Retention and repression: Fates of hyperedited RNAs in the nucleus

Current Opinion in Cell Biology

Volumn 17, Issue 3, 2005, Pages 302-308

  DeCerbo, Joshua ^a   Carmichael, Gordon G ^a  

^a UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; HELIX LOOP HELIX PROTEIN; RNA;

ALTERNATIVE RNA SPLICING; CELL NUCLEUS MEMBRANE; DNA REPAIR; DNA STRAND; DNA STRUCTURE; DNA SUPERCOILING; EXCISION REPAIR; GENE REPRESSION; HETEROCHROMATIN; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN NUCLEIC ACID INTERACTION; PROTEIN RNA BINDING; REVIEW; RNA BINDING; RNA EDITING; RNA SEQUENCE; RNA SPLICING; RNA STRUCTURE; STRUCTURAL HOMOLOGY; TRANSCRIPTION INITIATION;

ACTIVE TRANSPORT, CELL NUCLEUS; ADENOSINE DEAMINASE; ANIMALS; ANTIGENS, NUCLEAR; AUTOANTIGENS; CELL NUCLEUS; DEAD-BOX RNA HELICASES; DNA-BINDING PROTEINS; HUMANS; MODELS, BIOLOGICAL; NEOPLASM PROTEINS; NUCLEAR PROTEINS; RNA EDITING; RNA HELICASES; RNA INTERFERENCE; RNA TRANSPORT; RNA, DOUBLE-STRANDED; RNA-BINDING PROTEINS;

MAMMALIA;

EID: 19344368678     PISSN: 09550674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ceb.2005.04.008     Document Type: Review

References (55)

1. B. Lehner, G. Williams, R.D. Campbell, and C.M. Sanderson Antisense transcripts in the human genome Trends Genet 18 2002 63 65
2. J. Shendure, and G.M. Church Computational discovery of sense-antisense transcription in the human and mouse genomes Genome Biol 3 2002 44
3. H. Kiyosawa, I. Yamanaka, N. Osato, S. Kondo, and Y. Hayashizaki Antisense transcripts with FANTOM2 clone set and their implications for gene regulation Genome Res 13 2003 1324 1334
4. R. Yelin, D. Dahary, R. Sorek, E.Y. Levanon, O. Goldstein, A. Shoshan, A. Diber, S. Biton, Y. Tamir, and R. Khosravi Widespread occurrence of antisense transcription in the human genome Nat Biotechnol 21 2003 379 386 These authors use computational methods to show that antisense transcription in the human genome is far more extensive than had previously been appreciated.
5. J. Chen, M. Sun, W.J. Kent, X. Huang, H. Xie, W. Wang, G. Zhou, R.Z. Shi, and J.D. Rowley Over 20% of human transcripts might form sense-antisense pairs Nucleic Acids Res 32 2004 4812 4820
6. Q. Wang, and G.G. Carmichael Effects of length and location on the cellular response to double-stranded RNA Microbiol Mol Biol Rev 68 2004 432 452
7. B.L. Bass RNA editing by adenosine deaminases that act on RNA Annu Rev Biochem 71 2002 817 846
8. A.G. Polson, P.F. Crain, S.C. Pomerantz, J.A. McCloskey, and B.L. Bass The mechanism of adenosine to inosine conversion by the double-stranded RNA unwinding/modifying activity: a high-performance liquid chromatography-mass spectrometry analysis Biochemistry 30 1991 11507 11514
9. R.A. Reenan The RNA world meets behavior: A-I pre-mRNA editing in animals Trends Genet 17 2001 53 56
10. A.M. Kallman, M. Sahlin, and M. Ohman ADAR2 A-I editing: site selectivity and editing efficiency are separate events Nucleic Acids Res 31 2003 4874 4881
11. S.K. Wong, S. Sato, and D.W. Lazinski Substrate recognition by ADAR1 and ADAR2 RNA 7 2001 846 858
12. B. Hoopengardner, T. Bhalla, C. Staber, and R. Reenan Nervous system targets of RNA editing identified by comparative genomics Science 301 2003 832 836
13. C.R. Eckmann, and M.F. Jantsch The RNA-editing enzyme ADAR1 is localized to the nascent ribonucleoprotein matrix on Xenopus lampbrush chromosomes but specifically associates with an atypical loop J Cell Biol 144 1999 603 615
14. A. Strehblow, M. Hallegger, and M.F. Jantsch Nucleocytoplasmic distribution of human RNA-editing enzyme ADAR1 is modulated by double-stranded RNA-binding domains, a leucine-rich export signal, and a putative dimerization domain Mol Biol Cell 13 2002 3822 3835
15. O. Raitskin, D.S. Cho, J. Sperling, K. Nishikura, and R. Sperling RNA editing activity is associated with splicing factors in lnRNP particles: the nuclear pre-mRNA processing machinery Proc Natl Acad Sci USA 98 2001 6571 6576
16. K. Nishikura Modulation of double-stranded RNAs in vivo by RNA duplex unwindase Ann N Y Acad Sci 660 1992 240 250
17. B.L. Bass, and H. Weintraub An unwinding activity that covalently modifies its double-stranded RNA substrate Cell 55 1988 1089 1098
18. A.G. Polson, and B.L. Bass Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase EMBO J 13 1994 5701 5711
19. Z. Liu, D.B. Batt, and G.G. Carmichael Targeted nuclear antisense RNA mimics natural antisense-induced degradation of polyoma virus early RNA Proc Natl Acad Sci USA 91 1994 4258 4262
20. M. Kumar, and G.G. Carmichael Nuclear antisense RNA induces extensive adenosine modifications and nuclear retention of target transcripts Proc Natl Acad Sci USA 94 1997 3542 3547
21. 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 2001 465 475
22. B. Dong, D.S. Horowitz, R. Kobayashi, and A.R. Krainer 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 1993 4085 4092
23. S. Kameoka, P. Duque, and M.M. Konarska p54(nrb) associates with the 5′ splice site within large transcription/splicing complexes EMBO J 23 2004 1782 1791
24. Y.S. Yang, J.H. Hanke, L. Carayannopoulos, C.M. Craft, J.D. Capra, and P.W. Tucker NonO, a non-POU-domain-containing, octamer-binding protein, is the mammalian homolog of Drosophila nonAdiss Mol Cell Biol 13 1993 5593 5603
25. O. Gozani, J.G. Patton, and R. Reed A novel set of spliceosome-associated proteins and the essential splicing factor PSF bind stably to pre-mRNA prior to catalytic step II of the splicing reaction EMBO J 13 1994 3356 3367
26. J.G. Patton, E.B. Porro, J. Galceran, P. Tempst, and B. Nadal-Ginard Cloning and characterization of PSF, a novel pre-mRNA splicing factor Genes Dev 7 1993 393 406
27. L.A. Lindsey, A.J. Crow, and M.A. Garcia-Blanco A mammalian activity required for the second step of pre-messenger RNA splicing J Biol Chem 270 1995 13415 13421
28. W.W. Zhang, L.X. Zhang, R.K. Busch, J. Farres, and H. Busch Purification and characterization of a DNA-binding heterodimer of 52 and 100 kDa from HeLa cells Biochem J 290 1993 267 272
29. R.J. Urban, Y. Bodenburg, A. Kurosky, T.G. Wood, and S. Gasic Polypyrimidine tract-binding protein-associated splicing factor is a negative regulator of transcriptional activity of the porcine p450scc insulin-like growth factor response element Mol Endocrinol 14 2000 774 782
30. M. Mathur, P.W. Tucker, and H.H. Samuels PSF is a novel corepressor that mediates its effect through Sin3A and the DNA binding domain of nuclear hormone receptors Mol Cell Biol 21 2001 2298 2311
31. A.T. Akhmedov, and B.S. Lopez Human 100-kDa homologous DNA-pairing protein is the splicing factor PSF and promotes DNA strand invasion Nucleic Acids Res 28 2000 3022 3030
32. 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 2002 1102 1111
33. Bladen CL, Udayakumar D, Takeda Y, Dynan WS: Identification of the PSF-p54(nrb) complex as a candidate DNA double-strand break rejoining factor. J Biol Chem 2005, in press.
34. P. Belgrader, R. Dey, and R. Berezney Molecular cloning of matrin 3: a 125-kilodalton protein of the nuclear matrix contains an extensive acidic domain J Biol Chem 266 1991 9893 9899
35. Y. Hibino Functional arrangement of genomic DNA and structure of nuclear matrix Yakugaku Zasshi 120 2000 520 533
36. Y. Hibino, H. Ohzeki, N. Sugano, and K. Hiraga Transcription modulation by a rat nuclear scaffold protein, P130, and a rat highly repetitive DNA component or various types of animal and plant matrix or scaffold attachment regions Biochem Biophys Res Commun 279 2000 282 287
37. A.M. Denli, and G.J. Hannon RNAi: an ever-growing puzzle Trends Biochem Sci 28 2003 196 201 An excellent review of RNAi and the connection between dsRNA and gene silencing.
38. J.M. Bailis, and S.L. Forsburg RNAi hushes heterochromatin Genome Biol 3 2002 REVIEWS1035
39. R. Allshire Molecular biology. RNAi and heterochromatin - a hushed-up affair Science 297 2002 1818 1819
40. I.M. Hall, G.D. Shankaranarayana, K. Noma, N. Ayoub, A. Cohen, and S.I. Grewal Establishment and maintenance of a heterochromatin domain Science 297 2002 2232 2237
41. T.A. Volpe, C. Kidner, I.M. Hall, G. Teng, S.I. Grewal, and R.A. Martienssen Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi Science 297 2002 1833 1837
42. Q. Wang, Z. Zhang, K. Blackwell, and G.G. Carmichael Vigilins bind to promiscuously A-to-I edited RNAs and are involved in the formation of heterochromatin Curr Biol 15 2005 384 391 Both biochemical and cell biology approaches are used to show that vigilin family members bind to inosine-containing RNAs and exist in complexes that might act in heterochromatic gene silencing.
43. R.E. Dodson, and D.J. Shapiro Vigilin, a ubiquitous protein with 14 K homology domains, is the estrogen-inducible vitellogenin mRNA 3′-untranslated region-binding protein J Biol Chem 272 1997 12249 12252
44. H. Kanamori, R.E. Dodson, and D.J. Shapiro In vitro genetic analysis of the RNA binding site of vigilin, a multi-KH-domain protein Mol Cell Biol 18 1998 3991 4003
45. K.S. Cunningham, R.E. Dodson, M.A. Nagel, D.J. Shapiro, and D.R. Schoenberg Vigilin binding selectively inhibits cleavage of the vitellogenin mRNA 3′-untranslated region by the mRNA endonuclease polysomal ribonuclease 1 Proc Natl Acad Sci USA 97 2000 12498 12502
46. R.E. Dodson, and D.J. Shapiro Regulation of pathways of mRNA destabilization and stabilization Prog Nucleic Acid Res Mol Biol 72 2002 129 164
47. M.H. Klinger, and C. Kruse Immunocytochemical localization of vigilin, a tRNA-binding protein, after cell fractionation and within the exocrine pancreatic cell of the rat Anat Anz 178 1996 331 335
48. A. Cortes, D. Huertas, L. Fanti, S. Pimpinelli, F.X. Marsellach, B. Pina, and F. Azorin DDP1, a single-stranded nucleic acid-binding protein of Drosophila, associates with pericentric heterochromatin and is functionally homologous to the yeast Scp160p, which is involved in the control of cell ploidy EMBO J 18 1999 3820 3833
49. D. Huertas, A. Cortes, J. Casanova, and F. Azorin Drosophila DDP1, a multi-KH-domain protein, contributes to centromeric silencing and chromosome segregation Curr Biol 14 2004 1611 1620 Genetic approaches are used to show that DDP1 is essential for proper chromosome segregation in Drosophila, and that it appears to have a more general role as well in the formation of heterochromatin.
50. S.P. Lees-Miller, and K. Meek Repair of DNA double strand breaks by non-homologous end joining Biochimie 85 2003 1161 1173
51. D.P. Morse, P.J. Aruscavage, and B.L. Bass RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA Proc Natl Acad Sci USA 99 2002 7906 7911
52. D.D. Kim, T.T. Kim, T. Walsh, Y. Kobayashi, T.C. Matise, S. Buyske, and A. Gabriel Widespread RNA editing of embedded Alu elements in the human transcriptome Genome Res 14 2004 1719 1725
53. A. Athanasiadis, A. Rich, and S. Maas Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome PLoS Biol 2 2004 e391 Computational methods identify many instances of editing in human RNAs, most of which are in repetitive elements.
54. E.Y. Levanon, E. Eisenberg, R. Yelin, S. Nemzer, M. Hallegger, R. Shemesh, Z.Y. Fligelman, A. Shoshan, S.R. Pollock, and D. Sztybel Systematic identification of abundant A-to-I editing sites in the human transcriptome Nat Biotechnol 22 2004 1001 1005 Computational methods identify many instances of editing in human RNAs, most of which are in repetitive elements.
55. Eisenberg E, Nemzer S, Kinar Y, Sorek R, Rechavi G, Levanon EY: Is abundant A-to-I RNA editing primate-specific? Trends Genet 2005, in press. This study reveals that the great majority of editing in primates is in Alu elements, which are not found in non-primates. This raises questions about potential biological and evolutionary ramifications.