Paraspeckles: Nuclear bodies built on long noncoding RNA

Journal of Cell Biology

Volumn 186, Issue 5, 2009, Pages 637-644

  Bond, Charles S ^a   Fox, Archa H ^b  

^a UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

PARASPECKLE PROTEIN; RIBONUCLEOPROTEIN; TRANSCRIPTOME; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

CELL DIFFERENTIATION; CELL NUCLEUS; CELL NUCLEUS INCLUSION BODY; CELL STRUCTURE; CHROMATIN; DROSOPHILA MELANOGASTER; GENE EXPRESSION; MAMMAL CELL; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA SPLICING; RNA TRANSCRIPTION;

ANIMALS; CELL NUCLEUS; GENE EXPRESSION REGULATION; HUMANS; INTRANUCLEAR INCLUSION BODIES; NUCLEAR MATRIX-ASSOCIATED PROTEINS; NUCLEAR PROTEINS; OCTAMER TRANSCRIPTION FACTORS; RNA, UNTRANSLATED; RNA-BINDING PROTEINS;

DROSOPHILA MELANOGASTER; MAMMALIA;

EID: 69949132008     PISSN: 00219525     EISSN: 00219525     Source Type: Journal    
DOI: 10.1083/jcb.200906113     Document Type: Review

References (54)

1. Amelio, A.L., L.J. Miraglia, J.J. Conkright, B.A. Mercer, S. Batalov, V. Cavett, A.P. Orth, J. Busby, J.B. Hogenesch, and M.D. Conkright. 2007. A coactivator trap identifies NONO (p54nrb) as a component of the cAMP-signaling pathway. Proc. Natl. Acad. Sci. USA. 104:20314-20319.
2. Andersen, J.S., C.E. Lyon, A.H. Fox, A.K.L. Leung, Y.W. Lam, H. Steen, M. Mann, and A.I. Lamond. 2002. Directed proteomic analysis of the human nucleolus. Curr. Biol. 12:1-11. (Pubitemid 34063348)
3. Brown, S.A., J. Ripperger, S. Kadener, F. Fleury-Olela, F. Vilbois, M. Rosbash, and U. Schibler. 2005. PERIOD1-associated proteins modulate the negative limb of the mammalian circadian oscillator. Science. 308:693-696.
4. Cardinale, S., B. Cisterna, P. Bonetti, C. Aringhieri, M. Biggiogera, and S.M. Barabino. 2007. Subnuclear localization and dynamics of the Pre-mRNA 3′ end processing factor mammalian cleavage factor I 68-kDa subunit. Mol. Biol. Cell. 18:1282-1292. (Pubitemid 46626623)
5. Carninci, P., T. Kasukawa, S. Katayama, J. Gough, M.C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, et al. 2005. The transcriptional landscape of the mammalian genome. Science. 309:1559-1563.
6. Chen, L.L., and G.G. Carmichael. 2009. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol. Cell. doi:10.1016/j.molcel.2009.06.027.
7. Chen, L.L., J.N. DeCerbo, and G.G. Carmichael. 2008. Alu element-mediated gene silencing. EMBO J. 27:1694-1705.
8. Clemson, C.M., J.N. Hutchinson, S.A. Sara, A.W. Ensminger, A.H. Fox, A. Chess, and J.B. Lawrence. 2009. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol. Cell. 33:717-726.
9. Dettwiler, S., C. Aringhieri, S. Cardinale, W. Keller, and S.M. Barabino. 2004. Distinct sequence motifs within the 68-kDa subunit of cleavage factor Im mediate RNA binding, protein-protein interactions, and subcellular localization. J. Biol. Chem. 279:35788-35797. (Pubitemid 39100585)
10. Dong, B., D.S. Horowitz, R. Kobayashi, and A.R. Krainer. 1993. Purification and cDNA cloning of HeLa cell p54nrb, a nuclear protein with two RNA recognition motifs and extensive homology to human splicing factor PSF and Drosophila NONA/BJ6. Nucleic Acids Res. 21:4085-4092. (Pubitemid 23258726)
11. Dong, X., O. Shylnova, J.R. Challis, and S.J. Lye. 2005. Identification and characterization of the protein-associated splicing factor as a negative coregulator of the progesterone receptor. J. Biol. Chem. 280:13329-13340. (Pubitemid 40517219)
12. Dutton, J.R., D. Lahiri, and A. Ward. 2006. Different isoforms of the Wilms' tumour protein WT1 have distinct patterns of distribution and trafficking within the nucleus. Cell Prolif. 39:519-535.
13. Fox, A.H., Y.W. Lam, A.K. Leung, C.E. Lyon, J. Andersen, M. Mann, and A.I. Lamond. 2002. Paraspeckles: a novel nuclear domain. Curr. Biol. 12:13-25.
14. Fox, A.H., C.S. Bond, and A.I. Lamond. 2005. P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in an RNA-dependent manner. Mol. Biol. Cell. 16:5304-5315.
15. Hata, K., R. Nishimura, S. Muramatsu, A. Matsuda, T. Matsubara, K. Amano, F. Ikeda, V.R. Harley, and T. Yoneda. 2008. Paraspeckle protein p54nrb links Sox9-mediated transcription with RNA processing during chondrogenesis in mice. J. Clin. Invest. 118:3098-3108.
16. Hutchinson, J.N., A.W. Ensminger, C.M. Clemson, C.R. Lynch, J.B. Lawrence, and A. Chess. 2007. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics. 8:39.
17. Iseli, C., B.J. Stevenson, S.J. de Souza, H.B. Samaia, A.A. Camargo, K.H. Buetow, R.L. Strausberg, A.J. Simpson, P. Bucher, and C.V. Jongeneel. 2002. Long-range heterogeneity at the 3′ ends of human mRNAs. Genome Res. 12:1068-1074. (Pubitemid 34785199)
18. Ito, T., H. Watanabe, N. Yamamichi, S. Kondo, T. Tando, T. Haraguchi, T. Mizutani, K. Sakurai, S. Fujita, T. Izumi, et al. 2008. Brm transactivates the telomerase reverse transcriptase (TERT) gene and modulates the splicing patterns of its transcripts in concert with p54(nrb). Biochem. J. 411:201-209.
19. Kameoka, S., P. Duque, and M.M. Konarska. 2004. p54(nrb) associates with the 5′ splice site within large transcription/splicing complexes. EMBO J. 23:1782-1791. (Pubitemid 38649641)
20. Kaneko, S., O. Rozenblatt-Rosen, M. Meyerson, and J.L. Manley. 2007. The multifunctional protein p54nrb/PSF recruits the exonuclease XRN2 to facilitate pre-mRNA 3′ processing and transcription termination. Genes Dev. 21:1779-1789. (Pubitemid 47076477)
21. Kay, R.A., I.R. Ellis, S.J. Jones, S. Perrier, M.M. Florence, A.M. Schor, and S.L. Schor. 2005. The expression of migration stimulating factor, a potent oncofetal cytokine, is uniquely controlled by 3′-untranslated region-dependent nuclear sequestration of its precursor messenger RNA. Cancer Res. 65:10742-10749.
22. Kiesler, E., F. Miralles, A.K. Ostlund Farrants, and N. Visa. 2003. The Hrp65 self-interaction is mediated by an evolutionarily conserved domain and is required for nuclear import of Hrp65 isoforms that lack a nuclear localization signal. J. Cell Sci. 116:3949-3956. (Pubitemid 37279310)
23. Kuwahara, S., A. Ikei, Y. Taguchi, Y. Tabuchi, N. Fujimoto, M. Obinata, S. Uesugi, and Y. Kurihara. 2006. PSPC1, NONO, and SFPQ are expressed in mouse Sertoli cells and may function as coregulators of androgen receptor-mediated transcription. Biol. Reprod. 75:352-359. (Pubitemid 44268069)
24. Levanon, K., E. Eisenberg, G. Rechavi, and E.Y. Levanon. 2005. Letter from the editor: Adenosine-to-inosine RNA editing in Alu repeats in the human genome. EMBO Rep. 6:831-835. (Pubitemid 43108672)
25. Ling, S.H., C.J. Decker, M.A. Walsh, M. She, R. Parker, and H. Song. 2008. Crystal structure of human Edc3 and its functional implications. Mol. Cell. Biol. 28:5965-5976.
26. Liu, H., G.C. Ippolito, J.K. Wall, T. Niu, L. Probst, B.S. Lee, K. Pulford, A.H. Banham, L. Stockwin, A.L. Shaffer, et al. 2006. 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. (Pubitemid 44202722)
27. Mathur, M., P.W. Tucker, and H.H. Samuels. 2001. PSF is a novel corepressor that mediates its effect through Sin3A and the DNA binding domain of nuclear hormone receptors. Mol. Cell. Biol. 21:2298-2311. (Pubitemid 32222084)
28. Mercer, T.R., M.E. Dinger, and J.S. Mattick. 2009. Long noncoding RNAs: insights into functions. Nat. Rev. Genet. 10:155-159.
29. Myojin, R., S. Kuwahara, T. Yasaki, T. Matsunaga, T. Sakurai, M. Kimura, S. Uesugi, and Y. Kurihara. 2004. Expression and functional significance of mouse paraspeckle protein 1 on spermatogenesis. Biol. Reprod. 71:926-932. (Pubitemid 39108655)
30. O'Rourke, J.R., and M.S. Swanson. 2009. Mechanisms of RNA-mediated disease. J. Biol. Chem. 284:7419-7423.
31. Osenberg, S., D. Dominissini, G. Rechavi, and E. Eisenberg. 2009. Widespread cleavage of A-to-I hyperediting substrates. RNA.
32. Patton, J.G., E.B. Porro, J. Galceran, P. Tempst, and B. Nadal-Ginard. 1993. Cloning and characterization of PSF, a novel pre-mRNA splicing factor. Genes Dev. 7:393-406. (Pubitemid 23139233)
33. Peng, R., B.T. Dye, I. Pérez, D.C. Barnard, A.B. Thompson, and J.G. Patton. 2002. PSF and p54nrb bind a conserved stem in U5 snRNA. RNA. 8:1334-1347.
34. Platani, M., and A.I. Lamond. 2004. Nuclear organisation and subnuclear bodies. Prog. Mol. Subcell. Biol. 35:1-22.
35. Prasanth, K.V., and D.L. Spector. 2007. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev. 21:11-42.
36. Prasanth, K.V., S.G. Prasanth, Z. Xuan, S. Hearn, S.M. Freier, C.F. Bennett, M.Q. Zhang, and D.L. Spector. 2005. Regulating gene expression through RNA nuclear retention. Cell. 123:249-263.
37. Proteau, A., S. Blier, A.L. Albert, S.B. Lavoie, A.M. Traish, and M. Vincent. 2005. The multifunctional nuclear protein p54nrb is multiphosphorylated in mitosis and interacts with the mitotic regulator Pin1. J. Mol. Biol. 346:1163-1172. (Pubitemid 40215536)
38. Puvion-Dutilleul, F., S. Besse, E.K. Chan, E.M. Tan, and E. Puvion. 1995. p80coilin: a component of coiled bodies and interchromatin granule-associated zones. J. Cell Sci. 108:1143-1153.
39. Rivera, M.N., W.J. Kim, J. Wells, A. Stone, A. Burger, E.J. Coffman, J. Zhang, and D.A. Haber. 2009. The tumor suppressor WTX shuttles to the nucleus and modulates WT1 activity. Proc. Natl. Acad. Sci. USA. 106:8338-8343.
40. Royo, H., E. Basyuk, V. Marty, M. Marques, E. Bertrand, and J. Cavaillé. 2007. Bsr, a nuclear-retained RNA with monoallelic expression. Mol. Biol. Cell. 18:2817-2827. (Pubitemid 47235290)
41. Saha, S., S. Murthy, and P.N. Rangarajan. 2006. Identification and characterization of a virus-inducible noncoding RNA in mouse brain. J. Gen. Virol. 87:1991-1995. (Pubitemid 43985882)
42. Sasaki, Y.T., T. Ideue, M. Sano, T. Mituyama, and T. Hirose. 2009. MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc. Natl. Acad. Sci. USA. 106:2525-2530.
43. Shav-Tal, Y., and D. Zipori. 2002. PSF and p54(nrb)/NonO - multifunctional nuclear proteins. FEBS Lett. 531:109-114. (Pubitemid 35341179)
44. Shav-Tal, Y., J. Blechman, X. Darzacq, C. Montagna, B.T. Dye, J.G. Patton, R.H. Singer, and D. Zipori. 2005. Dynamic sorting of nuclear components into distinct nucleolar caps during transcriptional inhibition. Mol. Biol. Cell. 16:2395-2413. (Pubitemid 40632221)
45. Sone, M., T. Hayashi, H. Tarui, K. Agata, M. Takeichi, and S. Nakagawa. 2007. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J. Cell Sci. 120:2498-2506. (Pubitemid 47323859)
46. Sunwoo, H., M.E. Dinger, J.E. Wilusz, P.P. Amaral, J.S. Mattick, and D.L. Spector. 2009. MEN epsilon/beta nuclear-retained non-coding RNAs are upregulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 19:347-359.
47. Visa, N., F. Puvion-Dutilleul, J.P. Bachellerie, and E. Puvion. 1993. 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. 60:308-321. (Pubitemid 23139649)
48. Weis, K., S. Rambaud, C. Lavau, J. Jansen, T. Carvalho, M. Carmo-Fonseca, A. Lamond, and A. Dejean. 1994. Retinoic acid regulates aberrant nuclear localization of PML-RAR alpha in acute promyelocytic leukemia cells. Cell. 76:345-356. (Pubitemid 24046696)
49. Wilusz, J.E., S.M. Freier, and D.L. Spector. 2008. 3′ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell. 135:919-932.
50. Xie, S.Q., S. Martin, P.V. Guillot, D.L. Bentley, and A. Pombo. 2006. 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. 17:1723-1733.
51. Yang, Y.S., J.H. Hanke, L. Carayannopoulos, C.M. Craft, J.D. Capra, and P.W. Tucker. 1993. NonO, a non-POU-domain-containing, octamer-binding protein, is the mammalian homolog of Drosophila nonAdiss. Mol. Cell. Biol. 13:5593-5603. (Pubitemid 23260661)
52. Yang, Y.S., M.C. Yang, P.W. Tucker, and J.D. Capra. 1997. NonO enhances the association of many DNA-binding proteins to their targets. Nucleic Acids Res. 25:2284-2292.
53. Zhang, Z., and G.G. Carmichael. 2001. The fate of dsRNA in the nucleus: a p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell. 106:465-475. (Pubitemid 32786990)
54. Zolotukhin, A.S., D. Michalowski, J. Bear, S.V. Smulevitch, A.M. Traish, R. Peng, J. Patton, I.N. Shatsky, and B.K. Felber. 2003. PSF acts through the human immunodeficiency virus type 1 mRNA instability elements to regulate virus expression. Mol. Cell. Biol. 23:6618-6630.