancer Sci 2006; 97:106-12. (Pubitemid 43379477)
103. Guo F, Li Y, Liu Y, Wang J, Li Y, Li G. Inhibition of metastasis-associated lung adenocarcinoma transcript 1 in CaSki human cervical cancer cells suppresses cell proliferation and invasion. Acta biochimica et biophysica Sinica 2010; 42:224-9.
104. Spector DL, Lamond AI. Nuclear speckles. Cold Spring Harbor perspectives in biology 2011; 3.
105. Misteli T. RNA splicing: What has phosphorylation got to do with it? Curr Biol 1999; 9:198-200.
106. Misteli T, Spector DL. Protein phosphorylation and the nuclear organization of pre-mRNA splicing. Trends in cell biology 1997; 7:135-8. (Pubitemid 27135571)
107. Sanford JR, Wang X, Mort M, Vanduyn N, Cooper DN, Mooney SD, et al. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome research 2009; 19:381-94.
108. Ahn EY, Dekelver RC, Lo MC, Nguyen TA, Matsuura S, Boyapati A, et al. SON Controls Cell- Cycle Progression by Coordinated Regulation of RNA Splicing. Molecular cell 2011; 42:185-98.
109. Huen MS, Sy SM, Leung KM, Ching YP, Tipoe GL, Man C, et al. SON is a spliceosome-associated factor required for mitotic progression. Cell cycle (Georgetown, Tex) 2010; 9:2679-85.
110. Sharma A, Takata H, Shibahara K, Bubulya A, Bubulya PA. Son is essential for nuclear speckle organization and cell cycle progression. Molecular biology of the cell 2010; 21:650-63.
111. Polymenidou M, Lagier-Tourenne C, Hutt KR, Huelga SC, Moran J, Liang TY, et al. Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Nat Neurosci 2011; 14:459-68.
112. Tollervey JR, Curk T, Rogelj B, Briese M, Cereda M, Kayikci M, et al. Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci 2011; 14:452-8.
113. Makarov EM, Makarova OV, Achsel T, Luhrmann R. The human homologue of the yeast splicing factor prp6p contains multiple TPR elements and is stably associated with the U5 snRNP via protein-protein interactions. J Mol Biol 2000; 298:567-75.
114. Buratti E, Baralle FE. The multiple roles of TDP-43 in pre-mRNA processing and gene expression regulation. RNA biology 2010; 7:420-9.
115. Lagier-Tourenne C, Polymenidou M, Cleveland DW. TDP-43 and FUS/TLS: emerging roles in RNA processing and neurodegeneration. Human molecular genetics 2010; 19:46-64.
116. Lagier-Tourenne C, Cleveland DW. Rethinking ALS: the FUS about TDP-43. Cell 2009; 136:1001-4.
117. Caceres JF, Misteli T, Screaton GR, Spector DL, Krainer AR. Role of the modular domains of SR proteins in subnuclear localization and alternative splicing specificity. The Journal of cell biology 1997; 138:225-38. (Pubitemid 27323527)
118. Stamm S. Regulation of alternative splicing by reversible protein phosphorylation. The Journal of biological chemistry 2008; 283:1223-7.
119. Black DL. Mechanisms of alternative pre-messenger RNA splicing. Annual review of biochemistry 2003; 72:291-336. (Pubitemid 36930448)
120. Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS. Non-coding RNAs: regulators of disease. The Journal of pathology 2010; 220:126-39.
121. Tsai MC, Spitale RC, Chang HY. Long intergenic noncoding RNAs: new links in cancer progression. Cancer research 2011; 71:3-7.
122. Li L, Feng T, Lian Y, Zhang G, Garen A, Song X. Role of human noncoding RNAs in the control of tumorigenesis. Proceedings of the National Academy of Sciences of the United States of America 2009; 106:12956-61.
123. Xu C, Yang M, Tian J, Wang X, Li Z. MALAT-1: A long non-coding RNA and its important 3′ end functional motif in colorectal cancer metastasis. Int J Oncol 2011.
124. David CJ, Manley JL. Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. Genes & development 2010; 24:2343-64.
125. Ghigna C, Giordano S, Shen H, Benvenuto F, Castiglioni F, Comoglio PM, et al. Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene. Molecular cell 2005; 20:881-90. (Pubitemid 41814877)
126. Ghigna C, Valacca C, Biamonti G. Alternative splicing and tumor progression. Current genomics 2008; 9:556-70.
127. Karni R, de Stanchina E, Lowe SW, Sinha R, Mu D, Krainer AR. The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nature structural & molecular biology 2007; 14:185-93. (Pubitemid 46355578)
128. Karni R, Hippo Y, Lowe SW, Krainer AR. The splicing- factor oncoprotein SF2/ASF activates mTORC1. Proceedings of the National Academy of Sciences of the United States of America 2008; 105:15323-7.
129. Venables JP, Klinck R, Koh C, Gervais-Bird J, Bramard A, Inkel L, et al. Cancer-associated regulation of alternative splicing. Nature structural & molecular biology 2009; 16:670-6.
130. Shevtsov SP, Dundr M. Nucleation of nuclear bodies by RNA. Nat Cell Biol 2011; 13:167-73.
131. Bond CS, Fox AH. Paraspeckles: nuclear bodies built on long noncoding RNA. The Journal of cell biology 2009; 186:637-44.
132. nrb forms a heterodimer with PSP1 that localizes to paraspeckles in an RNA-dependent manner. Molecular biology of the cell 2005; 16:5304-15.
133. Fox AH, Lam YW, Leung AK, Lyon CE, Andersen J, Mann M, et al. Paraspeckles: a novel nuclear domain. Curr Biol 2002; 12:13-25. (Pubitemid 34063349)
134. Fox AH, Lamond AI. Paraspeckles. Cold Spring Harbor perspectives in biology 2010; 2:687.
135. Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM, Bennett CF, et al. Regulating gene expression through RNA nuclear retention. Cell 2005; 123:249-63. (Pubitemid 41457215)
136. Chen LL, DeCerbo JN, Carmichael GG. Alu element- mediated gene silencing. The EMBO journal 2008; 27:1694-705.
137. Mao YS, Sunwoo H, Zhang B, Spector DL. Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat Cell Biol 2011; 13:95-101.
138. Nakagawa S, Naganuma T, Shioi G, Hirose T. Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. The Journal of cell biology 2011; 193:31-9.
139. Lakhotia SC. The non-coding, developmentally active and stress inducible hsrw gene of Drosophila melanogaster integrates post-transcriptional processing of other nuclear transcripts. Georgetown, TX: Kluwer Acdemic/Plenum Publishers 2003.
140. Mutsuddi M, Lakhotia SC. Spatial expression of the hsr-omega (93D) gene in different tissues of Drosophila melanogaster and identification of promoter elements controlling its developmental expression. Dev Genet 1995; 17:303-11. (Pubitemid 26043679)
141. Prasanth KV, Rajendra TK, Lal AK, Lakhotia SC. Omega speckles - a novel class of nuclear speckles containing hnRNPs associated with noncoding hsromega RNA in Drosophila. Journal of cell science 2000; 113:3485-97.
142. Denegri M, Chiodi I, Corioni M, Cobianchi F, Riva S, Biamonti G. Stress-induced nuclear bodies are sites of accumulation of pre-mRNA processing factors. Molecular biology of the cell 2001; 12:3502-14. (Pubitemid 33108482)
143. Denegri M, Moralli D, Rocchi M, Biggiogera M, Raimondi E, Cobianchi F, et al. Human chromosomes 9, 12 and 15 contain the nucleation sites of stress-induced nuclear bodies. Molecular biology of the cell 2002; 13:2069-79. (Pubitemid 34651493)
144. Chiodi I, Biggiogera M, Denegri M, Corioni M, Weighardt F, Cobianchi F, et al. Structure and dynamics of hnRNP-labelled nuclear bodies induced by stress treatments. Journal of cell science 2000; 113:4043-53. (Pubitemid 32194529)
145. Jolly C, Metz A, Govin J, Vigneron M, Turner BM, Khochbin S, et al. Stress-induced transcription of satellite III repeats. The Journal of cell biology 2004; 164:25-33. (Pubitemid 38082454)
146. Jolly C, Lakhotia SC. Human sat III and Drosophila hsr{omega} transcripts: a common paradigm for regulation of nuclear RNA processing in stressed cells. Nucleic acids research 2006.
147. Wilusz JE, Freier SM, Spector DL. 3′ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 2008; 135:919-32.