23
Views
115
CrossRef citations to date
0
Altmetric
Gene Expression

Identification of cis Elements Directing Termination of Yeast Nonpolyadenylated snoRNA Transcripts

, , , &
Pages 6241-6252 | Received 18 Feb 2004, Accepted 14 Apr 2004, Published online: 27 Mar 2023

REFERENCES

  • Allison, D. S., and Hall B. D.. 1985. Effects of alterations in the 3′ flanking sequence on in vivo and in vitro expression of the yeast SUP4-o tRNATyr gene. EMBO J. 4:2657–2664.
  • Allmang, C., Kufel J., Chanfreau G., Mitchell P., Petfalski E., and Tollervey D.. 1999. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18:5399–5410.
  • Antson, A. A. 2000. Single-stranded-RNA binding proteins. Curr. Opin. Struct. Biol. 10:87–94.
  • Bentley, D. 2002. The mRNA assembly line: transcription and processing machines in the same factory. Curr. Opin. Cell Biol. 14:336–342.
  • 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.
  • 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.
  • Campbell, F. E., Jr., and Setzer D. R.. 1992. Transcription termination by RNA polymerase III: uncoupling of polymerase release from termination signal recognition. Mol. Cell. Biol. 12:2260–2272.
  • Clarke, N. D., and Granek J. A.. 2003. Rank order metrics for quantifying the association of sequence features with gene regulation. Bioinformatics 19:212–218.
  • 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.
  • Conrad, N. K., Wilson S. M., Steinmetz E. J., Patturajan M., Brow D. A., Swanson M. S., and Corden J. L.. 2000. A yeast heterogeneous nuclear ribonucleoprotein complex associated with RNA polymerase II. Genetics 154:557–571.
  • Deo, R. C., Bonanno J. B., Sonenberg N., and Burley S. K.. 1999. Recognition of polyadenylate RNA by the poly(A)-binding protein. Cell 98:835–845.
  • Dheur, S., Vo le T. A., Voisinet-Hakil F., Minet M., Schmitter J. M., Lacroute F., Wyers F., and Minvielle-Sebastia L.. 2003. Pti1p and Ref2p found in association with the mRNA 3′ end formation complex direct snoRNA maturation. EMBO J. 22:2831–2840.
  • Fatica, A., Morlando M., and Bozzoni I.. 2000. Yeast snoRNA accumulation relies on a cleavage-dependent/polyadenylation-independent 3′-processing apparatus. EMBO J. 19:6218–6229.
  • Handa, N., Nureki O., Kurimoto K., Kim I., Sakamoto H., Shimura Y., Muto Y., and Yokoyama S.. 1999. Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature 398:579–585.
  • Hanley, J. A., and McNeil B. J.. 1982. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143:29–36.
  • Henkin, T. M., and Yanofsky C.. 2002. Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions. Bioessays 24:700–707.
  • Hirose, Y., and Manley J. L.. 2000. RNA polymerase II and the integration of nuclear events. Genes Dev. 14:1415–1429.
  • Liu, X., and Clarke N. D.. 2002. Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. J. Mol. Biol. 323:1–8.
  • 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.
  • Maniatis, T., and Reed R.. 2002. An extensive network of coupling among gene expression machines. Nature 416:499–506.
  • McCracken, S., Fong N., Yankulov K., Ballantyne S., Pan G., Greenblatt J., Patterson S. D., Wickens M., and Bentley D. L.. 1997. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385:357–361.
  • Morlando, M., Greco P., Dichtl B., Fatica A., Keller W., and Bozzoni I.. 2002. Functional analysis of yeast snoRNA and snRNA 3′-end formation mediated by uncoupling of cleavage and polyadenylation. Mol. Cell. Biol. 22:1379–1389.
  • Nagai, K., Oubridge C., Jessen T. H., Li J., and Evans P. R.. 1990. Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A. Nature 348:515–520.
  • Nedea, E., He X., Kim M., Pootoolal J., Zhong G., Canadien V., Hughes T., Buratowski S., Moore C. L., and Greenblatt J.. 2003. Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3′-ends. J. Biol. Chem. 278:33000–33010.
  • Osheim, Y. N., Proudfoot N. J., and Beyer A. L.. 1999. EM visualization of transcription by RNA polymerase II: downstream termination requires a poly(A) signal but not transcript cleavage. Mol. Cell 3:379–387.
  • Proudfoot, N., and O'Sullivan J.. 2002. Polyadenylation: a tail of two complexes. Curr. Biol. 12:R855–R857.
  • Proudfoot, N. J., Furger A., and Dye M. J.. 2002. Integrating mRNA processing with transcription. Cell 108:501–512.
  • Reeder, R. H., Guevara P., and Roan J. G.. 1999. Saccharomyces cerevisiae RNA polymerase I terminates transcription at the Reb1 terminator in vivo. Mol. Cell. Biol. 19:7369–7376.
  • Richardson, J. P. 2002. Rho-dependent termination and ATPases in transcript termination. Biochim. Biophys. Acta 1577:251–260.
  • Sadowski, M., Dichtl B., Hubner W., and Keller W.. 2003. Independent functions of yeast Pcf11p in pre-mRNA 3′ end processing and in transcription termination. EMBO J. 22:2167–2177.
  • Schneider, T. D., and Stephens R. M.. 1990. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18:6097–6100.
  • Sikorski, R. S., and Hieter P.. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19–27.
  • Steinmetz, E. J., and Brow D. A.. 1998. Control of pre-mRNA accumulation by the essential yeast protein Nrd1 requires high-affinity transcript binding and a domain implicated in RNA polymerase II association. Proc. Natl. Acad. Sci. USA 95:6699–6704.
  • Steinmetz, E. J., and Brow D. A.. 1996. Repression of gene expression by an exogenous sequence element acting in concert with a heterogeneous nuclear ribonucleoprotein-like protein, Nrd1, and the putative helicase Sen1. Mol. Cell. Biol. 16:6993–7003.
  • Steinmetz, E. J., and Brow D. A.. 2003. Ssu72 protein mediates both poly(A)-coupled and poly(A)-independent termination of RNA polymerase II transcription. Mol. Cell. Biol. 23:6339–6349.
  • Steinmetz, E. J., Conrad N. K., Brow D. A., and Corden J. L.. 2001. RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts. Nature 413:327–331.
  • Thompson, J. D., Higgins D. G., and Gibson T. J.. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673–4680.
  • Tran, D. P., Kim S. J., Park N. J., Jew T. M., and Martinson H. G.. 2001. Mechanism of poly(A) signal transduction to RNA polymerase II in vitro. Mol. Cell. Biol. 21:7495–7508.
  • van Hoof, A., Lennertz P., and Parker R.. 2000. Yeast exosome mutants accumulate 3′-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol. Cell. Biol. 20:441–452.
  • Varani, G., and Nagai K.. 1998. RNA recognition by RNP proteins during RNA processing. Annu. Rev. Biophys. Biomol. Struct. 27:407–445.
  • Wang, X., and Tanaka Hall T. M.. 2001. Structural basis for recognition of AU-rich element RNA by the HuD protein. Nat. Struct. Biol. 8:141–145.
  • Yarnell, W. S., and Roberts J. W.. 1999. Mechanism of intrinsic transcription termination and antitermination. Science 284:611–615.
  • Zhao, J., Hyman L., and Moore C.. 1999. Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63:405–445.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.