The building process of the functional paraspeckle with long non-coding RNAs

Frontiers in Bioscience - Elite

Volumn 7E, Issue 1, 2015, Pages 1-47

  Yamazaki, Tomohiro ^a   Hirose, Tetsuro ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Long noncoding RNA; NEAT1 lncRNA; Neurodegenerative diseases; Nuclear body; Paraspeckle; Prion like domain; Review

Indexed keywords

DROSOPHILA MELANOGASTER BEHAVIOR HUMAN SPLICING PROTEIN; FET PROTEIN; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; LONG UNTRANSLATED RNA; NUCLEAR PARASPECKLE ASSEMBLY TRANSCRIPT 1 PROTEIN; RNA BINDING MOTIF PROTEIN; RNA BINDING PROTEIN; TET PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; ANNEXIN; ANNEXIN A10; CELL PROTEIN; CYTOCHROME B; CYTOCHROME B245; DROSOPHILA BEHAVIOR HUMAN SPLICING PROTEIN; DROSOPHILA PROTEIN; ECTOGRANULOMATOUS DISULFIDE THIOL EXCHANGER 1; LAMIN B; LAMIN B2; NUCLEAR PARASPECKLE ASSEMBLY TRANSCRIPT 1; NUCLEAR STRESS BODY; PROTEASOME; PROTEIN SH2; UBIQUITIN; NEAT1 LONG NON-CODING RNA, HUMAN; NUCLEAR PROTEIN; PSPC1 PROTEIN, HUMAN;

3' UNTRANSLATED REGION; ALTERNATIVE RNA SPLICING; ALZHEIMER DISEASE; CELL NUCLEUS INCLUSION BODY; CELL STRUCTURE; DEMENTIA; GENE EXPRESSION; GENE SILENCING; NONHUMAN; NUCLEAR LOCALIZATION SIGNAL; NUCLEAR STRESS BODY; NUCLEOLAR DETENTION CENTER; PARASPECKLE; POLYADENYLATION; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; REVIEW; RNA SEQUENCE; RNA STRUCTURE; SUMOYLATION; UBIQUITINATION; VIRUS INFECTION; CELL FUNCTION; CELL MATURATION; FETUS DISEASE; FRONTOTEMPORAL DEMENTIA; HUMAN; PATHOGENESIS; SIGNAL TRANSDUCTION; ANIMAL; CELL NUCLEUS; METABOLISM;

MAMMALIA;

ANIMALS; CELL NUCLEUS; HUMANS; NUCLEAR PROTEINS; RNA, LONG NONCODING; RNA-BINDING PROTEINS;

EID: 84918836602     PISSN: 19450494     EISSN: 19450508     Source Type: Journal    
DOI: 10.2741/E715     Document Type: Review

References (316)

1. P. Bertone, V. Stolc, T. E. Royce, J. S. Rozowsky, A. E. Urban, X. Zhu, J. L. Rinn, W. Tongprasit, M. Samanta, S. Weissman, M. Gerstein and M. Snyder: Global identification of human transcribed sequences with genome tiling arrays. Science, 306(5705), 2242-6 (2004) DOI: 10.1126/science.1103388
2. P. Carninci, T. Kasukawa, S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. E. Allen, A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, L. Baxter, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, Y. Hayashi, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. Krishnan, A. Kruger, S. K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, D. Lazarevic, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, G. Pesole, N. Petrovsky, S. Piazza, J. Reed, J. F. Reid, B. Z. Ring, M. Ringwald, B. Rost, Y. Ruan, S. L. Salzberg, A. Sandelin, C. Schneider, C. Schönbach, K. Sekiguchi, C. A. Semple, S. Seno, L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada, D. Silva, B. Sinclair, S. Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka, K. Taki, K. Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, H. R. Ueda, E. van Nimwegen, R. Verardo, C. L. Wei, K. Yagi, H. Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S. M. Grimmond, R. D. Teasdale, E. T. Liu, V. Brusic, J. Quackenbush, C. Wahlestedt, J. S. Mattick, D. A. Hume, C. Kai, D. Sasaki, Y. Tomaru, S. Fukuda, M. Kanamori-Katayama, M. Suzuki, J. Aoki, T. Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji, N. Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. Suzuki, M. Tagami, K. Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. Kawai, Y. Hayashizaki, F. Consortium and R. G. E. R. G. a. G. S. G. G. N. P. C. Group): The transcriptional landscape of the mammalian genome. Science, 309(5740), 1559-63 (2005) DOI: 10.1126/science.1112014
3. Z. Cheng, M. Ventura, X. She, P. Khaitovich, T. Graves, K. Osoegawa, D. Church, P. DeJong, R. K. Wilson, S. Pääbo, M. Rocchi and E. E. Eichler: A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature, 437(7055), 88-93 (2005) DOI: 10.1038/nature04000
4. S. Katayama, Y. Tomaru, T. Kasukawa, K. Waki, M. Nakanishi, M. Nakamura, H. Nishida, C. C. Yap, M. Suzuki, J. Kawai, H. Suzuki, P. Carninci, Y. Hayashizaki, C. Wells, M. Frith, T. Ravasi, K. C. Pang, J. Hallinan, J. Mattick, D. A. Hume, L. Lipovich, S. Batalov, P. G. Engström, Y. Mizuno, M. A. Faghihi, A. Sandelin, A. M. Chalk, S. Mottagui-Tabar, Z. Liang, B. Lenhard, C. Wahlestedt, R. G. E. R. Group, G. S. G. G. N. P. C. Group) and F. Consortium: Antisense transcription in the mammalian transcriptome. Science, 309(5740), 1564-6 (2005) DOI: 10.1126/science.1112009
5. E. Birney, J. A. Stamatoyannopoulos, A. Dutta, R. Guigó, T. R. Gingeras, E. H. Margulies, Z. Weng, M. Snyder, E. T. Dermitzakis, R. E. Thurman, M. S. Kuehn, C. M. Taylor, S. Neph, C. M. Koch, S. Asthana, A. Malhotra, I. Adzhubei, J. A. Greenbaum, R. M. Andrews, P. Flicek, P. J. Boyle, H. Cao, N. P. Carter, G. K. Clelland, S. Davis, N. Day, P. Dhami, S. C. Dillon, M. O. Dorschner, H. Fiegler, P. G. Giresi, J. Goldy, M. Hawrylycz, A. Haydock, R. Humbert, K. D. James, B. E. Johnson, E. M. Johnson, T. T. Frum, E. R. Rosenzweig, N. Karnani, K. Lee, G. C. Lefebvre, P. A. Navas, F. Neri, S. C. Parker, P. J. Sabo, R. Sandstrom, A. Shafer, D. Vetrie, M. Weaver, S. Wilcox, M. Yu, F. S. Collins, J. Dekker, J. D. Lieb, T. D. Tullius, G. E. Crawford, S. Sunyaev, W. S. Noble, I. Dunham, F. Denoeud, A. Reymond, P. Kapranov, J. Rozowsky, D. Zheng, R. Castelo, A. Frankish, J. Harrow, S. Ghosh, A. Sandelin, I. L. Hofacker, R. Baertsch, D. Keefe, S. Dike, J. Cheng, H. A. Hirsch, E. A. Sekinger, J. Lagarde, J. F. Abril, A. Shahab, C. Flamm, C. Fried, J. Hackermüller, J. Hertel, M. Lindemeyer, K. Missal, A. Tanzer, S. Washietl, J. Korbel, O. Emanuelsson, J. S. Pedersen, N. Holroyd, R. Taylor, D. Swarbreck, N. Matthews, M. C. Dickson, D. J. Thomas, M. T. Weirauch, J. Gilbert, J. Drenkow, I. Bell, X. Zhao, K. G. Srinivasan, W. K. Sung, H. S. Ooi, K. P. Chiu, S. Foissac, T. Alioto, M. Brent, L. Pachter, M. L. Tress, A. Valencia, S. W. Choo, C. Y. Choo, C. Ucla, C. Manzano, C. Wyss, E. Cheung, T. G. Clark, J. B. Brown, M. Ganesh, S. Patel, H. Tammana, J. Chrast, C. N. Henrichsen, C. Kai, J. Kawai, U. Nagalakshmi, J. Wu, Z. Lian, J. Lian, P. Newburger, X. Zhang, P. Bickel, J. S. Mattick, P. Carninci, Y. Hayashizaki, S. Weissman, T. Hubbard, R. M. Myers, J. Rogers, P. F. Stadler, T. M. Lowe, C. L. Wei, Y. Ruan, K. Struhl, M. Gerstein, S. E. Antonarakis, Y. Fu, E. D. Green, U. Karaöz, A. Siepel, J. Taylor, L. A. Liefer, K. A. Wetterstrand, P. J. Good, E. A. Feingold, M. S. Guyer, G. M. Cooper, G. Asimenos, C. N. Dewey, M. Hou, S. Nikolaev, J. I. Montoya-Burgos, A. Löytynoja, S. Whelan, F. Pardi, T. Massingham, H. Huang, N. R. Zhang, I. Holmes, J. C. Mullikin, A. Ureta-Vidal, B. Paten, M. Seringhaus, D. Church, K. Rosenbloom, W. J. Kent, E. A. Stone, S. Batzoglou, N. Goldman, R. C. Hardison, D. Haussler, W. Miller, A. Sidow, N. D. Trinklein, Z. D. Zhang, L. Barrera, R. Stuart, D. C. King, A. Ameur, S. Enroth, M. C. Bieda, J. Kim, A. A. Bhinge, N. Jiang, J. Liu, F. Yao, V. B. Vega, C. W. Lee, P. Ng, A. Yang, Z. Moqtaderi, Z. Zhu, X. Xu, S. Squazzo, M. J. Oberley, D. Inman, M. A. Singer, T. A. Richmond, K. J. Munn, A. Rada-Iglesias, O. Wallerman, J. Komorowski, J. C. Fowler, P. Couttet, A. W. Bruce, O. M. Dovey, P. D. Ellis, C. F. Langford, D. A. Nix, G. Euskirchen, S. Hartman, A. E. Urban, P. Kraus, S. Van Calcar, N. Heintzman, T. H. Kim, K. Wang, C. Qu, G. Hon, R. Luna, C. K. Glass, M. G. Rosenfeld, S. F. Aldred, S. J. Cooper, A. Halees, J. M. Lin, H. P. Shulha, M. Xu, J. N. Haidar, Y. Yu, V. R. Iyer, R. D. Green, C. Wadelius, P. J. Farnham, B. Ren, R. A. Harte, A. S. Hinrichs, H. Trumbower, H. Clawson, J. Hillman-Jackson, A. S. Zweig, K. Smith, A. Thakkapallayil, G. Barber, R. M. Kuhn, D. Karolchik, L. Armengol, C. P. Bird, P. I. de Bakker, A. D. Kern, N. Lopez-Bigas, J. D. Martin, B. E. Stranger, A. Woodroffe, E. Davydov, A. Dimas, E. Eyras, I. B. Hallgrímsdóttir, J. Huppert, M. C. Zody, G. R. Abecasis, X. Estivill, G. G. Bouffard, X. Guan, N. F. Hansen, J. R. Idol, V. V. Maduro, B. Maskeri, J. C. McDowell, M. Park, P. J. Thomas, A. C. Young, R. W. Blakesley, D. M. Muzny, E. Sodergren, D. A. Wheeler, K. C. Worley, H. Jiang, G. M. Weinstock, R. A. Gibbs, T. Graves, R. Fulton, E. R. Mardis, R. K. Wilson, M. Clamp, J. Cuff, S. Gnerre, D. B. Jaffe, J. L. Chang, K. Lindblad-Toh, E. S. Lander, M. Koriabine, M. Nefedov, K. Osoegawa, Y. Yoshinaga, B. Zhu, P. J. de Jong, E. P. Consortium, N. C. S. Program, B. C. o. M. H. G. S. Center, W. U. G. S. Center, B. Institute and C. s. H. O. R. Institute: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146), 799-816 (2007) DOI: 10.1038/nature05874
6. P. Kapranov, J. Cheng, S. Dike, D. A. Nix, R. Duttagupta, A. T. Willingham, P. F. Stadler, J. Hertel, J. Hackermüller, I. L. Hofacker, I. Bell, E. Cheung, J. Drenkow, E. Dumais, S. Patel, G. Helt, M. Ganesh, S. Ghosh, A. Piccolboni, V. Sementchenko, H. Tammana and T. R. Gingeras: RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316(5830), 1484-8 (2007) DOI: 10.1126/science.1138341
7. T. Hirose, Y. Mishima and Y. Tomari: Elements and machinery of non-coding RNAs: toward their taxonomy. EMBO Rep, 15(5), 489-507 (2014) DOI: 10.1002/embr.201338390
8. T. R. Cech and J. A. Steitz: The noncoding RNA revolution-trashing old rules to forge new ones. Cell, 157(1), 77-94 (2014) DOI: 10.1016/j.cell.2014.03.008
9. I. Ulitsky and D. P. BarTel: lincRNAs: genomics, evolution, and mechanisms. Cell, 154(1), 26-46 (2013) DOI: 10.1016/j.cell.2013.06.020
10. M. N. Cabili, C. Trapnell, L. Goff, M. Koziol, B. Tazon-Vega, A. Regev and J. L. Rinn: Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev, 25(18), 1915-27 (2011) DOI: 10.1101/gad.17446611
11. T. Derrien, R. Johnson, G. Bussotti, A. Tanzer, S. Djebali, H. Tilgner, G. Guernec, D. Martin, A. Merkel, D. G. Knowles, J. Lagarde, L. Veeravalli, X. Ruan, Y. Ruan, T. Lassmann, P. Carninci, J. B. Brown, L. Lipovich, J. M. Gonzalez, M. Thomas, C. A. Davis, R. Shiekhattar, T. R. Gingeras, T. J. Hubbard, C. Notredame, J. Harrow and R. Guigó: The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res, 22(9), 1775-89 (2012) DOI: 10.1101/gr.132159.111
12. K. V. Prasanth and D. L. Spector: Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev, 21(1), 11-42 (2007) DOI: 10.1101/gad.1484207
13. O. Yazgan and J. E. Krebs: Noncoding but nonexpendable: transcriptional regulation by large noncoding RNA in eukaryotes. Biochem Cell Biol, 85(4), 484-96 (2007) DOI: 10.1139/O07-061
14. R. Kurokawa, M. G. Rosenfeld and C. K. Glass: Transcriptional regulation through noncoding RNAs and epigenetic modifications. RNA Biol, 6(3), 233-6 (2009) DOI: 10.4161/rna.6.3.8329
15. J. E. Wilusz, H. Sunwoo and D. L. Spector: Long noncoding RNAs: functional surprises from the RNA world. Genes Dev, 23(13), 1494-504 (2009) DOI: 10.1101/gad.1800909
16. L. L. Chen and G. G. Carmichael: Decoding the function of nuclear long non-coding RNAs. Curr Opin Cell Biol, 22(3), 357-64 (2010) DOI: 10.1016/j.ceb.2010.03.003
17. X. Wang, X. Song, C. K. Glass and M. G. Rosenfeld: The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs. Cold Spring Harb Perspect Biol, 3(1), a003756 (2011) DOI: 10.1101/cshperspect.a003756
18. M. B. Clark and J. S. Mattick: Long noncoding RNAs in cell biology. Semin Cell Dev Biol, 22(4), 366-76 (2011) DOI: 10.1016/j.semcdb.2011.01.001
19. J. T. Lee: The X as model for RNA's niche in epigenomic regulation. Cold Spring Harb Perspect Biol, 2(9), a003749 (2010) DOI: 10.1101/cshperspect.a003749
20. J. T. Lee: Epigenetic regulation by long noncoding RNAs. Science, 338(6113), 1435-9 (2012) DOI: 10.1126/science.1231776
21. J. L. Rinn, M. Kertesz, J. K. Wang, S. L. Squazzo, X. Xu, S. A. Brugmann, L. H. Goodnough, J. A. Helms, P. J. Farnham, E. Segal and H. Y. Chang: Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 129(7), 1311-23 (2007) DOI: 10.1016/j.cell.2007.05.022
22. M. Sone, T. Hayashi, H. Tarui, K. Agata, M. Takeichi and S. Nakagawa: The mRNAlike noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci, 120(Pt 15), 2498-506 (2007) DOI: 10.1242/jcs.009357
23. J. Y. Ip and S. Nakagawa: Long noncoding RNAs in nuclear bodies. Dev Growth Differ, 54(1), 44-54 (2012) DOI: 10.1111/j.1440-169X.2011.01303.x
24. H. Tsuiji, R. Yoshimoto, Y. Hasegawa, M. Furuno, M. Yoshida and S. Nakagawa: Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1. Genes Cells, 16(5), 479-90 (2011) DOI: 10.1111/j.1365-2443.2011.01502.x
25. G. Barry, J. A. Briggs, D. P. Vanichkina, E. M. Poth, N. J. Beveridge, V. S. Ratnu, S. P. Nayler, K. Nones, J. Hu, T. W. Bredy, S. Nakagawa, F. Rigo, R. J. Taft, M. J. Cairns, S. Blackshaw, E. J. Wolvetang and J. S. Mattick: The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Mol Psychiatry, 19(4), 486-94 (2014) DOI: 10.1038/mp.2013.45
26. J. N. Hutchinson, A. W. Ensminger, C. M. Clemson, C. R. Lynch, J. B. Lawrence and A. Chess: A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics, 8, 39 (2007) DOI: 10.1186/1471-2164-8-39
27. V. Tripathi, J. D. Ellis, Z. Shen, D. Y. Song, Q. Pan, A. T. Watt, S. M. Freier, C. F. Bennett, A. Sharma, P. A. Bubulya, B. J. Blencowe, S. G. Prasanth and K. V. Prasanth: The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell, 39(6), 925-38 (2010) DOI: 10.1016/j.molcel.2010.08.011
28. B. Zhang, G. Arun, Y. S. Mao, Z. Lazar, G. Hung, G. Bhattacharjee, X. Xiao, C. J. Booth, J. Wu, C. Zhang and D. L. Spector: The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep, 2(1), 111-23 (2012) DOI: 10.1016/j.celrep.2012.06.003
29. S. Nakagawa, J. Y. Ip, G. Shioi, V. Tripathi, X. Zong, T. Hirose and K. V. Prasanth: Malat1 is not an essential component of nuclear speckles in mice. RNA, 18(8), 1487-99 (2012) DOI: 10.1261/rna.033217.112
30. T. Gutschner, M. Hämmerle, M. Eissmann, J. Hsu, Y. Kim, G. Hung, A. Revenko, G. Arun, M. Stentrup, M. Gross, M. Zörnig, A. R. MacLeod, D. L. Spector and S. Diederichs: The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res, 73(3), 1180-9 (2013) DOI: 10.1158/0008-5472.CAN-12-2850
31. M. Dundr and T. Misteli: Biogenesis of nuclear bodies. Cold Spring Harb Perspect Biol, 2(12), a000711 (2010) DOI: 10.1101/cshperspect.a000711
32. Y. S. Mao, B. Zhang and D. L. Spector: Biogenesis and function of nuclear bodies. Trends Genet, 27(8), 295-306 (2011) DOI: 10.1016/j.tig.2011.05.006
33. S. Boulon, B. J. Westman, S. Hutten, F. M. Boisvert and A. I. Lamond: The nucleolus under stress. Mol Cell, 40(2), 216-27 (2010) DOI: 10.1016/j.molcel.2010.09.024
34. T. Pederson: The nucleolus. Cold Spring Harb Perspect Biol, 3(3) (2011) DOI: 10.1101/cshperspect.a000638
35. C. Pollock and S. Huang: The perinucleolar compartment. Cold Spring Harb Perspect Biol, 2(2), a000679 (2010) DOI: 10.1101/cshperspect.a000679
36. A. I. Lamond and D. L. Spector: Nuclear speckles: a model for nuclear organelles. Nat Rev Mol Cell Biol, 4(8), 605-12 (2003) DOI: 10.1038/nrm1172
37. D. L. Spector and A. I. Lamond: Nuclear speckles. Cold Spring Harb Perspect Biol, 3(2) (2011) DOI: 10.1101/cshperspect.a000646
38. W. F. Marzluff, E. J. Wagner and R. J. Duronio: Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat Rev Genet, 9(11), 843-54 (2008) DOI: 10.1038/nrg2438
39. Z. F. Nizami, S. Deryusheva and J. G. Gall: Cajal bodies and histone locus bodies in Drosophila and Xenopus. Cold Spring Harb Symp Quant Biol, 75, 313-20 (2010) DOI: 10.1101/sqb.2010.75.005
40. V. Lallemand-Breitenbach and H. de Thé: PML nuclear bodies. Cold Spring Harb Perspect Biol, 2(5), a000661 (2010) DOI: 10.1101/cshperspect.a000661
41. M. Cioce and A. I. Lamond: Cajal bodies: a long history of discovery. Annu Rev Cell Dev Biol, 21, 105-31 (2005) DOI: 10.1146/annurev.cellbio.20.010403.103738
42. S. Paushkin, A. K. Gubitz, S. Massenet and G. Dreyfuss: The SMN complex, an assemblyosome of ribonucleoproteins. Curr Opin Cell Biol, 14(3), 305-12 (2002) DOI: 10.1016/S0955-0674(02)00332-0
43. A. K. Gubitz, W. Feng and G. Dreyfuss: The SMN complex. Exp Cell Res, 296(1), 51-6 (2004) DOI: 10.1016/j.yexcr.2004.03.022
44. D. J. Battle, M. Kasim, J. Yong, F. Lotti, C. K. Lau, J. Mouaikel, Z. Zhang, K. Han, L. Wan and G. Dreyfuss: The SMN complex: an assembly machine for RNPs. Cold Spring Harb Symp Quant Biol, 71, 313-20 (2006) DOI: 10.1101/sqb.2006.71.001
45. M. Carmo-Fonseca, M. T. Berciano and M. Lafarga: Orphan nuclear bodies. Cold Spring Harb Perspect Biol, 2(9), a000703 (2010) DOI: 10.1101/cshperspect.a000703
46. G. Biamonti and C. Vourc'h: Nuclear stress bodies. Cold Spring Harb Perspect Biol, 2(6), a000695 (2010) DOI: 10.1101/cshperspect.a000695
47. A. M. Dupuy-Coin, S. R. Kalifat and M. Bouteille: Nuclear bodies as proteinaceous structures containing ribonucleoproteins. J Ultrastruct Res, 38(1), 174-87 (1972) DOI: 10.1016/S0022-5320(72)90091-3
48. T. Kawaguchi and T. Hirose: Architectural roles of long noncoding RNAs in the intranuclear formation of functional paraspeckles. Front Biosci (Landmark Ed), 17, 1729-46 (2012) DOI: 10.2741/4015
49. A. H. Fox, Y. W. Lam, A. K. Leung, C. E. Lyon, J. Andersen, M. Mann and A. I. Lamond: Paraspeckles: a novel nuclear domain. Curr Biol, 12(1), 13-25 (2002) DOI: 10.1016/S0960-9822(01)00632-7
50. C. S. Bond and A. H. Fox: Paraspeckles: nuclear bodies built on long noncoding RNA. J Cell Biol, 186(5), 637-44 (2009) DOI: 10.1083/jcb.200906113
51. A. H. Fox and A. I. Lamond: Paraspeckles. Cold Spring Harb Perspect Biol, 2(7), a000687 (2010) DOI: 10.1101/cshperspect.a000687
52. N. Visa, F. Puvion-Dutilleul, J. P. Bachellerie and E. Puvion: Intranuclear distribution of U1 and U2 snRNAs visualized by high resolution in situ hybridization: revelation of a novel compartment containing U1 but not U2 snRNA in HeLa cells. Eur J Cell Biol, 60(2), 308-21 (1993)
53. S. Souquere, G. Beauclair, F. Harper, A. Fox and G. Pierron: Highly ordered spatial organization of the structural long noncoding NEAT1 RNAs within paraspeckle nuclear bodies. Mol Biol Cell, 21(22), 4020-7 (2010) DOI: 10.1091/mbc.E10-08-0690
54. A. H. Fox, C. S. Bond and A. I. Lamond: P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in an RNA-dependent manner. Mol Biol Cell, 16(11), 5304-15 (2005) DOI: 10.1091/mbc.E05-06-0587
55. Y. T. Sasaki, T. Ideue, M. Sano, T. Mituyama and T. Hirose: MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci U S A, 106(8), 2525-30 (2009) DOI: 10.1073/pnas.0807899106
56. L. L. Chen and G. G. Carmichael: Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell, 35(4), 467-78 (2009) DOI: 10.1016/j.molcel.2009.06.027
57. C. M. Clemson, J. N. Hutchinson, S. A. Sara, A. W. Ensminger, A. H. Fox, A. Chess and J. B. Lawrence: An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell, 33(6), 717-26 (2009) DOI: 10.1016/j.molcel.2009.01.026
58. H. Sunwoo, M. E. Dinger, J. E. Wilusz, P. P. Amaral, J. S. Mattick and D. L. Spector: MEN epsilon/beta nuclear-retained noncoding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res, 19(3), 347-59 (2009) DOI: 10.1101/gr.087775.108
59. S. C. Guru, S. K. Agarwal, P. Manickam, S. E. Olufemi, J. S. Crabtree, J. M. Weisemann, M. B. Kester, Y. S. Kim, Y. Wang, M. R. Emmert-Buck, L. A. Liotta, A. M. Spiegel, M. S. Boguski, B. A. Roe, F. S. Collins, S. J. Marx, L. Burns and S. C. Chandrasekharappa: A transcript map for the 2.8.-Mb region containing the multiple endocrine neoplasia type 1 locus. Genome Res, 7(7), 725-35 (1997)
60. J. A. Peyman: Repression of major histocompatibility complex genes by a human trophoblast ribonucleic acid. Biol Reprod, 60(1), 23-31 (1999) DOI: 10.1095/biolreprod60.1.23
61. A. Geirsson, R. J. Lynch, I. Paliwal, A. L. Bothwell and G. L. Hammond: Human trophoblast noncoding RNA suppresses CIITA promoter III activity in murine B-lymphocytes. Biochem Biophys Res Commun, 301(3), 718-24 (2003) DOI: 10.1016/S0006-291X(03)00028-7
62. S. Saha, P. Sugumar, P. Bhandari and P. N. Rangarajan: Identification of Japanese encephalitis virus-inducible genes in mouse brain and characterization of GARG39/IFIT2 as a microtubuleassociated protein. J Gen Virol, 87(Pt 11), 3285-9 (2006) DOI: 10.1099/vir.0.82107-0
63. P. F. Stadler: Evolution of the Long Noncoding RNAs MALAT1 and MENβ/ε. In: Advances in Bioinformatics and Computational Biology, 1-12. Eds: BSB 2010, LNBI6268 (2010)
64. Y. T. Sasaki and T. Hirose: How to build a paraspeckle. Genome Biol, 10(7), 227 (2009) DOI: 10.1186/gb-2009-10-7-227
65. T. Naganuma, S. Nakagawa, A. Tanigawa, Y. F. Sasaki, N. Goshima and T. Hirose: Alternative 3'-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. EMBO J, 31(20), 4020-34 (2012) DOI: 10.1038/emboj.2012.251
66. T. Naganuma and T. Hirose: Paraspeckle formation during the biogenesis of long non-coding RNAs. RNA Biol, 10(3), 456-61 (2013) DOI: 10.4161/rna.23547
67. K. T. Tycowski, M. D. Shu, S. Borah, M. Shi and J. A. Steitz: Conservation of a triple-helix-forming RNA stability element in noncoding and genomic RNAs of diverse viruses. Cell Rep, 2(1), 26-32 (2012) DOI: 10.1016/j.celrep.2012.05.020
68. J. E. Wilusz, C. K. JnBaptiste, L. Y. Lu, C. D. Kuhn, L. Joshua-Tor and P. A. Sharp: A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails. Genes Dev, 26(21), 2392-407 (2012) DOI: 10.1101/gad.204438.112
69. J. A. Brown, M. L. Valenstein, T. A. Yario, K. T. Tycowski and J. A. Steitz: Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MENinnodatabeta noncoding RNAs. Proc Natl Acad Sci U S A, 109(47), 19202-7 (2012) DOI: 10.1073/pnas.1217338109
70. J. A. Brown, D. Bulkley, J. Wang, M. L. Valenstein, T. A. Yario, T. A. Steitz and J. A. Steitz: Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. Nat Struct Mol Biol, 21(7), 633-40 (2014) DOI: 10.1038/nsmb.2844
71. J. E. Wilusz, J. M. Whipple, E. M. Phizicky and P. A. Sharp: tRNAs marked with CCACCA are targeted for degradation. Science, 334(6057), 817-21 (2011) DOI: 10.1126/science.1213671
72. M. B. Clark, R. L. Johnston, M. Inostroza-Ponta, A. H. Fox, E. Fortini, P. Moscato, M. E. Dinger and J. S. Mattick: Genome-wide analysis of long noncoding RNA stability. Genome Res, 22(5), 885-98 (2012) DOI: 10.1101/gr.131037.111
73. Y. B. Beaulieu, C. L. Kleinman, A. M. Landry-Voyer, J. Majewski and F. Bachand: Polyadenylation-dependent control of long noncoding RNA expression by the poly(A)-binding protein nuclear 1. PLoS Genet, 8(11), e1003078 (2012) DOI: 10.1371/journal.pgen.1003078
74. S. M. Bresson and N. K. Conrad: The human nuclear poly(a)-binding protein promotes RNA hyperadenylation and decay. PLoS Genet, 9(10), e1003893 (2013) DOI: 10.1371/journal.pgen.1003893
75. L. Jobert, N. Pinzón, E. Van Herreweghe, B. E. Jády, A. Guialis, T. Kiss and L. Tora: Human U1 snRNA forms a new chromatin-associated snRNP with TAF15. EMBO Rep, 10(5), 494-500 (2009) DOI: 10.1038/embor.2009.24
76. K. V. Prasanth, S. G. Prasanth, Z. Xuan, S. Hearn, S. M. Freier, C. F. Bennett, M. Q. Zhang and D. L. Spector: Regulating gene expression through RNA nuclear retention. Cell, 123(2), 249-63 (2005) DOI: 10.1016/j.cell.2005.08.033
77. S. Nakagawa, T. Naganuma, G. Shioi and T. Hirose: Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. J Cell Biol, 193(1), 31-9 (2011) DOI: 10.1083/jcb.201011110
78. S. Dettwiler, C. Aringhieri, S. Cardinale, W. Keller and S. M. Barabino: Distinct sequence motifs within the 68-kDa subunit of cleavage factor Im mediate RNA binding, protein-protein interactions, and subcellular localization. J Biol Chem, 279(34), 35788-97 (2004) DOI: 10.1074/jbc.M403927200
79. K. W. Fong, Y. Li, W. Wang, W. Ma, K. Li, R. Z. Qi, D. Liu, Z. Songyang and J. Chen: Whole-genome screening identifies proteins localized to distinct nuclear bodies. J Cell Biol, 203(1), 149-64 (2013) DOI: 10.1083/jcb.201303145
80. N. Quiskamp, M. Poeter, C. A. Raabe, U. M. Hohenester, S. König, V. Gerke and U. Rescher: The tumor suppressor annexin A10 is a novel component of nuclear paraspeckles. Cell Mol Life Sci, 71(2), 311-29 (2014) DOI: 10.1007/s00018-013-1375-4
81. W. J. Law, K. L. Cann and G. G. Hicks: TLS, EWS and TAF15: a model for transcriptional integration of gene expression. Brief Funct Genomic Proteomic, 5(1), 8-14 (2006) DOI: 10.1093/bfgp/ell015
82. N. Kim, P. Kim, S. Nam, S. Shin and S. Lee: ChimerDB - a knowledgebase for fusion sequences. Nucleic Acids Res, 34(Database issue), D21-4 (2006) DOI: 10.1093/nar/gkj019
83. P. Kim, S. Yoon, N. Kim, S. Lee, M. Ko, H. Lee, H. Kang and J. Kim: ChimerDB 2.0. - a knowledgebase for fusion genes updated. Nucleic Acids Res, 38(Database issue), D81-5 (2010) DOI: 10.1093/nar/gkp982
84. P. Brandal, I. Panagopoulos, B. Bjerkehagen and S. Heim: t(19;22) (q13;q12) Translocation leading to the novel fusion gene EWSR1-ZNF444 in soft tissue myoepithelial carcinoma. Genes Chromosomes Cancer, 48(12), 1051-6 (2009) DOI: 10.1002/gcc.20706
85. L. Brandimarte, V. Pierini, D. Di Giacomo, C. Borga, F. Nozza, P. Gorello, M. Giordan, G. Cazzaniga, G. Te Kronnie, R. La Starza and C. Mecucci: New MLLT10 gene recombinations in pediatric T-acute lymphoblastic leukemia. Blood, 121(25), 5064-7 (2013) DOI: 10.1182/blood-2013-02-487256
86. C. Thomsen, P. Grundevik, P. Elias, A. Sta˚hlberg and P. Aman: A conserved N-terminal motif is required for complex formation between FUS, EWSR1, TAF15 and their oncogenic fusion proteins. FASEB J, 27(12), 4965-74 (2013) DOI: 10.1096/fj.13-234435
87. O. D. King, A. D. Gitler and J. Shorter: The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease. Brain Res, 1462, 61-80 (2012) DOI: 10.1016/j.brainres.2012.01.016
88. Y. Nishimoto, S. Nakagawa, T. Hirose, H. J. Okano, M. Takao, S. Shibata, S. Suyama, K. Kuwako, T. Imai, S. Murayama, N. Suzuki and H. Okano: The long noncoding RNA nuclear-enriched abundant transcript 1-2 induces paraspeckle formation in the motor neuron during the early phase of amyotrophic lateral sclerosis. Mol Brain, 6, 31 (2013) DOI: 10.1186/1756-6606-6-31
89. A. Chesi, B. T. Staahl, A. Jovičić, J. Couthouis, M. Fasolino, A. R. Raphael, T. Yamazaki, L. Elias, M. Polak, C. Kelly, K. L. Williams, J. A. Fifita, N. J. Maragakis, G. A. Nicholson, O. D. King, R. Reed, G. R. Crabtree, I. P. Blair, J. D. Glass and A. D. Gitler: Exome sequencing to identify de novo mutations in sporadic ALS trios. Nat Neurosci, 16(7), 851-5 (2013) DOI: 10.1038/nn.3412
90. S. C. Ling, M. Polymenidou and D. W. Cleveland: Converging mechanisms in ALS and FTD: disrupted RNA and protein homeostasis. Neuron, 79(3), 416-38 (2013) DOI: 10.1016/j.neuron.2013.07.033
91. Y. R. Li, O. D. King, J. Shorter and A. D. Gitler: Stress granules as crucibles of ALS pathogenesis. J Cell Biol, 201(3), 361-72 (2013) DOI: 10.1083/jcb.201302044
92. J. Couthouis, M. P. Hart, J. Shorter, M. DeJesus-Hernandez, R. Erion, R. Oristano, A. X. Liu, D. Ramos, N. Jethava, D. Hosangadi, J. Epstein, A. Chiang, Z. Diaz, T. Nakaya, F. Ibrahim, H. J. Kim, J. A. Solski, K. L. Williams, J. Mojsilovic-Petrovic, C. Ingre, K. Boylan, N. R. Graff-Radford, D. W. Dickson, D. Clay-Falcone, L. Elman, L. McCluskey, R. Greene, R. G. Kalb, V. M. Lee, J. Q. Trojanowski, A. Ludolph, W. Robberecht, P. M. Andersen, G. A. Nicholson, I. P. Blair, O. D. King, N. M. Bonini, V. Van Deerlin, R. Rademakers, Z. Mourelatos and A. D. Gitler: A yeast functional screen predicts new candidate ALS disease genes. Proc Natl Acad Sci U S A, 108(52), 20881-90 (2011) DOI: 10.1073/pnas.1109434108
93. M. Salton, Y. Lerenthal, S. Y. Wang, D. J. Chen and Y. Shiloh: Involvement of Matrin 3 and SFPQ/NONO in the DNA damage response. Cell Cycle, 9(8), 1568-76 (2010) DOI: 10.4161/cc.9.8.11298
94. K. Ha, Y. Takeda and W. S. Dynan: Sequences in PSF/SFPQ mediate radioresistance and recruitment of PSF/SFPQ-containing complexes to DNA damage sites in human cells. DNA Repair (Amst), 10(3), 252-9 (2011) DOI: 10.1016/j.dnarep.2010.11.009
95. X. Gao, L. Kong, X. Lu, G. Zhang, L. Chi, Y. Jiang, Y. Wu, C. Yan, P. Duerksen-Hughes, X. Zhu and J. Yang: Paraspeckle protein 1 (PSPC1) is involved in the cisplatin induced DNA damage response - role in G1/S checkpoint. PLoS One, 9(5), e97174 (2014) DOI: 10.1371/journal.pone.0097174
96. M. P. Paronetto, B. Miñana and J. Valcárcel: The Ewing sarcoma protein regulates DNA damage-induced alternative splicing. Mol Cell, 43(3), 353-68 (2011) DOI: 10.1016/j.molcel.2011.05.035
97. A. S. Mastrocola, S. H. Kim, A. T. Trinh, L. A. Rodenkirch and R. S. Tibbetts: The RNA-binding protein fused in sarcoma (FUS) functions downstream of poly(ADP-ribose) polymerase (PARP) in response to DNA damage. J Biol Chem, 288(34), 24731-41 (2013) DOI: 10.1074/jbc.M113.497974
98. W. Y. Wang, L. Pan, S. C. Su, E. J. Quinn, M. Sasaki, J. C. Jimenez, I. R. Mackenzie, E. J. Huang and L. H. Tsai: Interaction of FUS and HDAC1 regulates DNA damage response and repair in neurons. Nat Neurosci, 16(10), 1383-91 (2013) DOI: 10.1038/nn.3514
99. S. Jungmichel, F. Rosenthal, M. Altmeyer, J. Lukas, M. O. Hottiger and M. L. Nielsen: Proteome-wide identification of poly(ADP-Ribosyl) ation targets in different genotoxic stress responses. Mol Cell, 52(2), 272-85 (2013) DOI: 10.1016/j.molcel.2013.08.026
100. S. Britton, E. Dernoncourt, C. Delteil, C. Froment, O. Schiltz, B. Salles, P. Frit and P. Calsou: DNA damage triggers SAF-A and RNA biogenesis factors exclusion from chromatin coupled to R-loops removal. Nucleic Acids Res (2014) DOI: 10.1093/nar/gku601
101. H. Qiu, S. Lee, Y. Shang, W. Y. Wang, K. F. Au, S. Kamiya, S. J. Barmada, S. Finkbeiner, H. Lui, C. E. Carlton, A. A. Tang, M. C. Oldham, H. Wang, J. Shorter, A. J. Filiano, E. D. Roberson, W. G. Tourtellotte, B. Chen, L. H. Tsai and E. J. Huang: ALS-associated mutation FUSR521C causes DNA damage and RNA splicing defects. J Clin Invest, 124(3), 981-99 (2014) DOI: 10.1172/JCI72723
102. Q. Deng, C. J. Holler, G. Taylor, K. F. Hudson, W. Watkins, M. Gearing, D. Ito, M. E. Murray, D. W. Dickson, N. T. Seyfried and T. Kukar: FUS is phosphorylated by DNA-PK and accumulates in the cytoplasm after DNA damage. J Neurosci, 34(23), 7802-13 (2014) DOI: 10.1523/JNEUROSCI.0172-14.2014
103. J. Fei and J. Chen: KIAA1530 protein is recruited by Cockayne syndrome complementation group protein A (CSA) to participate in transcription-coupled repair (TCR). J Biol Chem, 287(42), 35118-26 (2012) DOI: 10.1074/jbc.M112.398131
104. P. Schwertman, A. Lagarou, D. H. Dekkers, A. Raams, A. C. van der Hoek, C. Laffeber, J. H. Hoeijmakers, J. A. Demmers, M. Fousteri, W. Vermeulen and J. A. Marteijn: UV-sensitive syndrome protein UVSSA recruits USP7 to regulate transcription-coupled repair. Nat Genet, 44(5), 598-602 (2012) DOI: 10.1038/ng.2230
105. X. Zhang, K. Horibata, M. Saijo, C. Ishigami, A. Ukai, S. Kanno, H. Tahara, E. G. Neilan, M. Honma, T. Nohmi, A. Yasui and K. Tanaka: Mutations in UVSSA cause UV-sensitive syndrome and destabilize ERCC6 in transcription-coupled DNA repair. Nat Genet, 44(5), 593-7 (2012) DOI: 10.1038/ng.2228
106. Y. Nakazawa, K. Sasaki, N. Mitsutake, M. Matsuse, M. Shimada, T. Nardo, Y. Takahashi, K. Ohyama, K. Ito, H. Mishima, M. Nomura, A. Kinoshita, S. Ono, K. Takenaka, R. Masuyama, T. Kudo, H. Slor, A. Utani, S. Tateishi, S. Yamashita, M. Stefanini, A. R. Lehmann, K. Yoshiura and T. Ogi: Mutations in UVSSA cause UV-sensitive syndrome and impair RNA polymerase IIo processing in transcriptioncoupled nucleotide-excision repair. Nat Genet, 44(5), 586-92 (2012) DOI: 10.1038/ng.2229
107. M. Yuan, C. G. Eberhart and M. Kai: RNA binding protein RBM14 promotes radio-resistance in glioblastoma by regulating DNA repair and cell differentiation. Oncotarget, 5(9), 2820-2826 (2014)
108. A. Moumen, P. Masterson, M. J. O'Connor and S. P. Jackson: hnRNP K: An HDM2 target and transcriptional coactivator of p53 in response to DNA damage. Cell, 123(6), 1065-1078 (2005) DOI: 10.1016/j.cell.2005.09.032
109. S. E. Polo, A. N. Blackford, J. R. Chapman, L. Baskcomb, S. Gravel, A. Rusch, A. Thomas, R. Blundred, P. Smith, J. Kzhyshkowska, T. Dobner, A. M. R. Taylor, A. S. Turnell, G. S. Stewart, R. J. Grand and S. P. Jackson: Regulation of DNA-End Resection by hnRNPU-like Proteins Promotes DNA Double-Strand Break Signaling and Repair. Molecular Cell, 45(4), 505-516 (2012) DOI: 10.1016/j.molcel.2011.12.035
110. B. Adamson, A. Smogorzewska, F. D. Sigoillot, R. W. King and S. J. Elledge: A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nature Cell Biology, 14(3), 318-328 (2012) DOI: 10.1038/ncb2426
111. T. Ozaki, A. Nakagawara and H. Nagase: RUNX Family Participates in the Regulation of p53-Dependent DNA Damage Response. International Journal of Genomics (2013) DOI: 10.1155/2013/271347
112. P. C. Hanawalt and G. Spivak: Transcription-coupled DNA repair: two decades of progress and surprises. Nature Reviews Molecular Cell Biology, 9(12), 958-970 (2008) DOI: 10.1038/nrm2549
113. D. Auboeuf, D. H. Dowhan, M. Dutertre, N. Martin, S. M. Berget and B. W. O'Malley: A subset of nuclear receptor coregulators act as coupling proteins during synthesis and maturation of RNA transcripts. Mol Cell Biol, 25(13), 5307-16 (2005) DOI: 10.1128/MCB.25.13.5307-5316.2005
114. S. Kim, J. Yamamoto, Y. Chen, M. Aida, T. Wada, H. Handa and Y. Yamaguchi: Evidence that cleavage factor Im is a heterotetrameric protein complex controlling alternative polyadenylation. Genes Cells, 15(9), 1003-13 (2010) DOI: 10.1111/j.1365-2443.2010.01436.x
115. A. R. Gruber, G. Martin, W. Keller and M. Zavolan: Cleavage factor Im is a key regulator of 3' UTR length. RNA Biol, 9(12), 1405-12 (2012) DOI: 10.4161/rna.22570
116. R. Myojin, S. Kuwahara, T. Yasaki, T. Matsunaga, T. Sakurai, M. Kimura, S. Uesugi and Y. Kurihara: Expression and functional significance of mouse paraspeckle protein 1 on spermatogenesis. Biol Reprod, 71(3), 926-32 (2004) DOI: 10.1095/biolreprod.104.028159
117. D. M. Passon, M. Lee, O. Rackham, W. A. Stanley, A. Sadowska, A. Filipovska, A. H. Fox and C. S. Bond: Structure of the heterodimer of human NONO and paraspeckle protein component 1 and analysis of its role in subnuclear body formation. Proc Natl Acad Sci U S A, 109(13), 4846-50 (2012) DOI: 10.1073/pnas.1120792109
118. B. T. Dye and J. G. Patton: An RNA recognition motif (RRM) is required for the localization of PTB-associated splicing factor (PSF) to subnuclear speckles. Exp Cell Res, 263(1), 131-44 (2001) DOI: 10.1006/excr.2000.5097
119. A. Emili, M. Shales, S. McCracken, W. Xie, P. W. Tucker, R. Kobayashi, B. J. Blencowe and C. J. Ingles: Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD. RNA, 8(9), 1102-11 (2002) DOI: 10.1017/S1355838202025037
120. S. Kameoka, P. Duque and M. M. Konarska: p54(nrb) associates with the 5' splice site within large transcription/splicing complexes. EMBO J, 23(8), 1782-91 (2004) DOI: 10.1038/sj.emboj.7600187
121. Z. Zhang and G. G. Carmichael: The fate of dsRNA in the nucleus: a p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell, 106(4), 465-75 (2001) DOI: 10.1016/S0092-8674(01)00466-4
122. I. R. Mackenzie and M. Neumann: FET proteins in frontotemporal dementia and amyotrophic lateral sclerosis. Brain Res, 1462, 40-3 (2012) DOI: 10.1016/j.brainres.2011.12.010
123. C. Vance, B. Rogelj, T. Hortobágyi, K. J. De Vos, A. L. Nishimura, J. Sreedharan, X. Hu, B. Smith, D. Ruddy, P. Wright, J. Ganesalingam, K. L. Williams, V. Tripathi, S. Al-Saraj, A. Al-Chalabi, P. N. Leigh, I. P. Blair, G. Nicholson, J. de Belleroche, J. M. Gallo, C. C. Miller and C. E. Shaw: Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6. Science, 323(5918), 1208-11 (2009) DOI: 10.1126/science.1165942
124. T. J. Kwiatkowski, D. A. Bosco, A. L. Leclerc, E. Tamrazian, C. R. Vanderburg, C. Russ, A. Davis, J. Gilchrist, E. J. Kasarskis, T. Munsat, P. Valdmanis, G. A. Rouleau, B. A. Hosler, P. Cortelli, P. J. de Jong, Y. Yoshinaga, J. L. Haines, M. A. Pericak-Vance, J. Yan, N. Ticozzi, T. Siddique, D. McKenna-Yasek, P. C. Sapp, H. R. Horvitz, J. E. Landers and R. H. Brown: Mutations in the FUS/TLS gene on chromosome 16 cause familial amyotrophic lateral sclerosis. Science, 323(5918), 1205-8 (2009) DOI: 10.1126/science.1166066
125. D. Dormann and C. Haass: Fused in sarcoma (FUS): an oncogene goes awry in neurodegeneration. Mol Cell Neurosci, 56, 475-86 (2013) DOI: 10.1016/j.mcn.2013.03.006
126. T. Yamazaki, S. Chen, Y. Yu, B. Yan, T. C. Haertlein, M. A. Carrasco, J. C. Tapia, B. Zhai, R. Das, M. Lalancette-Hebert, A. Sharma, S. Chandran, G. Sullivan, A. L. Nishimura, C. E. Shaw, S. P. Gygi, N. A. Shneider, T. Maniatis and R. Reed: FUSSMN protein interactions link the motor neuron diseases ALS and SMA. Cell Rep, 2(4), 799-806 (2012) DOI: 10.1016/j.celrep.2012.08.025
127. J. C. Schwartz, C. C. Ebmeier, E. R. Podell, J. Heimiller, D. J. Taatjes and T. R. Cech: FUS binds the CTD of RNA polymerase II and regulates its phosphorylation at Ser2. Genes Dev, 26(24), 2690-5 (2012) DOI: 10.1101/gad.204602.112
128. X. Wang, S. Arai, X. Song, D. Reichart, K. Du, G. Pascual, P. Tempst, M. G. Rosenfeld, C. K. Glass and R. Kurokawa: Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature, 454(7200), 126-30 (2008) DOI: 10.1038/nature06992
129. J. I. Hoell, E. Larsson, S. Runge, J. D. Nusbaum, S. Duggimpudi, T. A. Farazi, M. Hafner, A. Borkhardt, C. Sander and T. Tuschl: RNA targets of wild-type and mutant FET family proteins. Nat Struct Mol Biol, 18(12), 1428-31 (2011) DOI: 10.1038/nsmb.2163
130. S. Ishigaki, A. Masuda, Y. Fujioka, Y. Iguchi, M. Katsuno, A. Shibata, F. Urano, G. Sobue and K. Ohno: Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions. Sci Rep, 2, 529 (2012) DOI: 10.1038/srep00529
131. C. Lagier-Tourenne, M. Polymenidou, K. R. Hutt, A. Q. Vu, M. Baughn, S. C. Huelga, K. M. Clutario, S. C. Ling, T. Y. Liang, C. Mazur, E. Wancewicz, A. S. Kim, A. Watt, S. Freier, G. G. Hicks, J. P. Donohue, L. Shiue, C. F. Bennett, J. Ravits, D. W. Cleveland and G. W. Yeo: Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long premRNAs. Nat Neurosci, 15(11), 1488-97 (2012) DOI: 10.1038/nn.3230
132. B. Rogelj, L. E. Easton, G. K. Bogu, L. W. Stanton, G. Rot, T. Curk, B. Zupan, Y. Sugimoto, M. Modic, N. Haberman, J. Tollervey, R. Fujii, T. Takumi, C. E. Shaw and J. Ule: Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain. Sci Rep, 2, 603 (2012) DOI: 10.1038/srep00603
133. T. Nakaya, P. Alexiou, M. Maragkakis, A. Chang and Z. Mourelatos: FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns. RNA, 19(4), 498-509 (2013) DOI: 10.1261/rna.037804.112
134. Y. Zhou, S. Liu, G. Liu, A. Oztürk and G. G. Hicks: ALS-associated FUS mutations result in compromised FUS alternative splicing and autoregulation. PLoS Genet, 9(10), e1003895 (2013) DOI: 10.1371/journal.pgen.1003895
135. S. M. Oh, Z. Liu, M. Okada, S. W. Jang, X. Liu, C. B. Chan, H. Luo and K. Ye: Ebp1 sumoylation, regulated by TLS/FUS E3 ligase, is required for its anti-proliferative activity. Oncogene, 29(7), 1017-30 (2010) DOI: 10.1038/onc.2009.411
136. E. C. Toomey, J. D. Schiffman and S. L. Lessnick: Recent advances in the molecular pathogenesis of Ewing's sarcoma. Oncogene, 29(32), 4504-16 (2010) DOI: 10.1038/onc.2010.205
137. M. P. Paronetto: Ewing sarcoma protein: a key player in human cancer. Int J Cell Biol, 2013, 642853 (2013) DOI: 10.1155/2013/642853
138. A. Bertolotti, T. Melot, J. Acker, M. Vigneron, O. Delattre and L. Tora: EWS, but not EWS-FLI-1, is associated with both TFIID and RNA polymerase II: interactions between two members of the TET family, EWS and hTAFII68, and subunits of TFIID and RNA polymerase II complexes. Mol Cell Biol, 18(3), 1489-97 (1998) No DOI Found
139. A. Bertolotti, Y. Lutz, D. J. Heard, P. Chambon and L. Tora: hTAF(II)68, a novel RNA/ssDNA-binding protein with homology to the pro-oncoproteins TLS/FUS and EWS is associated with both TFIID and RNA polymerase II. EMBO J, 15(18), 5022-31 (1996) No DOI Found
140. F. Ibrahim, M. Maragkakis, P. Alexiou, M. A. Maronski, M. A. Dichter and Z. Mourelatos: Identification of in vivo, conserved, TAF15 RNA binding sites reveals the impact of TAF15 on the neuronal transcriptome. Cell Rep, 3(2), 301-8 (2013) DOI: 10.1016/j.celrep.2013.01.021
141. R. Martinez-Contreras, P. Cloutier, L. Shkreta, J. F. Fisette, T. Revil and B. Chabot: hnRNP proteins and splicing control. Adv Exp Med Biol, 623, 123-47 (2007) DOI: 10.1007/978-0-387-77374-2-8
142. S. P. Han, Y. H. Tang and R. Smith: Functional diversity of the hnRNPs: past, present and perspectives. Biochem J, 430(3), 379-92 (2010) DOI: 10.1042/BJ20100396
143. J. Jean-Philippe, S. Paz and M. Caputi: hnRNP A1: the Swiss army knife of gene expression. Int J Mol Sci, 14(9), 18999-9024 (2013) DOI: 10.3390/ijms140918999
144. H. J. Kim, N. C. Kim, Y. D. Wang, E. A. Scarborough, J. Moore, Z. Diaz, K. S. MacLea, B. Freibaum, S. Li, A. Molliex, A. P. Kanagaraj, R. Carter, K. B. Boylan, A. M. Wojtas, R. Rademakers, J. L. Pinkus, S. A. Greenberg, J. Q. Trojanowski, B. J. Traynor, B. N. Smith, S. Topp, A. S. Gkazi, J. Miller, C. E. Shaw, M. Kottlors, J. Kirschner, A. Pestronk, Y. R. Li, A. F. Ford, A. D. Gitler, M. Benatar, O. D. King, V. E. Kimonis, E. D. Ross, C. C. Weihl, J. Shorter and J. P. Taylor: Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS. Nature, 495(7442), 467-73 (2013) DOI: 10.1038/nature11922
145. C. Dominguez, J. F. Fisette, B. Chabot and F. H. Allain: Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMs. Nat Struct Mol Biol, 17(7), 853-61 (2010) DOI: 10.1038/nsmb.1814
146. M. Caputi and A. M. Zahler: Determination of the RNA binding specificity of the heterogeneous nuclear ribonucleoprotein (hnRNP) H/H'/F/2H9 family. J Biol Chem, 276(47), 43850-9 (2001) DOI: 10.1074/jbc.M102861200
147. S. C. Huelga, A. Q. Vu, J. D. Arnold, T. Y. Liang, P. P. Liu, B. Y. Yan, J. P. Donohue, L. Shiue, S. Hoon, S. Brenner, M. Ares and G. W. Yeo: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep, 1(2), 167-78 (2012) DOI: 10.1016/j.celrep.2012.02.001
148. Y. Katz, E. T. Wang, E. M. Airoldi and C. B. Burge: Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods, 7(12), 1009-15 (2010) DOI: 10.1038/nmeth.1528
149. D. Mahé, P. Mähl, R. Gattoni, N. Fischer, M. G. Mattei, J. Stévenin and J. P. Fuchs: Cloning of human 2H9 heterogeneous nuclear ribonucleoproteins. Relation with splicing and early heat shock-induced splicing arrest. J Biol Chem, 272(3), 1827-36 (1997) DOI: 10.1074/jbc.272.3.1827
150. K. Bomsztyk, O. Denisenko and J. Ostrowski: hnRNP K: one protein multiple processes. Bioessays, 26(6), 629-38 (2004) DOI: 10.1002/bies.20048
151. M. Marko, M. Leichter, M. Patrinou-Georgoula and A. Guialis: hnRNP M interacts with PSF and p54(nrb) and co-localizes within defined nuclear structures. Exp Cell Res, 316(3), 390-400 (2010) DOI: 10.1016/j.yexcr.2009.10.021
152. Z. Mourelatos, L. Abel, J. Yong, N. Kataoka and G. Dreyfuss: SMN interacts with a novel family of hnRNP and spliceosomal proteins. EMBO J, 20(19), 5443-52 (2001) DOI: 10.1093/emboj/20.19.5443
153. W. Rossoll, A. K. Kröning, U. M. Ohndorf, C. Steegborn, S. Jablonka and M. Sendtner: Specific interaction of Smn, the spinal muscular atrophy determining gene product, with hnRNP-R and gryrbp/hnRNP-Q: a role for Smn in RNA processing in motor axons? Hum Mol Genet, 11(1), 93-105 (2002) DOI: 10.1093/hmg/11.1.93
154. M. Glinka, T. Herrmann, N. Funk, S. Havlicek, W. Rossoll, C. Winkler and M. Sendtner: The heterogeneous nuclear ribonucleoprotein-R is necessary for axonal beta-actin mRNA translocation in spinal motor neurons. Hum Mol Genet, 19(10), 1951-66 (2010) DOI: 10.1093/hmg/ddq073
155. A. Fukuda, M. Shimada, T. Nakadai, K. Nishimura and K. Hisatake: Heterogeneous nuclear ribonucleoprotein R cooperates with mediator to facilitate transcription reinitiation on the c-Fos gene. PLoS One, 8(8), e72496 (2013) DOI: 10.1371/journal.pone.0072496
156. T. Ideue, S. Adachi, T. Naganuma, A. Tanigawa, T. Natsume and T. Hirose: U7 small nuclear ribonucleoprotein represses histone gene transcription in cell cycle-arrested cells. Proc Natl Acad Sci U S A, 109(15), 5693-8 (2012) DOI: 10.1073/pnas.1200523109
157. T. B. Guo, L. G. Boros, K. C. Chan, A. P. Hikim, A. P. Hudson, R. S. Swerdloff, A. P. Mitchell and W. A. Salameh: Spermatogenetic expression of RNA-binding motif protein 7, a protein that interacts with splicing factors. J Androl, 24(2), 204-14 (2003) No DOI Found
158. M. Lubas, M. S. Christensen, M. S. Kristiansen, M. Domanski, L. G. Falkenby, S. Lykke-Andersen, J. S. Andersen, A. Dziembowski and T. H. Jensen: Interaction profiling identifies the human nuclear exosome targeting complex. Mol Cell, 43(4), 624-37 (2011) DOI: 10.1016/j.molcel.2011.06.028
159. T. Iwasaki, W. W. Chin and L. Ko: Identification and characterization of RRM-containing coactivator activator (CoAA) as TRBP-interacting protein, and its splice variant as a coactivator modulator (CoAM). J Biol Chem, 276(36), 33375-83 (2001) DOI: 10.1074/jbc.M101517200
160. D. Auboeuf, A. Hönig, S. M. Berget and B. W. O'Malley: Coordinate regulation of transcription and splicing by steroid receptor coregulators. Science, 298(5592), 416-9 (2002) DOI: 10.1126/science.1073734
161. M. Perani, P. Antonson, R. Hamoudi, C. J. Ingram, C. S. Cooper, M. D. Garrett and G. H. Goodwin: The proto-oncoprotein SYT interacts with SYT-interacting protein/ co-activator activator (SIP/CoAA), a human nuclear receptor co-activator with similarity to EWS and TLS/FUS family of proteins. J Biol Chem, 280(52), 42863-76 (2005) DOI: 10.1074/jbc.M502963200
162. J. I. Wu, J. Lessard, I. A. Olave, Z. Qiu, A. Ghosh, I. A. Graef and G. R. Crabtree: Regulation of dendritic development by neuron-specific chromatin remodeling complexes. Neuron, 56(1), 94-108 (2007) DOI: 10.1016/j.neuron.2007.08.021
163. R. Kanhoush, B. Beenders, C. Perrin, J. Moreau, M. Bellini and M. Penrad-Mobayed: Novel domains in the hnRNP G/RBMX protein with distinct roles in RNA binding and targeting nascent transcripts. Nucleus, 1(1), 109-22 (2010) No DOI Found
164. S. Matsunaga, H. Takata, A. Morimoto, K. Hayashihara, T. Higashi, K. Akatsuchi, E. Mizusawa, M. Yamakawa, M. Ashida, T. M. Matsunaga, T. Azuma, S. Uchiyama and K. Fukui: RBMX: a regulator for maintenance and centromeric protection of sister chromatid cohesion. Cell Rep, 1(4), 299-308 (2012) DOI: 10.1016/j.celrep.2012.02.005
165. E. Tsend-Ayush, L. A. O'Sullivan, F. S. Grützner, S. M. Onnebo, R. S. Lewis, M. L. Delbridge, J. A. Marshall Graves and A. C. Ward: RBMX gene is essential for brain development in zebrafish. Dev Dyn, 234(3), 682-8 (2005) DOI: 10.1002/dvdy.20432
166. M. Neumann, D. M. Sampathu, L. K. Kwong, A. C. Truax, M. C. Micsenyi, T. T. Chou, J. Bruce, T. Schuck, M. Grossman, C. M. Clark, L. F. McCluskey, B. L. Miller, E. Masliah, I. R. Mackenzie, H. Feldman, W. Feiden, H. A. Kretzschmar, J. Q. Trojanowski and V. M. Lee: Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Science, 314(5796), 130-3 (2006) DOI: 10.1126/science.1134108
167. T. Arai, M. Hasegawa, H. Akiyama, K. Ikeda, T. Nonaka, H. Mori, D. Mann, K. Tsuchiya, M. Yoshida, Y. Hashizume and T. Oda: TDP-43 is a component of ubiquitin-positive tau-negative inclusions in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Biochem Biophys Res Commun, 351(3), 602-11 (2006) DOI: 10.1016/j.bbrc.2006.10.093
168. E. Kabashi, P. N. Valdmanis, P. Dion, D. Spiegelman, B. J. McConkey, C. Vande Velde, J. P. Bouchard, L. Lacomblez, K. Pochigaeva, F. Salachas, P. F. Pradat, W. Camu, V. Meininger, N. Dupre and G. A. Rouleau: TARDBP mutations in individuals with sporadic and familial amyotrophic lateral sclerosis. Nat Genet, 40(5), 572-4 (2008) DOI: 10.1038/ng.132
169. J. Sreedharan, I. P. Blair, V. B. Tripathi, X. Hu, C. Vance, B. Rogelj, S. Ackerley, J. C. Durnall, K. L. Williams, E. Buratti, F. Baralle, J. de Belleroche, J. D. Mitchell, P. N. Leigh, A. Al-Chalabi, C. C. Miller, G. Nicholson and C. E. Shaw: TDP-43 mutations in familial and sporadic amyotrophic lateral sclerosis. Science, 319(5870), 1668-72 (2008) DOI: 10.1126/science.1154584
170. M. A. Gitcho, R. H. Baloh, S. Chakraverty, K. Mayo, J. B. Norton, D. Levitch, K. J. Hatanpaa, C. L. White, E. H. Bigio, R. Caselli, M. Baker, M. T. Al-Lozi, J. C. Morris, A. Pestronk, R. Rademakers, A. M. Goate and N. J. Cairns: TDP-43 A315T mutation in familial motor neuron disease. Ann Neurol, 63(4), 535-8 (2008) DOI: 10.1002/ana.21344
171. X. Shan, P. M. Chiang, D. L. Price and P. C. Wong: Altered distributions of Gemini of coiled bodies and mitochondria in motor neurons of TDP-43 transgenic mice. Proc Natl Acad Sci U S A, 107(37), 16325-30 (2010) DOI: 10.1073/pnas.1003459107
172. H. Tsuiji, Y. Iguchi, A. Furuya, A. Kataoka, H. Hatsuta, N. Atsuta, F. Tanaka, Y. Hashizume, H. Akatsu, S. Murayama, G. Sobue and K. Yamanaka: Spliceosome integrity is defective in the motor neuron diseases ALS and SMA. EMBO Mol Med, 5(2), 221-34 (2013) DOI: 10.1002/emmm.201202303
173. L. C. Hsu, H. Y. Chen, Y. W. Lin, W. C. Chu, M. J. Lin, Y. T. Yan and P. H. Yen: DAZAP1, an hnRNP protein, is required for normal growth and spermatogenesis in mice. RNA, 14(9), 1814-22 (2008) DOI: 10.1261/rna.1152808
174. E. Goina, N. Skoko and F. Pagani: Binding of DAZAP1 and hnRNPA1/A2 to an exonic splicing silencer in a natural BRCA1 exon 18 mutant. Mol Cell Biol, 28(11), 3850-60 (2008) DOI: 10.1128/MCB.02253-07
175. T. Pastor and F. Pagani: Interaction of hnRNPA1/A2 and DAZAP1 with an Alu-derived intronic splicing enhancer regulates ATM aberrant splicing. PLoS One, 6(8), e23349 (2011) DOI: 10.1371/journal.pone.0023349
176. R. W. Smith, R. C. Anderson, J. W. Smith, M. Brook, W. A. Richardson and N. K. Gray: DAZAP1, an RNA-binding protein required for development and spermatogenesis, can regulate mRNA translation. RNA, 17(7), 1282-95 (2011) DOI: 10.1261/rna.2717711
177. R. Choudhury, S. G. Roy, Y. S. Tsai, A. Tripathy, L. M. Graves and Z. Wang: The splicing activator DAZAP1 integrates splicing control into MEK/Erk-regulated cell proliferation and migration. Nat Commun, 5, 3078 (2014) DOI: 10.1038/ncomms4078
178. Y. Vera, T. Dai, A. P. Hikim, Y. Lue, E. C. Salido, R. S. Swerdloff and P. H. Yen: Deleted in azoospermia associated protein 1 shuttles between nucleus and cytoplasm during normal germ cell maturation. J Androl, 23(5), 622-8 (2002)
179. Y. Kurihara, H. Watanabe, A. Kawaguchi, T. Hori, K. Mishiro, M. Ono, H. Sawada and S. Uesugi: Dynamic changes in intranuclear and subcellular localizations of mouse Prrp/DAZAP1 during spermatogenesis: the necessity of the C-terminal proline-rich region for nuclear import and localization. Arch Histol Cytol, 67(4), 325-33 (2004) DOI: 10.1679/aohc.67.325
180. Y. T. Lin and P. H. Yen: A novel nucleocytoplasmic shuttling sequence of DAZAP1, a testis-abundant RNA-binding protein. RNA, 12(8), 1486-93 (2006) DOI: 10.1261/rna.42206
181. Y. T. Lin, W. C. Wen and P. H. Yen: Transcription-dependent nuclear localization of DAZAP1 requires an N-terminal signal. Biochem Biophys Res Commun, 428(3), 422-6 (2012) DOI: 10.1016/j.bbrc.2012.10.076
182. A. N. Ladd, N. H. Nguyen, K. Malhotra and T. A. Cooper: CELF6, a member of the CELF family of RNA-binding proteins, regulates muscle-specific splicing enhancer-dependent alternative splicing. J Biol Chem, 279(17), 17756-64 (2004) DOI: 10.1074/jbc.M310687200
183. J. D. Dougherty, S. E. Maloney, D. F. Wozniak, M. A. Rieger, L. Sonnenblick, G. Coppola, N. G. Mahieu, J. Zhang, J. Cai, G. J. Patti, B. S. Abrahams, D. H. Geschwind and N. Heintz: The disruption of Celf6, a gene identified by translational profiling of serotonergic neurons, results in autism-related behaviors. J Neurosci, 33(7), 2732-53 (2013) DOI: 10.1523/JNEUROSCI.4762-12.2013
184. C. Shin, Y. Feng and J. L. Manley: Dephosphorylated SRp38 acts as a splicing repressor in response to heat shock. Nature, 427(6974), 553-8 (2004) DOI: 10.1038/nature02288
185. Y. Shi and J. L. Manley: A complex signaling pathway regulates SRp38 phosphorylation and pre-mRNA splicing in response to heat shock. Mol Cell, 28(1), 79-90 (2007) DOI: 10.1016/j.molcel.2007.08.028
186. G. Biamonti and J. F. Caceres: Cellular stress and RNA splicing. Trends Biochem Sci, 34(3), 146-53 (2009) DOI: 10.1016/j.tibs.2008.11.004
187. X. Zhou, W. Wu, H. Li, Y. Cheng, N. Wei, J. Zong, X. Feng, Z. Xie, D. Chen, J. L. Manley, H. Wang and Y. Feng: Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation. Nucleic Acids Res, 42(6), 4019-30 (2014) DOI: 10.1093/nar/gkt1387
188. J. Pihlajamäki, C. Lerin, P. Itkonen, T. Boes, T. Floss, J. Schroeder, F. Dearie, S. Crunkhorn, F. Burak, J. C. Jimenez-Chillaron, T. Kuulasmaa, P. Miettinen, P. J. Park, I. Nasser, Z. Zhao, Z. Zhang, Y. Xu, W. Wurst, H. Ren, A. J. Morris, S. Stamm, A. B. Goldfine, M. Laakso and M. E. Patti: Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis. Cell Metab, 14(2), 208-18 (2011) DOI: 10.1016/j.cmet.2011.06.007
189. C. F. Kennedy, A. Krämer and S. M. Berget: A role for SRp54 during intron bridging of small introns with pyrimidine tracts upstream of the branch point. Mol Cell Biol, 18(9), 5425-34 (1998) No DOI Found
190. S. Wellmann, C. Bührer, E. Moderegger, A. Zelmer, R. Kirschner, P. Koehne, J. Fujita and K. Seeger: Oxygen-regulated expression of the RNA-binding proteins RBM3 and CIRP by a HIF-1-independent mechanism. J Cell Sci, 117(Pt 9), 1785-94 (2004) DOI: 10.1242/jcs.01026
191. M. E. Lleonart: A new generation of protooncogenes: cold-inducible RNA binding proteins. Biochim Biophys Acta, 1805(1), 43-52 (2010) DOI: 10.1016/j.bbcan.2009.11.001
192. Y. Liu, W. Hu, Y. Murakawa, J. Yin, G. Wang, M. Landthaler and J. Yan: Coldinduced RNA-binding proteins regulate circadian gene expression by controlling alternative polyadenylation. Sci Rep, 3, 2054 (2013) DOI: 10.1038/srep02054
193. T. Wagner, J. Wirth, J. Meyer, B. Zabel, M. Held, J. Zimmer, J. Pasantes, F. D. Bricarelli, J. Keutel, E. Hustert, U. Wolf, N. Tommerup, W. Schempp and G. Scherer: Autosomal sex reversal and campomelic dysplasia are caused by mutations in and around the SRY-related gene SOX9. Cell, 79(6), 1111-20 (1994) DOI: 10.1016/0092-8674(94)90041-8
194. J. W. Foster, M. A. Dominguez-Steglich, S. Guioli, C. Kwok, P. A. Weller, M. Stevanović, J. Weissenbach, S. Mansour, I. D. Young and P. N. Goodfellow: Campomelic dysplasia and autosomal sex reversal caused by mutations in an SRY-related gene. Nature, 372(6506), 525-30 (1994) DOI: 10.1038/372525a0
195. J. A. Price, D. W. Bowden, J. T. Wright, M. J. Pettenati and T. C. Hart: Identification of a mutation in DLX3 associated with tricho-dento-osseous (TDO) syndrome. Hum Mol Genet, 7(3), 563-9 (1998) DOI: 10.1093/hmg/7.3.563
196. H. Liu, G. C. Ippolito, J. K. Wall, T. Niu, L. Probst, B. S. Lee, K. Pulford, A. H. Banham, L. Stockwin, A. L. Shaffer, L. M. Staudt, C. Das, M. J. Dyer and P. W. Tucker: Functional studies of BCL11A: characterization of the conserved BCL11A-XL splice variant and its interaction with BCL6 in nuclear paraspeckles of germinal center B cells. Mol Cancer, 5, 18 (2006) DOI: 10.1186/1476-4598-5-18
197. R. Shimizu, J. D. Engel and M. Yamamoto: GATA1-related leukaemias. Nat Rev Cancer, 8(4), 279-87 (2008) DOI: 10.1038/nrc2348
198. L. S. Chuang and Y. Ito: RUNX3 is multifunctional in carcinogenesis of multiple solid tumors. Oncogene, 29(18), 2605-15 (2010) DOI: 10.1038/onc.2010.88
199. Y. J. Yang, A. E. Baltus, R. S. Mathew, E. A. Murphy, G. D. Evrony, D. M. Gonzalez, E. P. Wang, C. A. Marshall-Walker, B. J. Barry, J. Murn, A. Tatarakis, M. A. Mahajan, H. H. Samuels, Y. Shi, J. A. Golden, M. Mahajnah, R. Shenhav and C. A. Walsh: Microcephaly gene links trithorax and REST/NRSF to control neural stem cell proliferation and differentiation. Cell, 151(5), 1097-112 (2012) DOI: 10.1016/j.cell.2012.10.043
200. C. L. Balduini and A. Savoia: Genetics of familial forms of thrombocytopenia. Hum Genet, 131(12), 1821-32 (2012) DOI: 10.1007/s00439-012-1215-x
201. V. G. Sankaran, R. Ghazvinian, R. Do, P. Thiru, J. A. Vergilio, A. H. Beggs, C. A. Sieff, S. H. Orkin, D. G. Nathan, E. S. Lander and H. T. Gazda: Exome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia. J Clin Invest, 122(7), 2439-43 (2012) DOI: 10.1172/JCI63597
202. J. Boultwood and A. Pellagatti: Reduced translation of GATA1 in Diamond-Blackfan anemia. Nat Med, 20(7), 703-4 (2014) DOI: 10.1038/nm.3630
203. L. S. Ludwig, H. T. Gazda, J. C. Eng, S. W. Eichhorn, P. Thiru, R. Ghazvinian, T. I. George, J. R. Gotlib, A. H. Beggs, C. A. Sieff, H. F. Lodish, E. S. Lander and V. G. Sankaran: Altered translation of GATA1 in Diamond-Blackfan anemia. Nat Med, 20(7), 748-53 (2014) DOI: 10.1038/nm.3557
204. Y. Y. Chau and N. D. Hastie: The role of Wt1 in regulating mesenchyme in cancer, development, and tissue homeostasis. Trends Genet, 28(10), 515-24 (2012) DOI: 10.1016/j.tig.2012.04.004
205. A. M. Kaindl: Autosomal recessive primary microcephalies (MCPH). Eur J Paediatr Neurol, 18(4), 547-8 (2014) DOI: 10.1016/j.ejpn.2014.03.010
206. F. Xia, M. N. Bainbridge, T. Y. Tan, M. F. Wangler, A. E. Scheuerle, E. H. Zackai, M. H. Harr, V. R. Sutton, R. L. Nalam, W. Zhu, M. Nash, M. M. Ryan, J. Yaplito-Lee, J. V. Hunter, M. A. Deardorff, S. J. Penney, A. L. Beaudet, S. E. Plon, E. A. Boerwinkle, J. R. Lupski, C. M. Eng, D. M. Muzny, Y. Yang and R. A. Gibbs: De novo truncating mutations in AHDC1 in individuals with syndromic expressive language delay, hypotonia, and sleep apnea. Am J Hum Genet, 94(5), 784-9 (2014) DOI: 10.1016/j.ajhg.2014.04.006
207. K. Takahashi and S. Yamanaka: Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell, 126(4), 663-76 (2006) DOI: 10.1016/j.cell.2006.07.024
208. D. Jia, S. M. Hasso, J. Chan, D. Filingeri, P. A. D'Amore, L. Rice, C. Pampo, D. W. Siemann, D. Zurakowski, S. J. Rodig and M. A. Moses: Transcriptional repression of VEGF by ZNF24: mechanistic studies and vascular consequences in vivo. Blood, 121(4), 707-15 (2013) DOI: 10.1182/blood-2012-05-433045
209. A. J. Lopez-Contreras, I. Ruppen, M. Nieto-Soler, M. Murga, S. Rodriguez-Acebes, S. Remeseiro, S. Rodrigo-Perez, A. M. Rojas, J. Mendez, J. Muñoz and O. Fernandez-Capetillo: A proteomic characterization of factors enriched at nascent DNA molecules. Cell Rep, 3(4), 1105-16 (2013) DOI: 10.1016/j.celrep.2013.03.009
210. H. Akiyama, M. C. Chaboissier, J. F. Martin, A. Schedl and B. de Crombrugghe: The transcription factor Sox9 has essential roles in successive steps of the chondrocyte differentiation pathway and is required for expression of Sox5 and Sox6. Genes Dev, 16(21), 2813-28 (2002) DOI: 10.1101/gad.1017802
211. Y. Kawaguchi: Sox9 and programming of liver and pancreatic progenitors. J Clin Invest, 123(5), 1881-6 (2013) DOI: 10.1172/JCI66022
212. K. Hata, R. Nishimura, S. Muramatsu, A. Matsuda, T. Matsubara, K. Amano, F. Ikeda, V. R. Harley and T. Yoneda: Paraspeckle protein p54nrb links Sox9-mediated transcription with RNA processing during chondrogenesis in mice. J Clin Invest, 118(9), 3098-108 (2008) DOI: 10.1172/JCI31373
213. W. M. Schmidt, C. Kraus, H. Höger, S. Hochmeister, F. Oberndorfer, M. Branka, S. Bingemann, H. Lassmann, M. Müller, L. I. Macedo-Souza, M. Vainzof, M. Zatz, A. Reis and R. E. Bittner: Mutation in the Scyl1 gene encoding amino-terminal kinase-like protein causes a recessive form of spinocerebellar neurodegeneration. EMBO Rep, 8(7), 691-7 (2007) DOI: 10.1038/sj.embor.7401001
214. S. Pelletier, S. Gingras, S. Howell, P. Vogel and J. N. Ihle: An early onset progressive motor neuron disorder in Scyl1-deficient mice is associated with mislocalization of TDP-43. J Neurosci, 32(47), 16560-73 (2012) DOI: 10.1523/JNEUROSCI.1787-12.2012
215. S. Q. Xie, S. Martin, P. V. Guillot, D. L. Bentley and A. Pombo: Splicing speckles are not reservoirs of RNA polymerase II, but contain an inactive form, phosphorylated on serine2 residues of the C-terminal domain. Mol Biol Cell, 17(4), 1723-33 (2006) DOI: 10.1091/mbc.E05-08-0726
216. D. Rotin and S. Kumar: Physiological functions of the HECT family of ubiquitin ligases. Nat Rev Mol Cell Biol, 10(6), 398-409 (2009) DOI: 10.1038/nrm2690
217. S. Galbán and C. S. Duckett: XIAP as a ubiquitin ligase in cellular signaling. Cell Death Differ, 17(1), 54-60 (2010) DOI: 10.1038/cdd.2009.81
218. M. B. Metzger, V. A. Hristova and A. M. Weissman: HECT and RING finger families of E3 ubiquitin ligases at a glance. J Cell Sci, 125(Pt 3), 531-7 (2012) DOI: 10.1242/jcs.091777
219. T. K. Oberoi-Khanuja, A. Murali and K. Rajalingam: IAPs on the move: role of inhibitors of apoptosis proteins in cell migration. Cell Death Dis, 4, e784 (2013) DOI: 10.1038/cddis.2013.311
220. B. Pereira, M. Le Borgne, N. T. Chartier, M. Billaud and R. Almeida: MEX-3 proteins: recent insights on novel post-transcriptional regulators. Trends Biochem Sci, 38(10), 477-9 (2013) DOI: 10.1016/j.tibs.2013.08.004
221. I. B. Wilde, M. Brack, J. M. Winget and T. Mayor: Proteomic characterization of aggregating proteins after the inhibition of the ubiquitin proteasome system. J Proteome Res, 10(3), 1062-72 (2011) DOI: 10.1021/pr1008543
222. D. Li and Y. Huang: Knockdown of ubiquitin associated protein 2-like inhibits the growth and migration of prostate cancer cells. Oncol Rep (2014) DOI: 10.3892/or.2014.3360
223. A. Castello, B. Fischer, K. Eichelbaum, R. Horos, B. M. Beckmann, C. Strein, N. E. Davey, D. T. Humphreys, T. Preiss, L. M. Steinmetz, J. Krijgsveld and M. W. Hentze: Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell, 149(6), 1393-406 (2012) DOI: 10.1016/j.cell.2012.04.031
224. A. G. Baltz, M. Munschauer, B. Schwanhäusser, A. Vasile, Y. Murakawa, M. Schueler, N. Youngs, D. Penfold- Brown, K. Drew, M. Milek, E. Wyler, R. Bonneau, M. Selbach, C. Dieterich and M. Landthaler: The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell, 46(5), 674-90 (2012) DOI: 10.1016/j.molcel.2012.05.021
225. I. Kwon, M. Kato, S. Xiang, L. Wu, P. Theodoropoulos, H. Mirzaei, T. Han, S. Xie, J. L. Corden and S. L. McKnight: Phosphorylation-regulated binding of RNA polymerase II to fibrous polymers of low-complexity domains. Cell, 155(5), 1049-60 (2013) DOI: 10.1016/j.cell.2013.10.033
226. F. Cano, H. Bye, L. M. Duncan, K. Buchet-Poyau, M. Billaud, M. R. Wills and P. J. Lehner: The RNA-binding E3 ubiquitin ligase MEX-3C links ubiquitination with MHC-I mRNA degradation. EMBO J, 31(17), 3596-606 (2012) DOI: 10.1038/emboj.2012.218
227. R. A. Burrell, S. E. McClelland, D. Endesfelder, P. Groth, M. C. Weller, N. Shaikh, E. Domingo, N. Kanu, S. M. Dewhurst, E. Gronroos, S. K. Chew, A. J. Rowan, A. Schenk, M. Sheffer, M. Howell, M. Kschischo, A. Behrens, T. Helleday, J. Bartek, I. P. Tomlinson and C. Swanton: Replication stress links structural and numerical cancer chromosomal instability. Nature, 494(7438), 492-6 (2013) DOI: 10.1038/nature11935
228. Y. Jiao, S. K. George, Q. Zhao, M. W. Hulver, S. M. Hutson, C. E. Bishop and B. Lu: Mex3c mutation reduces adiposity and increases energy expenditure. Mol Cell Biol, 32(21), 4350-62 (2012) DOI: 10.1128/MCB.00452-12
229. L. Zhang, L. Kang, W. Bond and N. Zhang: Interaction between syntaxin 8 and HECTd3, a HECT domain ligase. Cell Mol Neurobiol, 29(1), 115-21 (2009) DOI: 10.1007/s10571-008-9303-0
230. Y. Zhu, C. Wang, J. Lan, J. Yu, C. Jin and H. Huang: Phosphorylation of Tara by Plk1 is essential for faithful chromosome segregation in mitosis. Exp Cell Res, 318(18), 2344-52 (2012) DOI: 10.1016/j.yexcr.2012.07.001
231. Y. Li, Y. Kong, Z. Zhou, H. Chen, Z. Wang, Y. C. Hsieh, D. Zhao, X. Zhi, J. Huang, J. Zhang, H. Li and C. Chen: The HECTD3 E3 ubiquitin ligase facilitates cancer cell survival by promoting K63-linked polyubiquitination of caspase-8. Cell Death Dis, 4, e935 (2013) DOI: 10.1038/cddis.2013.464
232. Y. Li, X. Chen, Z. Wang, D. Zhao, H. Chen, W. Chen, Z. Zhou, J. Zhang, H. Li and C. Chen: The HECTD3 E3 ubiquitin ligase suppresses cisplatin-induced apoptosis via stabilizing MALT1. Neoplasia, 15(1), 39-48 (2013) No DOI Found
233. N. S. Kenneth and C. S. Duckett: IAP proteins: regulators of cell migration and development. Curr Opin Cell Biol, 24(6), 871-5 (2012) DOI: 10.1016/j.ceb.2012.11.004
234. S. Rigaud, M. C. Fondanèche, N. Lambert, B. Pasquier, V. Mateo, P. Soulas, L. Galicier, F. Le Deist, F. Rieux-Laucat, P. Revy, A. Fischer, G. de Saint Basile and S. Latour: XIAP deficiency in humans causes an X-linked lymphoproliferative syndrome. Nature, 444(7115), 110-4 (2006) DOI: 10.1038/nature05257
235. C. C. Akoh, G. C. Lee, Y. C. Liaw, T. H. Huang and J. F. Shaw: GDSL family of serine esterases/lipases. Prog Lipid Res, 43(6), 534-52 (2004) DOI: 10.1016/j.plipres.2004.09.002
236. V. Anantharaman and L. Aravind: Novel eukaryotic enzymes modifying cell-surface biopolymers. Biol Direct, 5, 1 (2010) DOI: 10.1186/1745-6150-5-1
237. Z. A. Jenkins, M. van Kogelenberg, T. Morgan, A. Jeffs, R. Fukuzawa, E. Pearl, C. Thaller, A. V. Hing, M. E. Porteous, S. Garcia-Miñaur, A. Bohring, D. Lacombe, F. Stewart, T. Fiskerstrand, L. Bindoff, S. Berland, L. C. Adès, M. Tchan, A. David, L. C. Wilson, R. C. Hennekam, D. Donnai, S. Mansour, V. Cormier-Daire and S. P. Robertson: Germline mutations in WTX cause a sclerosing skeletal dysplasia but do not predispose to tumorigenesis. Nat Genet, 41(1), 95-100 (2009) DOI: 10.1038/ng.270
238. S. B. Herman, S. K. Holman, S. P. Robertson, L. Davidson, B. Taragin and J. Samanich: Severe osteopathia striata with cranial sclerosis in a female case with whole WTX gene deletion. Am J Med Genet A, 161A(3), 594-9 (2013) DOI: 10.1002/ajmg.a.35716
239. A. Fujita, N. Ochi, H. Fujimaki, H. Muramatsu, Y. Takahashi, J. Natsume, S. Kojima, M. Nakashima, Y. Tsurusaki, H. Saitsu, N. Matsumoto and N. Miyake: A novel WTX mutation in a female patient with osteopathia striata with cranial sclerosis and hepatoblastoma. Am J Med Genet A, 164A(4), 998-1002 (2014) DOI: 10.1002/ajmg.a.36369
240. J. R. Dutton, D. Lahiri and A. Ward: Different isoforms of the Wilms' tumour protein WT1 have distinct patterns of distribution and trafficking within the nucleus. Cell Prolif, 39(6), 519-35 (2006) DOI: 10.1111/j.1365-2184.2006.00409.x
241. M. N. Rivera, W. J. Kim, J. Wells, A. Stone, A. Burger, E. J. Coffman, J. Zhang and D. A. Haber: The tumor suppressor WTX shuttles to the nucleus and modulates WT1 activity. Proc Natl Acad Sci U S A, 106(20), 8338-43 (2009) DOI: 10.1073/pnas.0811349106
242. C. Westberg, J. P. Yang, H. Tang, T. R. Reddy and F. Wong-Staal: A novel shuttle protein binds to RNA helicase A and activates the retroviral constitutive transport element. J Biol Chem, 275(28), 21396-401 (2000) DOI: 10.1074/jbc.M909887199
243. J. P. Yang, H. Tang, T. R. Reddy and F. Wong-Staal: Mapping the functional domains of HAP95, a protein that binds RNA helicase A and activates the constitutive transport element of type D retroviruses. J Biol Chem, 276(33), 30694-700 (2001) DOI: 10.1074/jbc.M102809200
244. Y. Yang, C. L. Mahaffey, N. Bérubé, A. Nystuen and W. N. Frankel: Functional characterization of fidgetin, an AAA-family protein mutated in fidget mice. Exp Cell Res, 304(1), 50-8 (2005) DOI: 10.1016/j.yexcr.2004.11.014
245. Y. Yang, C. L. Mahaffey, N. Bérubé and W. N. Frankel: Interaction between fidgetin and protein kinase A-anchoring protein AKAP95 is critical for palatogenesis in the mouse. J Biol Chem, 281(31), 22352-9 (2006) DOI: 10.1074/jbc.M603626200
246. T. J. Maures, J. H. Kurzer and C. Carter-Su: SH2B1 (SH2-B) and JAK2: a multifunctional adaptor protein and kinase made for each other. Trends Endocrinol Metab, 18(1), 38-45 (2007) DOI: 10.1016/j.tem.2006.11.007
247. B. Desbuquois, N. Carré and A. F. Burnol: Regulation of insulin and type 1 insulinlike growth factor signaling and action by the Grb10/14 and SH2B1/B2 adaptor proteins. FEBS J, 280(3), 794-816 (2013) DOI: 10.1111/febs.12080
248. M. E. Doche, E. G. Bochukova, H. W. Su, L. R. Pearce, J. M. Keogh, E. Henning, J. M. Cline, S. Saeed, A. Dale, T. Cheetham, I. Barroso, L. S. Argetsinger, S. O'Rahilly, L. Rui, C. Carter-Su and I. S. Farooqi: Human SH2B1 mutations are associated with maladaptive behaviors and obesity. J Clin Invest, 122(12), 4732-6 (2012) DOI: 10.1172/JCI62696
249. R. A. Hegele, H. Cao, D. M. Liu, G. A. Costain, V. Charlton-Menys, N. W. Rodger and P. N. Durrington: Sequencing of the reannotated LMNB2 gene reveals novel mutations in patients with acquired partial lipodystrophy. Am J Hum Genet, 79(2), 383-9 (2006) DOI: 10.1086/505885
250. H. J. Worman and G. Bonne: "Laminopathies": a wide spectrum of human diseases. Exp Cell Res, 313(10), 2121-33 (2007) DOI: 10.1016/j.yexcr.2007.03.028
251. H. J. Worman, L. G. Fong, A. Muchir and S. G. Young: Laminopathies and the long strange trip from basic cell biology to therapy. J Clin Invest, 119(7), 1825-36 (2009) DOI: 10.1172/JCI37679
252. N. M. Maraldi, C. Capanni, V. Cenni, M. Fini and G. Lattanzi: Laminopathies and lamin-associated signaling pathways. J Cell Biochem, 112(4), 979-92 (2011) DOI: 10.1002/jcb.22992
253. P. O. Simsek-Kiper, E. Roach, G. E. Utine and K. Boduroglu: Barraquer-Simons syndrome: a rare clinical entity. Am J Med Genet A, 164(7), 1756-60 (2014) DOI: 10.1002/ajmg.a.36491
254. D. Roos, D. B. Kuhns, A. Maddalena, J. Bustamante, C. Kannengiesser, M. de Boer, K. van Leeuwen, M. Y. Köker, B. Wolach, J. Roesler, H. L. Malech, S. M. Holland, J. I. Gallin and M. J. Stasia: Hematologically important mutations: the autosomal recessive forms of chronic granulomatous disease (second update). Blood Cells Mol Dis, 44(4), 291-9 (2010) DOI: 10.1016/j.bcmd.2010.01.009
255. D. J. Scarlett, P. M. Herst and M. V. Berridge: Multiple proteins with single activities or a single protein with multiple activities: the conundrum of cell surface NADH oxidoreductases. Biochim Biophys Acta, 1708(1), 108-19 (2005) DOI: 10.1016/j.bbabio.2005.03.006
256. Y. S. Mao, H. Sunwoo, B. Zhang and D. L. Spector: Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat Cell Biol, 13(1), 95-101 (2011) DOI: 10.1038/ncb2140
257. M. Dundr: Seed and grow: a two-step model for nuclear body biogenesis. J Cell Biol, 193(4), 605-6 (2011) DOI: 10.1083/jcb.201104087
258. M. Kato, T. W. Han, S. Xie, K. Shi, X. Du, L. C. Wu, H. Mirzaei, E. J. Goldsmith, J. Longgood, J. Pei, N. V. Grishin, D. E. Frantz, J. W. Schneider, S. Chen, L. Li, M. R. Sawaya, D. Eisenberg, R. Tycko and S. L. McKnight: Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell, 149(4), 753-67 (2012) DOI: 10.1016/j.cell.2012.04.017
259. T. W. Han, M. Kato, S. Xie, L. C. Wu, H. Mirzaei, J. Pei, M. Chen, Y. Xie, J. Allen, G. Xiao and S. L. McKnight: Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies. Cell, 149(4), 768-79 (2012) DOI: 10.1016/j.cell.2012.04.016
260. T. Thisted, D. L. Lyakhov and S. A. Liebhaber: Optimized RNA targets of two closely related triple KH domain proteins, heterogeneous nuclear ribonucleoprotein K and alphaCP-2KL, suggest Distinct modes of RNA recognition. J Biol Chem, 276(20), 17484-96 (2001) DOI: 10.1074/jbc.M010594200
261. T. A. Shelkovnikova, H. K. Robinson, C. Troakes, N. Ninkina and V. L. Buchman: Compromised paraspeckle formation as a pathogenic factor in FUSopathies. Hum Mol Genet, 23(9), 2298-312 (2014) DOI: 10.1093/hmg/ddt622
262. N. Gilks, N. Kedersha, M. Ayodele, L. Shen, G. Stoecklin, L. M. Dember and P. Anderson: Stress granule assembly is mediated by prion-like aggregation of TIA-1. Mol Biol Cell, 15(12), 5383-98 (2004) DOI: 10.1091/mbc.E04-08-0715
263. C. J. Decker, D. Teixeira and R. Parker: Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae. J Cell Biol, 179(3), 437-49 (2007) DOI: 10.1083/jcb.200704147
264. D. Dormann, R. Rodde, D. Edbauer, E. Bentmann, I. Fischer, A. Hruscha, M. E. Than, I. R. Mackenzie, A. Capell, B. Schmid, M. Neumann and C. Haass: ALS-associated fused in sarcoma (FUS) mutations disrupt Transportin-mediated nuclear import. EMBO J, 29(16), 2841-57 (2010) DOI: 10.1038/emboj.2010.143
265. J. C. Schwartz, X. Wang, E. R. Podell and T. R. Cech: RNA seeds higher-order assembly of FUS protein. Cell Rep, 5(4), 918-25 (2013) DOI: 10.1016/j.celrep.2013.11.017
266. W. Shen, X. H. Liang and S. T. Crooke: Phosphorothioate oligonucleotides can displace NEAT1 RNA and form nuclear paraspeckle-like structures. Nucleic Acids Res, 42(13), 8648-62 (2014) DOI: 10.1093/nar/gku579
267. T. Hirose, G. Virnicchi, A. Tanigawa, T. Naganuma, R. Li, H. Kimura, T. Yokoi, S. Nakagawa, M. Bénard, A. H. Fox and G. Pierron: NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies. Mol Biol Cell, 25(1), 169-83 (2014) DOI: 10.1091/mbc.E13-09-0558
268. K. Imamura, N. Imamachi, G. Akizuki, M. Kumakura, A. Kawaguchi, K. Nagata, A. Kato, Y. Kawaguchi, H. Sato, M. Yoneda, C. Kai, T. Yada, Y. Suzuki, T. Yamada, T. Ozawa, K. Kaneki, T. Inoue, M. Kobayashi, T. Kodama, Y. Wada, K. Sekimizu and N. Akimitsu: Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli. Mol Cell, 53(3), 393-406 (2014) DOI: 10.1016/j.molcel.2014.01.009
269. Q. Zhang, C. Y. Chen, V. S. Yedavalli and K. T. Jeang: NEAT1 long noncoding RNA and paraspeckle bodies modulate HIV-1 posttranscriptional expression. MBio, 4(1), e00596-12 (2013) DOI: 10.1128/mBio.00596-12
270. H. Choudhry, J. Schödel, S. Oikonomopoulos, C. Camps, S. Grampp, A. L. Harris, P. J. Ratcliffe, J. Ragoussis and D. R. Mole: Extensive regulation of the non-coding transcriptome by hypoxia: role of HIF in releasing paused RNApol2. EMBO Rep, 15(1), 70-6 (2014) DOI: 10.1002/embr.201337642
271. S. Gremlich, F. Damnon, D. Reymondin, O. Braissant, J. C. Schittny, D. Baud, S. Gerber and M. Roth-Kleiner: The long non-coding RNA NEAT1 is increased in IUGR placentas, leading to potential new hypotheses of IUGR origin/development. Placenta, 35(1), 44-9 (2014) DOI: 10.1016/j.placenta.2013.11.003
272. J. R. Tollervey, T. Curk, B. Rogelj, M. Briese, M. Cereda, M. Kayikci, J. König, T. Hortobágyi, A. L. Nishimura, V. Zupunski, R. Patani, S. Chandran, G. Rot, B. Zupan, C. E. Shaw and J. Ule: Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci, 14(4), 452-8 (2011) DOI: 10.1038/nn.2778
273. Y. D. Ke, Y. Ke, J. Dramiga, U. Schütz, J. J. Kril, L. M. Ittner, H. Schröder and J. Götz: Tau-mediated nuclear depletion and cytoplasmic accumulation of SFPQ in Alzheimer's and Pick's disease. PLoS One, 7(4), e35678 (2012) DOI: 10.1371/journal.pone.0035678
274. N. T. Seyfried, Y. M. Gozal, L. E. Donovan, J. H. Herskowitz, E. B. Dammer, Q. Xia, L. Ku, J. Chang, D. M. Duong, H. D. Rees, D. S. Cooper, J. D. Glass, M. Gearing, M. G. Tansey, J. J. Lah, Y. Feng, A. I. Levey and J. Peng: Quantitative analysis of the detergent-insoluble brain proteome in frontotemporal lobar degeneration using SILAC internal standards. J Proteome Res, 11(5), 2721-38 (2012) DOI: 10.1021/pr2010814
275. J. Cotto, S. Fox and R. Morimoto: HSF1 granules: a novel stress-induced nuclear compartment of human cells. J Cell Sci, 110 (Pt 23), 2925-34 (1997) No DOI Found
276. I. Chiodi, M. Biggiogera, M. Denegri, M. Corioni, F. Weighardt, F. Cobianchi, S. Riva and G. Biamonti: Structure and dynamics of hnRNP-labelled nuclear bodies induced by stress treatments. J Cell Sci, 113 (Pt 22), 4043-53 (2000) No DOI Found
277. M. Denegri, D. Moralli, M. Rocchi, M. Biggiogera, E. Raimondi, F. Cobianchi, L. De Carli, S. Riva and G. Biamonti: Human chromosomes 9, 12, and 15 contain the nucleation sites of stress-induced nuclear bodies. Mol Biol Cell, 13(6), 2069-79 (2002) DOI: 10.1091/mbc.01-12-0569
278. G. Biamonti: Nuclear stress bodies: a heterochromatin affair? Nat Rev Mol Cell Biol, 5(6), 493-8 (2004) DOI: 10.1038/nrm1405
279. R. Valgardsdottir, I. Chiodi, M. Giordano, F. Cobianchi, S. Riva and G. Biamonti: Structural and functional characterization of noncoding repetitive RNAs transcribed in stressed human cells. Mol Biol Cell, 16(6), 2597-604 (2005) DOI: 10.1091/mbc.E04-12-1078
280. C. Jolly and S. C. Lakhotia: Human sat III and Drosophila hsr omega transcripts: a common paradigm for regulation of nuclear RNA processing in stressed cells. Nucleic Acids Res, 34(19), 5508-14 (2006) DOI: 10.1093/nar/gkl711
281. K. H. Choo, E. Earle and C. McQuillan: A homologous subfamily of satellite III DNA on human chromosomes 14 and 22. Nucleic Acids Res, 18(19), 5641-8 (1990) DOI: 10.1093/nar/18.19.5641
282. I. Chiodi, M. Corioni, M. Giordano, R. Valgardsdottir, C. Ghigna, F. Cobianchi, R. M. Xu, S. Riva and G. Biamonti: RNA recognition motif 2 directs the recruitment of SF2/ASF to nuclear stress bodies. Nucleic Acids Res, 32(14), 4127-36 (2004) DOI: 10.1093/nar/gkh759
283. S. P. Shevtsov and M. Dundr: Nucleation of nuclear bodies by RNA. Nat Cell Biol, 13(2), 167-73 (2011) DOI: 10.1038/ncb2157
284. T. E. Audas, M. D. Jacob and S. Lee: Immobilization of proteins in the nucleolus by ribosomal intergenic spacer noncoding RNA. Mol Cell, 45(2), 147-57 (2012) DOI: 10.1016/j.molcel.2011.12.012
285. T. E. Audas, M. D. Jacob and S. Lee: The nucleolar detention pathway: A cellular strategy for regulating molecular networks. Cell Cycle, 11(11), 2059-62 (2012) DOI: 10.4161/cc.20140
286. M. D. Jacob, T. E. Audas, S. T. Mullineux and S. Lee: Where no RNA polymerase has gone before: novel functional transcripts derived from the ribosomal intergenic spacer. Nucleus, 3(4), 315-9 (2012) DOI: 10.4161/nucl.20585
287. M. D. Jacob, T. E. Audas, J. Uniacke, L. Trinkle-Mulcahy and S. Lee: Environmental cues induce a long noncoding RNA-dependent remodeling of the nucleolus. Mol Biol Cell, 24(18), 2943-53 (2013) DOI: 10.1091/mbc.E13-04-0223
288. T. Chen, F. M. Boisvert, D. P. Bazett-Jones and S. Richard: A role for the GSG domain in localizing Sam68 to novel nuclear structures in cancer cell lines. Mol Biol Cell, 10(9), 3015-33 (1999) DOI: 10.1091/mbc.10.9.3015
289. M. A. Karreman, A. V. Agronskaia, A. J. Verkleij, F. F. Cremers, H. C. Gerritsen and B. M. Humbel: Discovery of a new RNA-containing nuclear structure in UVC=induced apoptotic cells by integrated laser electron microscopy. Biol Cell, 101(5), 287-99 (2009) DOI: 10.1042/BC20080076
290. Q. F. Yin, L. Yang, Y. Zhang, J. F. Xiang, Y. W. Wu, G. G. Carmichael and L. L. Chen: Long noncoding RNAs with snoRNA ends. Mol Cell, 48(2), 219-30 (2012) DOI: 10.1016/j.molcel.2012.07.033
291. S. B. Cassidy, S. Schwartz, J. L. Miller and D. J. Driscoll: Prader-Willi syndrome. Genet Med, 14(1), 10-26 (2012) DOI: 10.1038/gim.0b013e31822bead0
292. M. D. Blower, M. Nachury, R. Heald and K. Weis: A Rae1-containing ribonucleoprotein complex is required for mitotic spindle assembly. Cell, 121(2), 223-34 (2005) DOI: 10.1016/j.cell.2005.02.016
293. M. D. Blower, E. Feric, K. Weis and R. Heald: Genome-wide analysis demonstrates conserved localization of messenger RNAs to mitotic microtubules. J Cell Biol, 179(7), 1365-73 (2007) DOI: 10.1083/jcb.200705163
294. A. Jambhekar, A. B. Emerman, C. T. Schweidenback and M. D. Blower: RNA stimulates Aurora B kinase activity during mitosis. PLoS One, 9(6), e100748 (2014) DOI: 10.1371/journal.pone.0100748
295. M. Kloc, K. Wilk, D. Vargas, Y. Shirato, S. Bilinski and L. D. Etkin: Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes. Development, 132(15), 3445-57 (2005) DOI: 10.1242/dev.01919
296. M. Kloc, S. Bilinski and M. T. Dougherty: Organization of cytokeratin cytoskeleton and germ plasm in the vegetal cortex of Xenopus laevis oocytes depends on coding and non-coding RNAs: threedimensional and ultrastructural analysis. Exp Cell Res, 313(8), 1639-51 (2007) DOI: 10.1016/j.yexcr.2007.02.018
297. C. L. de Hoog, L. J. Foster and M. Mann: RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centers. Cell, 117(5), 649-62 (2004) DOI: 10.1016/S0092-8674(04)00456-8
298. M. Wojciechowska and W. J. Krzyzosiak: Cellular toxicity of expanded RNA repeats: focus on RNA foci. Hum Mol Genet, 20(19), 3811-21 (2011) DOI: 10.1093/hmg/ddr299
299. M. Ramaswami, J. P. Taylor and R. Parker: Altered ribostasis: RNA-protein granules in degenerative disorders. Cell, 154(4), 727-36 (2013) DOI: 10.1016/j.cell.2013.07.038
300. V. V. Belzil, T. F. Gendron and L. Petrucelli: RNA-mediated toxicity in neurodegenerative disease. Mol Cell Neurosci, 56, 406-19 (2013) DOI: 10.1016/j.mcn.2012.12.006
301. D. L. Nelson, H. T. Orr and S. T. Warren: The unstable repeats - three evolving faces of neurological disease. Neuron, 77(5), 825-43 (2013) DOI: 10.1016/j.neuron.2013.02.022
302. A. Mohan, M. Goodwin and M. S. Swanson: RNA-protein interactions in unstable microsatellite diseases. Brain Res (2014) DOI: 10.1016/j.brainres.2014.03.039
303. R. N. Kanadia, K. A. Johnstone, A. Mankodi, C. Lungu, C. A. Thornton, D. Esson, A. M. Timmers, W. W. Hauswirth and M. S. Swanson: A muscleblind knockout model for myotonic dystrophy. Science, 302(5652), 1978-80 (2003) DOI: 10.1126/science.1088583
304. R. N. Kanadia, J. Shin, Y. Yuan, S. G. Beattie, T. M. Wheeler, C. A. Thornton and M. S. Swanson: Reversal of RNA missplicing and myotonia after muscleblind overexpression in a mouse poly(CUG) model for myotonic dystrophy. Proc Natl Acad Sci U S A, 103(31), 11748-53 (2006) DOI: 10.1073/pnas.0604970103
305. C. Sellier, F. Rau, Y. Liu, F. Tassone, R. K. Hukema, R. Gattoni, A. Schneider, S. Richard, R. Willemsen, D. J. Elliott, P. J. Hagerman and N. Charlet-Berguerand: Sam68 sequestration and partial loss of function are associated with splicing alterations in FXTAS patients. EMBO J, 29(7), 1248-61 (2010) DOI: 10.1038/emboj.2010.21
306. A. E. Renton, E. Majounie, A. Waite, J. Simón-Sánchez, S. Rollinson, J. R. Gibbs, J. C. Schymick, H. Laaksovirta, J. C. van Swieten, L. Myllykangas, H. Kalimo, A. Paetau, Y. Abramzon, A. M. Remes, A. Kaganovich, S. W. Scholz, J. Duckworth, J. Ding, D. W. Harmer, D. G. Hernandez, J. O. Johnson, K. Mok, M. Ryten, D. Trabzuni, R. J. Guerreiro, R. W. Orrell, J. Neal, A. Murray, J. Pearson, I. E. Jansen, D. Sondervan, H. Seelaar, D. Blake, K. Young, N. Halliwell, J. B. Callister, G. Toulson, A. Richardson, A. Gerhard, J. Snowden, D. Mann, D. Neary, M. A. Nalls, T. Peuralinna, L. Jansson, V. M. Isoviita, A. L. Kaivorinne, M. Hölttä-Vuori, E. Ikonen, R. Sulkava, M. Benatar, J. Wuu, A. Chiò, G. Restagno, G. Borghero, M. Sabatelli, D. Heckerman, E. Rogaeva, L. Zinman, J. D. Rothstein, M. Sendtner, C. Drepper, E. E. Eichler, C. Alkan, Z. Abdullaev, S. D. Pack, A. Dutra, E. Pak, J. Hardy, A. Singleton, N. M. Williams, P. Heutink, S. Pickering-Brown, H. R. Morris, P. J. Tienari, B. J. Traynor and I. Consortium: A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron, 72(2), 257-68 (2011) DOI: 10.1016/j.neuron.2011.09.010
307. M. DeJesus-Hernandez, I. R. Mackenzie, B. F. Boeve, A. L. Boxer, M. Baker, N. J. Rutherford, A. M. Nicholson, N. A. Finch, H. Flynn, J. Adamson, N. Kouri, A. Wojtas, P. Sengdy, G. Y. Hsiung, A. Karydas, W. W. Seeley, K. A. Josephs, G. Coppola, D. H. Geschwind, Z. K. Wszolek, H. Feldman, D. S. Knopman, R. C. Petersen, B. L. Miller, D. W. Dickson, K. B. Boylan, N. R. Graff-Radford and R. Rademakers: Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron, 72(2), 245-56 (2011) DOI: 10.1016/j.neuron.2011.09.011
308. A. Ghetti, S. Piñol-Roma, W. M. Michael, C. Morandi and G. Dreyfuss: hnRNP I, the polypyrimidine tract-binding protein: distinct nuclear localization and association with hnRNAs. Nucleic Acids Res, 20(14), 3671-8 (1992) DOI: 10.1093/nar/20.14.3671
309. W. Schul, B. Groenhout, K. Koberna, Y. Takagaki, A. Jenny, E. M. Manders, I. Raska, R. van Driel and L. de Jong: The RNA 3' cleavage factors CstF 64 kDa and CPSF 100 kDa are concentrated in nuclear domains closely associated with coiled bodies and newly synthesized RNA. EMBO J, 15(11), 2883-92 (1996) No DOI Found
310. S. Bléoo, X. Sun, M. J. Hendzel, J. M. Rowe, M. Packer and R. Godbout: Association of human DEAD box protein DDX1 with a cleavage stimulation factor involved in 3'-end processing of preMRNA. Mol Biol Cell, 12(10), 3046-59 (2001) DOI: 10.1091/mbc.12.10.3046
311. L. Li, K. Roy, S. Katyal, X. Sun, S. Bléoo and R. Godbout: Dynamic nature of cleavage bodies and their spatial relationship to DDX1 bodies, Cajal bodies, and gems. Mol Biol Cell, 17(3), 1126-40 (2006) DOI: 10.1091/mbc.E05-08-0768
312. P. Mähl, Y. Lutz, E. Puvion and J. P. Fuchs: Rapid effect of heat shock on two heterogeneous nuclear ribonucleoprotein-associated antigens in HeLa cells. J Cell Biol, 109(5), 1921-35 (1989) DOI: 10.1083/jcb.109.5.1921
313. P. Buchenau, J. Hodgson, H. Strutt and D. J. Arndt-Jovin: The distribution of polycomb-group proteins during cell division and development in Drosophila embryos: impact on models for silencing. J Cell Biol, 141(2), 469-81 (1998) DOI: 10.1083/jcb.141.2.469
314. A. J. Saurin, C. Shiels, J. Williamson, D. P. Satijn, A. P. Otte, D. Sheer and P. S. Freemont: The human polycomb group complex associates with pericentromeric heterochromatin to form a novel nuclear domain. J Cell Biol, 142(4), 887-98 (1998) DOI: 10.1083/jcb.142.4.887
315. A. Pombo, P. Cuello, W. Schul, J. B. Yoon, R. G. Roeder, P. R. Cook and S. Murphy: Regional and temporal specialization in the nucleus: a transcriptionally-active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle. EMBO J, 17(6), 1768-78 (1998) DOI: 10.1093/emboj/17.6.1768
316. M. Lafarga, M. T. Berciano, E. Pena, I. Mayo, J. G. Castaño, D. Bohmann, J. P. Rodrigues, J. P. Tavanez and M. Carmo-Fonseca: Clastosome: a subtype of nuclear body enriched in 19S and 20S proteasomes, ubiquitin, and protein substrates of proteasome. Mol Biol Cell, 13(8), 2771-82 (2002)