38
Views
71
CrossRef citations to date
0
Altmetric
Gene Expression

The Essential WD Repeat Protein Swd2 Has Dual Functions in RNA Polymerase II Transcription Termination and Lysine 4 Methylation of Histone H3

, &
Pages 2932-2943 | Received 17 Oct 2003, Accepted 06 Jan 2004, Published online: 27 Mar 2023

REFERENCES

  • Alen, C., Kent N. A., Jones H. S., O'Sullivan J., Aranda A., and Proudfoot N. J.. 2002. A role for chromatin remodeling in transcriptional termination by RNA polymerase II. Mol. Cell 10:1441–1452.
  • Barilla, D., Lee B. A., and Proudfoot N. J.. 2001. Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 98:445–450.
  • Bernstein, B. E., Humphrey E. L., Erlich R. L., Schneider R., Bouman P., Liu J. S., Kouzarides T., and Schreiber S. L.. 2002. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc. Natl. Acad. Sci. USA 99:8695–8700.
  • Betz, J. L., Chang M., Washburn T. M., Porter S. E., Mueller C. L., and Jaehning J. A.. 2002. Phenotypic analysis of Paf1/RNA polymerase II complex mutations reveals connections to cell cycle regulation, protein synthesis, and lipid and nucleic acid metabolism. Mol. Genet. Genomics 268:272–285.
  • 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.
  • Briggs, S. D., Bryk M., Strahl B. D., Cheung W. L., Davie J. K., Dent S. Y., Winston F., and Allis C. D.. 2001. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev. 15:3286–3295.
  • Cid, V. J., Duran A., del Rey F., Snyder M. P., Nombela C., and Sanchez M.. 1995. Molecular basis of cell integrity and morphogenesis in Saccharomyces cerevisiae. Microbiol. Rev. 59:345–386.
  • Corda, Y., Schramke V., Longhese M. P., Smokvina T., Paciotti V., Brevet V., Gilson E., and Geli V.. 1999. Interaction between Set1p and checkpoint protein Mec3p in DNA repair and telomere functions. Nat. Genet. 21:204–208.
  • Dheur, S., Vo L. 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.
  • Dichtl, B., Blank D., Ohnacker M., Friedlein A., Roeder D., Langen H., and Keller W.. 2002. A role for SSU72 in balancing RNA polymerase II transcription elongation and termination. Mol. Cell 10:1139–1150.
  • Dichtl, B., Blank D., Sadowski M., Hubner W., Weiser S., and Keller W.. 2002. Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination. EMBO J. 21:4125–4135.
  • Dohmen, R. J., Wu P., and Varshavsky A.. 1994. Heat-inducible degron: a method for constructing temperature-sensitive mutants. Science 263:1273–1276.
  • Edmonds, M. 2002. A history of poly (A) sequences: from formation to factors to function. Prog. Nucleic Acid Res. Mol. Biol. 71:285–389.
  • Elion, E. A., and Warner J. R.. 1986. An RNA polymerase I enhancer in Saccharomyces cerevisiae. Mol. Cell. Biol. 6:2089–2097.
  • Ganem, C., Devaux F., Torchet C., Jacq C., Quevillon-Cheruel S., Labesse G., Facca C., and Faye G.. 2003. Ssu72 is a phosphatase essential for transcription termination of snoRNAs and specific mRNAs in yeast. EMBO J. 22:1588–1598.
  • Gavin, A. C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J. M., Michon A. M., Cruciat C. M., Remor M., Hofert C., Schelder M., Brajenovic M., Ruffner H., Merino A., Klein K., Hudak M., Dickson D., Rudi T., Gnau V., Bauch A., Bastuck S., Huhse B., Leutwein C., Heurtier M. A., Copley R. R., Edelmann A., Querfurth E., Rybin V., Drewes G., Raida M., Bouwmeester T., Bork P., Seraphin B., Kuster B., Neubauer G., and Superti-Furga G.. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141–147.
  • Gilbert, W., Siebel C. W., and Guthrie C.. 2001. Phosphorylation by Sky1p promotes Npl3p shuttling and mRNA dissociation. RNA 7:302–313.
  • Hammell, C. M., Gross S., Zenklusen D., Heath C. V., Stutz F., Moore C., and Cole C. N.. 2002. Coupling of termination, 3′ processing, and mRNA export. Mol. Cell. Biol. 22:6441–6457.
  • Hampsey, M. 1997. A review of phenotypes in Saccharomyces cerevisiae. Yeast 13:1099–1133.
  • Hampsey, M., and Reinberg D.. 2003. Tails of intrigue: phosphorylation of RNA polymerase II mediates histone methylation. Cell 113:429–432.
  • He, X., Khan A. U., Cheng H., Pappas D. L., Jr., Hampsey M., and Moore C. L.. 2003. Functional interactions between the transcription and mRNA 3′ end processing machineries mediated by Ssu72 and Sub1. Genes Dev. 17:1030–1042.
  • Henikoff, S. 2003. Versatile assembler. Nature 423:814–817.
  • Kanoh, J., Francesconi S., Collura A., Schramke V., Ishikawa F., Baldacci G., and Geli V.. 2003. The fission yeast spSet1p is a histone H3-K4 methyltransferase that functions in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. J. Mol. Biol. 326:1081–1094.
  • Komachi, K., and Johnson A.. 1997. Residues in the WD repeats of Tup1 required for interaction with α2. Mol. Cell. Biol. 17:6023–6028.
  • Krogan, N. J., Dover J., Khorrami S., Greenblatt J. F., Schneider J., Johnston M., and Shilatifard A.. 2002. COMPASS, a histone H3 (lysine 4) methyltransferase required for telomeric silencing of gene expression. J. Biol. Chem. 277:10753–10755.
  • Krogan, N. J., Dover J., Wood A., Schneider J., Heidt J., Boateng M. A., Dean K., Ryan O. W., Golshani A., Johnston M., Greenblatt J. F., and Shilatifard A.. 2003. The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol. Cell 11:721–729.
  • Landry, J., Sutton A., Hesman T., Min J., Xu R., Johnston M., and Sternglanz R.. 2003. Set2-catalyzed methylation of histone H3 represses basal expression of GAL4 in Saccharomyces cerevisiae. Mol. Cell. Biol. 23:5972–5978.
  • Madison, J. M., and Winston F.. 1997. Evidence that Spt3 functionally interacts with Mot1, TFIIA, and TATA-binding protein to confer promoter-specific transcriptional control in Saccharomyces cerevisiae. Mol. Cell. Biol. 17:287–295.
  • McNeil, J. B., Agah H., and Bentley D.. 1998. Activated transcription independent of the RNA polymerase II holoenzyme in budding yeast. Genes Dev. 12:2510–2521.
  • Meinhart, A., Silberzahn T., and Cramer P.. 2003. The mRNA transcription/processing factor Ssu72 is a potential tyrosine phosphatase. J. Biol. Chem. 278:15917–15921.
  • Miller, T., Krogan N. J., Dover J., Erdjument-Bromage H., Tempst P., Johnston M., Greenblatt J. F., and Shilatifard A.. 2001. COMPASS: a complex of proteins associated with a trithorax-related SET domain protein. Proc. Natl. Acad. Sci. USA 98:12902–12907.
  • Morillon, A., Karabetsou N., O'Sullivan J., Kent N., Proudfoot N., and Mellor J.. 2003. Isw1 chromatin remodeling ATPase coordinates transcription elongation and termination by RNA polymerase II. Cell 115:425–435.
  • 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.
  • Nagy, P. L., Griesenbeck J., Kornberg R. D., and Cleary M. L.. 2002. A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3. Proc. Natl. Acad. Sci. USA 99:90–94.
  • Nakamura, T., Mori T., Tada S., Krajewski W., Rozovskaia T., Wassell R., Dubois G., Mazo A., Croce C. M., and Canaani E.. 2002. ALL-1 is a histone methyltransferase that assembles a supercomplex of proteins involved in transcriptional regulation. Mol. Cell 10:1119–1128.
  • Nedea, E., He S., Kim M., Pootoolal J., Zhong G., Canadien V., Hughes T., Buratwoski S., Moore C., and Greenblatt J.. 2003. Organization and function of APT, a sub-complex of the yeast cleavage and polyadenylation factor involved in the formation of snoRNA 3′ ends. J. Biol. Chem. 278:33000–33010.
  • Ng, H. H., Robert F., Young R. A., and Struhl K.. 2003. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell 11:709–719.
  • Nislow, C., Ray E., and Pillus L.. 1997. SET1, a yeast member of the trithorax family, functions in transcriptional silencing and diverse cellular processes. Mol. Biol. Cell 8:2421–2436.
  • Ohnacker, M., Barabino S. M., Preker P. J., and Keller W.. 2000. The WD-repeat protein Pfs2p bridges two essential factors within the yeast pre-mRNA 3′-end-processing complex. EMBO J. 19:37–47.
  • Orphanides, G., and Reinberg D.. 2002. A unified theory of gene expression. Cell 108:439–451.
  • Parthun, M. R., Widom J., and Gottschling D. E.. 1996. The major cytoplasmic histone acetyltransferase in yeast: links to chromatin replication and histone metabolism. Cell 87:85–94.
  • Pemberton, L., and Blobel G.. 1997. Characterization of the Wtm proteins, a novel family of Saccharomyces cerevisiae transcriptional modulators with roles in meiotic regulation and silencing. Mol. Cell. Biol. 17:4830–4841.
  • Roguev, A., Schaft D., Shevchenko A., Aasland R., and Stewart A. F.. 2003. High conservation of the Set1/Rad6 axis of histone 3 lysine 4 methylation in budding and fission yeasts. J. Biol. Chem. 278:8487–8493.
  • Roguev, A., Schaft D., Shevchenko A., Pijnappel W., Wilm M., Aasland R., and Stewart A.. 2001. The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4. EMBO J. 20:7137–7148.
  • Roguev, A., Shevchenko A., Schaft D., Thomas H., and Stewart A. F.. 15 November 2003, posting date. A comparative analysis of an orthologous proteomic environment in the yeasts S. cerevisiae and S. pombe. Mol. Cell. Proteomics [Online.] http://www.mcponline.org.
  • Russnak, R., Nehrke K., and Platt T.. 1995. REF2 encodes an RNA-binding protein directly involved in yeast mRNA 3′-end formation. Mol. Cell. Biol. 15:1689–1697.
  • 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.
  • Santos-Rosa, H., Schneider R., Bannister A. J., Sherriff J., Bernstein B. E., Emre N. C., Schreiber S. L., Mellor J., and Kouzarides T.. 2002. Active genes are tri-methylated at K4 of histone H3. Nature 419:407–411.
  • Santos-Rosa, H., Schneider R., Bernstein B. E., Karabetsou N., Morillon A., Weise C., Schreiber S. L., Mellor J., and Kouzarides T.. 2003. Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. Mol. Cell 12:1325–1332.
  • Schramke, V., Neecke H., Brevet V., Corda Y., Lucchini G., Longhese M. P., Gilson E., and Geli V.. 2001. The set1Δ mutation unveils a novel signaling pathway relayed by the Rad53-dependent hyperphosphorylation of replication protein A that leads to transcriptional activation of repair genes. Genes Dev. 15:1845–1858.
  • Sims, R. J., III, Nishioka K., and Reinberg D.. 2003. Histone lysine methylation: a signature for chromatin function. Trends Genet. 19:629–639.
  • Skaar, D., and Greenleaf A.. 2002. The RNA polymerase II CTD kinase CTDK-1 affects pre-mRNA 3′ cleavage/polyadenylation through the processing component Pti1p. Mol. Cell 10:1429–1439.
  • Smith, T. F., Gaitatzes C., Saxena K., and Neer E. J.. 1999. The WD repeat: a common architecture for diverse functions. Trends Biochem. Sci. 24:181–185.
  • Sparks, K. A., and Dieckmann C. L.. 1998. Regulation of poly(A) site choice of several yeast mRNAs. Nucleic Acids Res. 26:4676–4687.
  • Spector, M., Raff A., DeSilva H., Lee K., and Osley M.. 1997. Hir1p and Hir2p function as transcriptional corepressors to regulate histone gene transcription in the Saccharomyces cerevisiae cell cycle. Mol. Cell. Biol. 17:545–552.
  • Stark, M. J. 1996. Yeast protein serine/threonine phosphatases: multiple roles and diverse regulation. Yeast 12:1647–1675.
  • Steinmetz, E., and Brow D.. 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., Conrad N., Brow D., and Corden J.. 2001. RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts. Nature 413:327–331.
  • Strahl, B. D., Grant P. S., Briggs S. D., Sun Z. W., Bone J. R., Caldwell J. A., Mollah S., Cook R. G., Shabanowitz J., Hunt D. F., and Allis C. D.. 2002. Set2 is a nucleosomal histone H3 methyltransferase that mediates transcriptional repression. Mol. Cell. Biol. 22:1298–1306.
  • Sun, Z. W., and Hampsey M.. 1996. Synthetic enhancement of a TFIIB defect by a mutation in SSU72, an essential yeast gene encoding a novel protein that affects transcription start site selection in vivo. Mol. Cell. Biol. 16:1557–1566.
  • Thomas, D., Kuras L., Barbey R., Cherest H., Blaiseau P., and Surdin-Kerjan Y.. 1995. Met30p, a yeast transcriptional inhibitor that responds to S-adenysylmethionine, is an essential protein with WD40 repeats. Mol. Cell. Biol. 15:6526–6534.
  • Vo, L. T. A., Minet M., Schmitter J.-M., Lacroute F., and Wyers F.. 2001. Mpe1, a zinc knuckle protein, is an essential component of yeast cleavage and polyadenylation factor required for the cleavage and polyadenylation of mRNA. Mol. Cell. Biol. 21:8346–8356.
  • Wysocka, J., Myers M. P., Laherty C. D., Eisenman R. N., and Herr W.. 2003. Human Sin3 deacetylase and thrithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1. Genes Dev. 17:896–911.
  • Zhang, Y., Sun Z. W., Iratni R., Erdjument-Bromage H., Tempst P., Hampesy M., and Reinberg D.. 1998. Sap30, a novel protein conserved between human and yeast, is a component of a histone deacetylase complex. Mol. Cell 1:1021–1031.
  • Zhao, J., Kessler M., Helmling S., O'Connor J. P., and Moore C.. 1999. Pta1, a component of yeast CF II, is required for both cleavage and poly(A) addition of mRNA precursor. Mol. Cell. Biol. 19:7733–7740.

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.