Regulation of transcription termination in the nematode Caenorhabditis elegans

Nucleic Acids Research

Volumn 37, Issue 20, 2009, Pages 6723-6736

  Haenni, Simon ^a   Sharpe, Helen E ^a   Gravato nobre, Maria ^a   Zechner, Kerstin ^a   Browne, Cathy ^a   Hodgkin, Jonathan ^a   Furger, André ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA PRECURSOR; RNA POLYMERASE II; DNA DIRECTED DNA POLYMERASE ALPHA; MESSENGER RNA; SMALL NUCLEAR RIBONUCLEOPROTEIN;

ARTICLE; CAENORHABDITIS ELEGANS; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA FLANKING REGION; GENE EXPRESSION; GENE LOCATION; INTRON; MICROBIAL GENETICS; NONHUMAN; OPERON; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SPLICING; RNA TRANSCRIPTION; TRANSCRIPTION TERMINATION; ANIMAL; CAENORHABDITIS; DRUG ANTAGONISM; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; RNA INTERFERENCE; TRANS SPLICING;

CAENORHABDITIS ELEGANS; EUKARYOTA;

ANIMALS; CAENORHABDITIS; DNA POLYMERASE II; GENE EXPRESSION REGULATION; INTRONS; OPERON; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RNA INTERFERENCE; RNA SPLICING; RNA, MESSENGER; TRANS-SPLICING; TRANSCRIPTION, GENETIC;

EID: 73349137357     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp744     Document Type: Article

References (51)

1. Greger, I.H., Demarchi, F., Giacca, M. and Proudfoot, N.J. (1998) Transcriptional interference perturbs the binding of Sp1 to the HIV-1 promoter. Nucleic Acids Res., 26, 1294-1301.
2. Bauren, G., Belikov, S. and Wieslander, L. (1998) Transcriptional termination in the Balbiani ring 1 gene is closely coupled to 3′-end formation and excision of the 3′-terminal intron. Genes Dev., 12, 2759-2769.
3. Dye, M.J. and Proudfoot, N.J. (1999) Terminal exon definition occurs cotranscriptionally and promotes termination of RNA polymerase II. Mol. Cell, 3, 371-378.
4. Glover-Cutter, K., Kim, S., Espinosa, J. and Bentley, D.L. (2008) RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat. Struct. Mol. Biol., 15, 71-78.
5. Birse, C.E., Minvielle-Sebastia, L., Lee, B.A., Keller, W. and Proudfoot, N.J. (1998) Coupling termination of transcription to messenger RNA maturation in yeast. Science, 280, 298-301.
6. Kim, M., Ahn, S.H., Krogan, N.J., Greenblatt, J.F. and Buratowski, S. (2004) Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes. EMBO J., 23, 354-364.
7. Birse, C.E., Lee, B.A., Hansen, K. and Proudfoot, N.J. (1997) Transcriptional termination signals for RNA polymerase II infission yeast. EMBO J., 16, 3633-3643.
8. Logan, J., Falck-Pedersen, E., Darnell, J.E. Jr. and Shenk, T. (1987) A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene. Proc. Natl Acad. Sci. USA, 84, 8306-8310.
9. Rosonina, E., Kaneko, S. and Manley, J.L. (2006) Terminating the transcript: breaking up is hard to do. Genes Dev., 20, 1050-1056.
10. Connelly, S. and Manley, J.L. (1988) A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. Genes Dev., 2, 440-452.
11. Whitelaw, E. and Proudfoot, N. (1986) Alpha-thalassaemia caused by a poly(A) site mutation reveals that transcriptional termination is linked to 3′ end processing in the human alpha 2 globin gene. EMBO J., 5, 2915-2922.
12. Proudfoot, N. (2004) New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr. Opin. Cell Biol., 16, 272-278.
13. Luo, W., Johnson, A.W. and Bentley, D.L. (2006) The role of Rat1 in coupling mRNA 3′-end processing to transcription termination: implications for a unified allosteric-torpedo model. Genes Dev., 20, 954-965.
14. Kaneko, S., Rozenblatt-Rosen, O., Meyerson, M. and Manley, J.L. (2007) The multifunctional protein p54nrb/PSF recruits the exonuclease XRN2 to facilitate pre-mRNA 3′ processing and transcription termination. Genes Dev., 21, 1779-1789.
15. West, S., Proudfoot, N.J. and Dye, M.J. (2008) Molecular dissection of mammalian RNA polymerase II transcriptional termination. Mol. Cell, 29, 600-610.
16. Blumenthal, T. (2004) Operons in eukaryotes. Brief Funct. Genomic Proteomic, 3, 199-211.
17. Spieth, J., Brooke, G., Kuersten, S., Lea, K. and Blumenthal, T. (1993) Operons in C. elegans: polycistronic mRNA precursors are processed by trans-splicing of SL2 to downstream coding regions. Cell, 73, 521-532.
18. Hannon, G.J., Maroney, P.A. and Nilsen, T.W. (1991) U small nuclear ribonucleoprotein requirements for nematode cis- and trans-splicing in vitro. J. Biol. Chem., 266, 22792-22795.
19. Huang, T., Kuersten, S., Deshpande, A.M., Spieth, J., MacMorris, M. and Blumenthal, T. (2001) Intercistronic region required for polycistronic pre-mRNA processing in Caenorhabditis elegans. Mol. Cell Biol., 21, 1111-1120.
20. Kuersten, S., Lea, K., MacMorris, M., Spieth, J. and Blumenthal, T. (1997) Relationship between 3′-end formation and SL2-specific trans-splicing in polycistronic Caenorhabditis elegans pre-mRNA processing. RNA, 3, 269-278.
21. Liu, Y., Huang, T., MacMorris, M. and Blumenthal, T. (2001) Interplay between AAUAAA and the trans-splice site in processing of a Caenorhabditis elegans operon pre-mRNA. RNA, 7, 176-181.
22. Liu, Y., Kuersten, S., Huang, T., Larsen, A., MacMorris, M. and Blumenthal, T. (2003) An uncapped RNA suggests a model for Caenorhabditis elegans polycistronic pre-mRNA processing. RNA, 9, 677-687.
23. Evans, D., Perez, I., MacMorris, M., Leake, D., Wilusz, C.J. and Blumenthal, T. (2001) A complex containing CstF-64 and the SL2 snRNP connects mRNA 3′ end formation and trans-splicing in C. elegans operons. Genes Dev., 15, 2562-2571.
24. Johnstone, I.L. (1999) In Hope, I.A. (ed.), C. elegans, A Practical Approach. Oxford University Press, Oxford, Chapter 11, pp. 201-225.
25. Dalziel, M., Nunes, N.M. and Furger, A. (2007) Two G-rich regulatory elements located adjacent to and 440 nucleotides downstream of the core poly(A) site of the intronless melanocortin receptor 1 gene are critical for efficient 3′ end processing. Mol. Cell Biol., 27, 1568-1580.
26. Morillon, A., Karabetsou, N., Nair, A. and Mellor, J. (2005) Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. Mol. Cell, 18, 723-734.
27. Kamath, R.S., Martinez-Campos, M., Zipperlen, P., Fraser, A.G. and Ahringer, J. (2001) Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans. Genome Biol., 2, RESEARCH0002.
28. Blumenthal, T., Evans, D., Link, C.D., Guffanti, A., Lawson, D., Thierry-Mieg, J., Thierry-Mieg, D., Chiu, W.L., Duke, K., Kiraly, M. et al. (2002) A global analysis of Caenorhabditis elegans operons. Nature, 417, 851-854.
29. Oka, T., Yamamoto, R. and Futai, M. (1997) Three vha genes encode proteolipids of Caenorhabditis elegans vacuolar-type ATPase. Gene structures and preferential expression in an H-shaped excretory cell and rectal cells. J. Biol. Chem., 272, 24387-24392.
30. Le Hir, H., Nott, A. and Moore, M.J. (2003) How introns influence and enhance eukaryotic gene expression. Trends Biochem. Sci., 28, 215-220.
31. Ashe, M.P., Griffin, P., James, W. and Proudfoot, N.J. (1995) Poly(A) site selection in the HIV-1 provirus: inhibition of promoter-proximal polyadenylation by the downstream major splice donor site. Genes Dev., 9, 3008-3025.
32. Sonnichsen, B., Koski, L.B., Walsh, A., Marschall, P., Neumann, B., Brehm, M., Alleaume, A.M., Artelt, J., Bettencourt, P., Cassin, E. et al. (2005) Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature, 434, 462-469.
33. Guiliano, D.B. and Blaxter, M.L. (2006) Operon conservation and the evolution of trans-splicing in the phylum Nematoda. PLoS Genet., 2, e198.
34. Ganot, P., Kallesoe, T., Reinhardt, R., Chourrout, D. and Thompson, E.M. (2004) Spliced-leader RNA trans splicing in a chordate, Oikopleura dioica, with a compact genome. Mol. Cell Biol., 24, 7795-7805.
35. Davis, R.E. and Hodgson, S. (1997) Gene linkage and steady state RNAs suggest trans-splicing may be associated with a polycistronic transcript in Schistosoma mansoni. Mol. Biochem. Parasitol., 89, 25-39.
36. Jager, A.V., De Gaudenzi, J.G., Cassola, A., D'Orso, I. and Frasch, A.C. (2007) mRNA maturation by two-step trans-splicing/polyadenylation processing in trypanosomes. Proc. Natl Acad. Sci. USA, 104, 2035-2042.
37. Fong, Y.W. and Zhou, Q. (2001) Stimulatory effect of splicing factors on transcriptional elongation. Nature, 414, 929-933.
38. Furger, A., O'Sullivan, J.M., Binnie, A., Lee, B.A. and Proudfoot, N.J. (2002) Promoter proximal splice sites enhance transcription. Genes Dev., 16, 2792-2799.
39. Tange, T.O., Nott, A. and Moore, M.J. (2004) The ever-increasing complexities of the exon junction complex. Curr. Opin. Cell Biol., 16, 279-284.
40. Hachet, O. and Ephrussi, A. (2004) Splicing of oskar RNA in the nucleus is coupled to its cytoplasmic localization. Nature, 428, 959-963.
41. Nott, A., Le Hir, H. and Moore, M.J. (2004) Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Genes Dev., 18, 210-222.
42. Liu, C., de Oliveira, A., Higazi, T.B., Ghedin, E., DePasse, J. and Unnasch, T.R. (2007) Sequences necessary for trans-splicing in transiently transfected Brugia malayi. Mol. Biochem. Parasitol., 156, 62-73.
43. Ashe, M.P., Furger, A. and Proudfoot, N.J. (2000) Stem-loop 1 of the U1 snRNP plays a critical role in the suppression of HIV-1 polyadenylation. RNA, 6, 170-177.
44. Proudfoot, N.J., Furger, A. and Dye, M.J. (2002) Integrating Mrna processing with transcription. Cell, 108, 501-512.
45. Ashe, M.P., Pearson, L.H. and Proudfoot, N.J. (1997) The HIV-1 50 LTR poly(A) site is inactivated by U1 snRNP interaction with the downstream major splice donor site. EMBO J., 16, 5752-5763.
46. Nag, A., Narsinh, K. and Martinson, H.G. (2007) The poly(A)-dependent transcriptional pause is mediated by CPSF acting on the body of the polymerase. Nat. Struct. Mol. Biol., 14, 662-669.
47. Dantonel, J.C., Murthy, K.G., Manley, J.L. and Tora, L. (1997) Transcription factor TFIID recruits factor CPSF for formation of 3′ end of mRNA. Nature, 389, 399-402.
48. Calvo, O. and Manley, J.L. (2001) Evolutionarily conserved interaction between CstF-64 and PC4 links transcription, polyadenylation, and termination. Mol. Cell, 7, 1013-1023.
49. Venkataraman, K., Brown, K.M. and Gilmartin, G.M. (2005) Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition. Genes Dev., 19, 1315-1327.
50. Rigo, F. and Martinson, H.G. (2009) Polyadenylation releases mRNA from RNA polymerase II in a process that is licensed by splicing. RNA, 15, 823-836.
51. Lin, K. and Zhang, D.Y. (2005) The excess of 50 introns in eukaryotic genomes. Nucleic Acids Res., 33, 6522-6527.