The Prp19 Complex Is a Novel Transcription Elongation Factor Required for Trex Occupancy at Transcribed Genes Functional Analysis of the Rna Polymerase Ii C-terminal Domain Kinase Ctk1 in the Yeast

Different steps in gene expression are intimately linked. In Saccharomyces cerevisiae, the conserved TREX complex couples transcription to nuclear messenger RNA (mRNA) export. However, it is unknown how TREX is recruited to actively transcribed genes. Here, we show that the Prp19 splicing complex functions in transcription elongation. The Prp19 complex is recruited to transcribed genes, interacts with RNA polymerase II (RNAPII) and TREX, and is absolutely required for TREX occupancy at transcribed genes. Importantly, the Prp19 complex is necessary for full transcriptional activity. Taken together, we identify the Prp19 splicing complex as a novel transcription elongation factor that is essential for TREX occupancy at transcribed genes and that thus provides a novel link between transcription and messenger ribonucleoprotein (mRNP) formation.

[1]  K. Nakayama,et al.  U Box Proteins as a New Family of Ubiquitin-Protein Ligases* , 2001, The Journal of Biological Chemistry.

[2]  W. Tarn,et al.  Functional association of essential splicing factor(s) with PRP19 in a protein complex. , 1994, The EMBO journal.

[3]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[4]  R. Luna,et al.  The yeast THO complex and mRNA export factors link RNA metabolism with transcription and genome instability , 2002, The EMBO journal.

[5]  C. Will,et al.  Spliceosome structure and function. , 2011, Cold Spring Harbor perspectives in biology.

[6]  B. Séraphin,et al.  The tandem affinity purification (TAP) method: a general procedure of protein complex purification. , 2001, Methods.

[7]  J. Manley,et al.  The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex. , 2011, Genes & development.

[8]  T. Maniatis,et al.  An extensive network of coupling among gene expression machines , 2002, Nature.

[9]  Daniel Zenklusen,et al.  Stable mRNP Formation and Export Require Cotranscriptional Recruitment of the mRNA Export Factors Yra1p and Sub2p by Hpr1p , 2002, Molecular and Cellular Biology.

[10]  Catherine Dargemont,et al.  Ubiquitin-associated domain of Mex67 synchronizes recruitment of the mRNA export machinery with transcription , 2006, Proceedings of the National Academy of Sciences.

[11]  W. Tsai,et al.  The Prp19p-Associated Complex in Spliceosome Activation , 2003, Science.

[12]  K Strässer,et al.  Yra1p, a conserved nuclear RNA‐binding protein, interacts directly with Mex67p and is required for mRNA export , 2000, The EMBO journal.

[13]  K. Gould,et al.  Structural insights into the U-box, a domain associated with multi-ubiquitination , 2003, Nature Structural Biology.

[14]  Danny Reinberg,et al.  RNA polymerase II elongation through chromatin , 2000, Nature.

[15]  P. Hieter,et al.  Tetratrico peptide repeat interactions: to TPR or not to TPR? , 1995, Trends in biochemical sciences.

[16]  D. Libri,et al.  Multiple roles for the yeast SUB2/yUAP56 gene in splicing. , 2001, Genes & development.

[17]  Kevin Struhl,et al.  Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. , 2005, Molecular cell.

[18]  S. Elledge,et al.  The Prp19 complex and the Usp4Sart3 deubiquitinating enzyme control reversible ubiquitination at the spliceosome. , 2010, Genes & development.

[19]  S. R. Wente,et al.  mRNA nuclear export at a glance , 2009, Journal of Cell Science.

[20]  D. Barford,et al.  The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR‐mediated protein–protein interactions , 1998, The EMBO journal.

[21]  Richard A Young,et al.  Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. , 2002, Molecular cell.

[22]  C. Guthrie,et al.  The essential yeast RNA binding protein Np13p is methylated. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[23]  J. Ranish,et al.  Intermediates in formation and activity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. , 1999, Genes & development.

[24]  Y. Yoneda,et al.  Roles of the TREX complex in nuclear export of mRNA , 2009, RNA biology.

[25]  B. Kuster,et al.  Functional analysis of the human CDC5L complex and identification of its components by mass spectrometry , 2000, The EMBO journal.

[26]  Seiji Masuda,et al.  Recruitment of the human TREX complex to mRNA during splicing. , 2005, Genes & development.

[27]  F. Stutz,et al.  Regulation of mRNP dynamics along the export pathway , 2008, FEBS letters.

[28]  J. Hoeijmakers,et al.  XAB2, a Novel Tetratricopeptide Repeat Protein Involved in Transcription-coupled DNA Repair and Transcription* , 2000, The Journal of Biological Chemistry.

[29]  P. Silver,et al.  Intron status and 3'-end formation control cotranscriptional export of mRNA. , 2002, Genes & development.

[30]  Frédéric Devaux,et al.  THO/Sub2p Functions to Coordinate 3′-End Processing with Gene-Nuclear Pore Association , 2008, Cell.

[31]  R. Reed,et al.  Coupling transcription, splicing and mRNA export. , 2003, Current opinion in cell biology.

[32]  D. Bentley,et al.  Cotranscriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3' end processing factor Pcf11. , 2009, Molecular cell.

[33]  Ed Hurt,et al.  Cotranscriptional recruitment of the serine-arginine-rich (SR)-like proteins Gbp2 and Hrb1 to nascent mRNA via the TREX complex , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Rodney Rothstein,et al.  Elevated recombination rates in transcriptionally active DNA , 1989, Cell.

[35]  Kae-Jiun Chang,et al.  Ntc90 is required for recruiting first step factor Yju2 but not for spliceosome activation. , 2009, RNA.

[36]  E. Izaurralde,et al.  The interplay of nuclear mRNP assembly, mRNA surveillance and export. , 2003, Trends in cell biology.

[37]  Daniel Zenklusen,et al.  The Yeast hnRNP-Like Proteins Yra1p and Yra2p Participate in mRNA Export through Interaction with Mex67p , 2001, Molecular and Cellular Biology.

[38]  Ed Hurt,et al.  Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p , 2001, Nature.

[39]  J. Manley,et al.  RNA polymerase II and the integration of nuclear events. , 2000, Genes & development.

[40]  D. Bentley,et al.  "Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions. , 2009, Molecular cell.

[41]  Melanie D Ohi,et al.  Characterization of interactions among the Cef1p-Prp19p-associated splicing complex. , 2002, RNA.

[42]  C. Will,et al.  The Spliceosome: Design Principles of a Dynamic RNP Machine , 2009, Cell.

[43]  M. Wilm,et al.  A subset of human 35S U5 proteins, including Prp19, function prior to catalytic step 1 of splicing , 2004, The EMBO journal.

[44]  S. Lacadie,et al.  Biochemical analysis of TREX complex recruitment to intronless and intron‐containing yeast genes , 2004, The EMBO journal.

[45]  J. Qin,et al.  Isolation of XAB2 Complex Involved in Pre-mRNA Splicing, Transcription, and Transcription-coupled Repair* , 2008, Journal of Biological Chemistry.

[46]  J D Beggs,et al.  Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. , 2000, Genetics.

[47]  Pamela A. Silver,et al.  Coupling and coordination in gene expression processes: a systems biology view , 2008, Nature Reviews Genetics.

[48]  J. Manley,et al.  Cotranscriptional processes and their influence on genome stability. , 2006, Genes & development.

[49]  Kevin Struhl,et al.  TREX is a conserved complex coupling transcription with messenger RNA export , 2002, Nature.

[50]  S. Chávez,et al.  The yeast HPR1 gene has a functional role in transcriptional elongation that uncovers a novel source of genome instability. , 1997, Genes & development.

[51]  N. Krogan,et al.  Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes , 2004, The EMBO journal.

[52]  Ed Hurt,et al.  Exporting RNA from the nucleus to the cytoplasm , 2007, Nature Reviews Molecular Cell Biology.

[53]  Andreas Mayer,et al.  Nucleocytoplasmic shuttling of the La motif-containing protein Sro9 might link its nuclear and cytoplasmic functions. , 2010, RNA.

[54]  R. Reed,et al.  TREX, SR proteins and export of mRNA. , 2005, Current opinion in cell biology.

[55]  A. Aguilera,et al.  A new connection of mRNP biogenesis and export with transcription-coupled repair , 2007, Nucleic acids research.

[56]  S. Buratowski,et al.  Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3' end processing. , 2004, Molecular cell.

[57]  G. Orphanides,et al.  A Unified Theory of Gene Expression , 2002, Cell.

[58]  M. Mann,et al.  Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly , 2001, Nature.

[59]  K. Yano,et al.  Human Transcription Elongation Factor NELF: Identification of Novel Subunits and Reconstitution of the Functionally Active Complex , 2003, Molecular and Cellular Biology.

[60]  C. Will,et al.  13 Spliceosome Structure and Function , 2006 .

[61]  P. Cramer,et al.  Identification, structure, and functional requirement of the Mediator submodule Med7N/31 , 2009, The EMBO journal.

[62]  R. Sikorski,et al.  A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. , 1989, Genetics.

[63]  Andrés Aguilera,et al.  The interface between transcription and mRNP export: from THO to THSC/TREX-2. , 2010, Biochimica et biophysica acta.

[64]  Andrés Aguilera,et al.  Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. , 2003, Molecular cell.

[65]  A. Aguilera,et al.  Molecular Evidence That the Eukaryotic THO/TREX Complex Is Required for Efficient Transcription Elongation* , 2003, Journal of Biological Chemistry.

[66]  H. Urlaub,et al.  Hierarchical, clustered protein interactions with U4/U6 snRNA: a biochemical role for U4/U6 proteins , 2002, The EMBO journal.

[67]  G. Blatch,et al.  The tetratricopeptide repeat: a structural motif mediating protein-protein interactions. , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.