Adventures in time and space

Control of pre-mRNA splicing is a critical part of the eukaryotic gene expression process. Extensive evidence indicates that transcription and splicing are spatiotemporally coordinated and that most splicing events occur co-transcriptionally. A kinetic coupling model has been proposed in metazoans to describe how changing RNA Polymerase II (RNAPII) elongation rate can impact which alternative splice sites are used. In Saccharomyces cerevisiae, in which most spliced genes have only a single intron and splice sites adhere to a strong consensus sequence, we recently observed that splicing efficiency was sensitive to mutations in RNAPII that increase or decrease its elongation rate. Our data revealed that RNAPII speed and splicing efficiency are generally anti-correlated: at many genes, increased elongation rate caused decreased splicing efficiency, while decreased elongation rate increased splicing efficiency. An improved splicing phenotype was also observed upon deletion of SUB1, a condition in which elongation rate is slowed. We discuss these data in the context of a growing field and expand the kinetic coupling model to apply to both alternative splicing and splicing efficiency.

[1]  Y. Zhang,et al.  In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features , 2013, Nature.

[2]  G. Chanfreau,et al.  Sequential RNA degradation pathways provide a fail-safe mechanism to limit the accumulation of unspliced transcripts in Saccharomyces cerevisiae. , 2012, RNA.

[3]  R. F. Luco,et al.  Epigenetics in Alternative Pre-mRNA Splicing , 2011, Cell.

[4]  Craig D. Kaplan,et al.  Dissection of Pol II Trigger Loop Function and Pol II Activity–Dependent Control of Start Site Selection In Vivo , 2012, PLoS genetics.

[5]  Paul Tempst,et al.  Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. , 2007, Molecular cell.

[6]  C. Guthrie,et al.  Essential Yeast Protein with Unexpected Similarity to Subunits of Mammalian Cleavage and Polyadenylation Specificity Factor (CPSF) , 1996, Science.

[7]  J. Jaehning,et al.  The Paf1 complex: platform or player in RNA polymerase II transcription? , 2010, Biochimica et biophysica acta.

[8]  K. Neugebauer,et al.  Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells , 2006, Nature Structural &Molecular Biology.

[9]  F. Rigo,et al.  Functional Coupling of Last-Intron Splicing and 3′-End Processing to Transcription In Vitro: the Poly(A) Signal Couples to Splicing before Committing to Cleavage , 2007, Molecular and Cellular Biology.

[10]  Evan C. Merkhofer,et al.  Dynamic histone acetylation is critical for cotranscriptional spliceosome assembly and spliceosomal rearrangements , 2011, Proceedings of the National Academy of Sciences.

[11]  B. Shafer,et al.  Mutations in the Saccharomyces cerevisiae RPB1 Gene Conferring Hypersensitivity to 6-Azauracil , 2006, Genetics.

[12]  C. Guthrie,et al.  Rapid, transcript-specific changes in splicing in response to environmental stress. , 2007, Molecular cell.

[13]  Stuart Aitken,et al.  Modelling Reveals Kinetic Advantages of Co-Transcriptional Splicing , 2011, PLoS Comput. Biol..

[14]  C. Guthrie,et al.  Transcript Specificity in Yeast Pre-mRNA Splicing Revealed by Mutations in Core Spliceosomal Components , 2007, PLoS biology.

[15]  J. Weissman,et al.  Nascent transcript sequencing visualizes transcription at nucleotide resolution , 2011, Nature.

[16]  Lily Shiue,et al.  Competition between pre-mRNAs for the splicing machinery drives global regulation of splicing. , 2013, Molecular cell.

[17]  N. Proudfoot,et al.  Terminal exon definition occurs cotranscriptionally and promotes termination of RNA polymerase II. , 1999, Molecular cell.

[18]  X. Darzacq,et al.  The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing , 2011, PLoS biology.

[19]  M. Rosbash,et al.  Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. , 2011, Genes & development.

[20]  Amanda E. Jones,et al.  USP49 deubiquitinates histone H2B and regulates cotranscriptional pre-mRNA splicing. , 2013, Genes & development.

[21]  T. Huffaker,et al.  A Quantitative, High-Throughput Reverse Genetic Screen Reveals Novel Connections between Pre–mRNA Splicing and 5′ and 3′ End Transcript Determinants , 2012, PLoS genetics.

[22]  D. Black,et al.  Co-transcriptional splicing of constitutive and alternative exons. , 2009, RNA.

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

[24]  I. Graham,et al.  Effects of RNA secondary structure on alternative splicing of Pre-mRNA: Is folding limited to a region behind the transcribing RNA polymerase? , 1988, Cell.

[25]  I. Schor,et al.  Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation , 2013, The EMBO journal.

[26]  Ross D. Alexander,et al.  Splicing-Dependent RNA Polymerase Pausing in Yeast , 2010, Molecular cell.

[27]  D. Lockshon,et al.  Cotranscriptional Recruitment of the U1 snRNP to Intron-Containing Genes in Yeast , 2003, Molecular and Cellular Biology.

[28]  Craig D. Kaplan,et al.  From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II , 2013, Cell.

[29]  L. Steinmetz,et al.  Extensive degradation of RNA precursors by the exosome in wild-type cells. , 2012, Molecular cell.

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

[31]  Yael Mandel-Gutfreund,et al.  Exploring functional relationships between components of the gene expression machinery , 2005, Nature Structural &Molecular Biology.

[32]  C. Guthrie,et al.  Identification of novel genes required for yeast pre-mRNA splicing by means of cold-sensitive mutations. , 1996, Genetics.

[33]  Daniel F Tardiff,et al.  In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants. , 2006, Genes & development.

[34]  Tracy L. Johnson,et al.  Acetylation by the Transcriptional Coactivator Gcn5 Plays a Novel Role in Co-Transcriptional Spliceosome Assembly , 2009, PLoS genetics.

[35]  K. Neugebauer,et al.  Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. , 2005, Molecular cell.

[36]  L. Vasiljeva,et al.  Spliceosome-mediated decay (SMD) regulates expression of nonintronic genes in budding yeast , 2013, Genes & development.

[37]  K. Neugebauer,et al.  Counting on co-transcriptional splicing , 2013, F1000prime reports.

[38]  M. Alló,et al.  Transcriptional elongation and alternative splicing. , 2013, Biochimica et biophysica acta.

[39]  J. Acker,et al.  Genome-wide location analysis reveals a role for Sub1 in RNA polymerase III transcription , 2009, Proceedings of the National Academy of Sciences.

[40]  C. Guthrie,et al.  Diverse environmental stresses elicit distinct responses at the level of pre-mRNA processing in yeast. , 2011, RNA.

[41]  Leighton J. Core,et al.  Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.

[42]  B. Blencowe,et al.  Regulation of Alternative Splicing by Histone Modifications , 2010, Science.

[43]  Lily Shiue,et al.  Integration of a splicing regulatory network within the meiotic gene expression program of Saccharomyces cerevisiae. , 2010, Genes & development.

[44]  S. Preibisch,et al.  Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. , 2010, Molecular cell.

[45]  Jaroslav Icha,et al.  Histone Deacetylase Activity Modulates Alternative Splicing , 2011, PloS one.

[46]  N. Krogan,et al.  The Yeast SR-Like Protein Npl3 Links Chromatin Modification to mRNA Processing , 2012, PLoS genetics.

[47]  T. R. Hebbes,et al.  A direct link between core histone acetylation and transcriptionally active chromatin. , 1988, The EMBO journal.

[48]  M. Carmo-Fonseca,et al.  Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3′ end of human genes , 2011, Nature Structural &Molecular Biology.

[49]  M. Ares,et al.  Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. , 2003, RNA.

[50]  W. Keller,et al.  Position-dependent inhibition of the cleavage step of pre-mRNA 3'-end processing by U1 snRNP. , 2000, RNA.

[51]  J. Remme,et al.  Coupling of rRNA transcription and ribosomal assembly in vivo. Formation of active ribosomal subunits in Escherichia coli requires transcription of rRNA genes by host RNA polymerase which cannot be replaced by bacteriophage T7 RNA polymerase. , 1993, Journal of molecular biology.

[52]  S. Marquardt,et al.  Kinetic competition between RNA Polymerase II and Sen1-dependent transcription termination. , 2013, Molecular cell.

[53]  Manolis Kellis,et al.  Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo , 2013, Nature.

[54]  B. Pugh,et al.  Genome-wide structure and organization of eukaryotic pre-initiation complexes , 2011, Nature.

[55]  Xiaochun Yu,et al.  WAC, a functional partner of RNF20/40, regulates histone H2B ubiquitination and gene transcription. , 2011, Molecular cell.

[56]  A. Kornblihtt,et al.  A slow RNA polymerase II affects alternative splicing in vivo. , 2003, Molecular cell.

[57]  P. Silver,et al.  Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicing. , 2006, Molecular cell.

[58]  D. Black,et al.  Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions , 2012, Cell.

[59]  Alicia García,et al.  Sub1 associates with Spt5 and influences RNA polymerase II transcription elongation rate , 2012, Molecular biology of the cell.

[60]  C. Guthrie,et al.  Mechanical Devices of the Spliceosome: Motors, Clocks, Springs, and Things , 1998, Cell.

[61]  N. Proudfoot,et al.  Disengaging polymerase: Terminating RNA polymerase II transcription in budding yeast☆ , 2013, Biochimica et biophysica acta.

[62]  G. Roeder,et al.  Meiosis-specific RNA splicing in yeast , 1991, Cell.

[63]  Daniel F Tardiff,et al.  A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional. , 2006, Molecular cell.

[64]  S. Lacadie,et al.  Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5'ss base pairing in yeast. , 2005, Molecular cell.

[65]  M. Alló,et al.  RNA Polymerase II Elongation at the Crossroads of Transcription and Alternative Splicing , 2011, Genetics research international.

[66]  L. Guarente,et al.  Yeast SUB1 is a suppressor of TFIIB mutations and has homology to the human co‐activator PC4. , 1996, The EMBO journal.