Abstract
The discovery that many intron-containing genes can be cotranscriptionally spliced has led to an increased understanding of how splicing and transcription are intricately intertwined. Cotranscriptional splicing has been demonstrated in a number of different organisms and has been shown to play roles in coordinating both constitutive and alternative splicing. The nature of cotranscriptional splicing suggests that changes in transcription can dramatically affect splicing, and new evidence suggests that splicing can, in turn, influence transcription. In this chapter, we discuss the mechanisms and consequences of cotranscriptional splicing and introduce some of the tools used to measure this process.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Osheim YN, Miller OL Jr et al (1985) RNP particles at splice junction sequences on Drosophila chorion transcripts. Cell 43(1): 143–151
Beyer AL, Bouton AH, Miller OL Jr (1981) Correlation of hnRNP structure and nascent transcript cleavage. Cell 26(2 Pt 2):155–165
Wu ZA, Murphy C, Callan HG et al (1991) Small nuclear ribonucleoproteins and heterogeneous nuclear ribonucleoproteins in the amphibian germinal vesicle: loops, spheres, and snurposomes. J Cell Biol 113(3):465–483
Perales R, Bentley D (2009) “Cotranscriptionality”: the transcription elongation complex as a nexus for nuclear transactions. Mol Cell 36(2):178–191
Gornemann J, Kotovic KM, Hujer K et al (2005) Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol Cell 19(1):53–63
Lacadie SA, Rosbash M (2005) Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5′ss base pairing in yeast. Mol Cell 19(1):65–75
Listerman I, Sapra AK, Neugebauer KM (2006) Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nat Struct Mol Biol 13(9):815–822
Wetterberg I, Zhao J, Masich S et al (2001) In situ transcription and splicing in the Balbiani ring 3 gene. EMBO J 20(10):2564–2574
Kotovic KM, Lockshon D, Boric L et al (2003) Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast. Mol Cell Biol 23(16):5768–5779
Gunderson FQ, Johnson TL (2009) Acetylation by the transcriptional coactivator Gcn5 plays a novel role in co-transcriptional spliceosome assembly. PLoS Genet 5(10):e1000682
Carrillo Oesterreich F, Bieberstein N, Neugebauer KM (2011) Pause locally, splice globally. Trends Cell Biol 21(6):328–335
Tardiff DF, Lacadie SA, Rosbash M (2006) A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional. Mol Cell 24(6):917–929
Carrillo Oesterreich F, Preibisch S, Neugebauer KM (2010) Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol Cell 40(4):571–581
Alexander RD, Innocente SA, Barrass JD et al (2010) Splicing-dependent RNA polymerase pausing in yeast. Mol Cell 40(4):582–593
Khodor YL, Rodriguez J, Abruzzi KC et al (2011) Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. Genes Dev 25(23):2502–2512
Ameur A, Zaghlool A, Halvardson J et al (2011) Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat Struct Mol Biol 18(12):1435–1440
Tilgner H, Knowles DG, Johnson R et al (2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res 22(9):1616–1625
Girard C, Will CL, Peng J et al (2012) Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion. Nat Commun 3:994
Windhager L, Bonfert T, Burger K et al (2012) Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Res 22(10): 2031–2042
Bhatt DM, Pandya-Jones A, Tong AJ et al (2012) Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 150(2):279–290
Pandya-Jones A, Bhatt DM, Lin CH et al (2013) Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression. RNA 19(6):811–827
Hsin JP, Manley JL (2012) The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev 26(19):2119–2137
de Almeida SF, Carmo-Fonseca M (2008) The CTD role in cotranscriptional RNA processing and surveillance. FEBS lett 582(14): 1971–1976
Pandit S, Wang D, Fu XD (2008) Functional integration of transcriptional and RNA processing machineries. Curr Opin Cell Biol 20(3):260–265
Corden JL (1990) Tails of RNA polymerase II. Trends Biochem Sci 15(10):383–387
West ML, Corden JL (1995) Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations. Genetics 140(4):1223–1233
Buratowski S (2009) Progression through the RNA polymerase II CTD cycle. Mol Cell 36(4):541–546
Barboric M, Lenasi T, Chen H et al (2009) 7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development. Proc Natl Acad Sci USA 106(19):7798–7803
Lin S, Coutinho-Mansfield G, Wang D et al (2008) The splicing factor SC35 has an active role in transcriptional elongation. Nat Struct Mol Biol 15(8):819–826
Mortillaro MJ, Blencowe BJ, Wei X et al (1996) A hyperphosphorylated form of the large subunit of RNA polymerase II is associated with splicing complexes and the nuclear matrix. Proc Natl Acad Sci USA 93(16):8253–8257
McCracken S, Fong N, Yankulov K et al (1997) The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385(6614):357–361
Hirose Y, Tacke R, Manley JL (1999) Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev 13(10): 1234–1239
David CJ, Boyne AR, Millhouse SR et al (2011) The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex. Genes Dev 25(9):972–983
Gu B, Eick D, Bensaude O (2012) CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo. Nucleic Acids Res 41(3):1591–1603
Yuryev A, Patturajan M, Litingtung Y et al (1996) The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc Natl Acad Sci USA 93(14):6975–6980
de la Mata M, Kornblihtt AR (2006) RNA polymerase II C-terminal domain mediates regulation of alternative splicing by SRp20. Nat Struct Mol Biol 13(11):973–980
Das R, Yu J, Zhang Z et al (2007) SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol Cell 26(6):867–881
Ghosh S, Garcia-Blanco MA (2000) Coupled in vitro synthesis and splicing of RNA polymerase II transcripts. RNA 6(9):1325–1334
Das R, Dufu K, Romney B et al (2006) Functional coupling of RNAP II transcription to spliceosome assembly. Genes Dev 20(9):1100–1109
Abruzzi KC, Lacadie S, Rosbash M (2004) Biochemical analysis of TREX complex recruitment to intronless and intron-containing yeast genes. EMBO J 23(13):2620–2631
Neugebauer KM (2002) On the importance of being co-transcriptional. J Cell Sci 115(Pt 20):3865–3871
Fong YW, Zhou Q (2001) Stimulatory effect of splicing factors on transcriptional elongation. Nature 414(6866):929–933
de la Mata M, Alonso CR, Kadener S et al (2003) A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell 12(2): 525–532
Munoz MJ, Perez Santangelo MS, Paronetto MP et al (2009) DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell 137(4):708–720
Ip JY, Schmidt D, Pan Q et al (2011) Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res 21(3):390–401
Dujardin G, Lafaille C, Petrillo E et al (2012) Transcriptional elongation and alternative splicing. Biochimica et Biophysica Acta 1829(1):134–140
Kornblihtt AR, de la Mata M, Fededa JP et al (2004) Multiple links between transcription and splicing. RNA 10(10):1489–1498
Howe KJ, Kane CM, Ares M Jr (2003) Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA 9(8):993–1006
Chen Y, Chafin D, Price DH et al (1996) Drosophila RNA polymerase II mutants that affect transcription elongation. J Biol Chem 271(11):5993–5999
Hodges C, Bintu L, Lubkowska L et al (2009) Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science 325(5940):626–628
Churchman LS, Weissman JS (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469(7330): 368–373
Schwartz S, Meshorer E, Ast G (2009) Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 16(9): 990–995
Tilgner H, Nikolaou C, Althammer S et al (2009) Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol 16(9):996–1001
Cramer P, Pesce CG, Baralle FE et al (1997) Functional association between promoter structure and transcript alternative splicing. Proc Natl Acad Sci USA 94(21):11456–11460
Monsalve M, Wu Z, Adelmant G et al (2000) Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1. Mol Cell 6(2):307–316
Huang Y, Li W, Yao X et al (2012) Mediator complex regulates alternative mRNA processing via the MED23 subunit. Mol Cell 45(4):459–469
Brinster RL, Allen JM, Behringer RR et al (1988) Introns increase transcriptional efficiency in transgenic mice. Proc Natl Acad Sci USA 85(3):836–840
Choi T, Huang M, Gorman C et al (1991) A generic intron increases gene expression in transgenic mice. Mol Cell Biol 11(6):3070–3074
Palmiter RD, Sandgren EP, Avarbock MR et al (1991) Heterologous introns can enhance expression of transgenes in mice. Proc Natl Acad Sci USA 88(2):478–482
Loomis RJ, Naoe Y, Parker JB et al (2009) Chromatin binding of SRp20 and ASF/SF2 and dissociation from mitotic chromosomes is modulated by histone H3 serine 10 phosphorylation. Mol Cell 33(4):450–461
Huang Y, Steitz JA (2001) Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA. Mol Cell 7(4):899–905
Pozzoli U, Riva L, Menozzi G et al (2004) Over-representation of exonic splicing enhancers in human intronless genes suggests multiple functions in mRNA processing. Biochem Biophys Res Commun 322(2):470–476
Lenasi T, Peterlin BM, Barboric M (2011) Cap-binding protein complex links pre-mRNA capping to transcription elongation and alternative splicing through positive transcription elongation factor b (P-TEFb). J Biol Chem 286(26):22758–22768
Hossain MA, Chung C, Pradhan SK et al (2013) The yeast cap binding complex modulates transcription factor recruitment and establishes proper histone H3K36 trimethylation during active transcription. Mol Cell Biol 33(4):785–799
Damgaard CK, Kahns S, Lykke-Andersen S et al (2008) A 5′ splice site enhances the recruitment of basal transcription initiation factors in vivo. Mol Cell 29(2):271–278
Kwek KY, Murphy S, Furger A et al (2002) U1 snRNA associates with TFIIH and regulates transcriptional initiation. Nat Struct Biol 9(11):800–805
Furger A, O’Sullivan JM, Binnie A et al (2002) Promoter proximal splice sites enhance transcription. Genes Dev 16(21):2792–2799
Zhou HL, Hinman MN, Barron VA et al (2011) Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner. Proc Natl Acad Sci USA 108(36):E627–E635
Kim S, Kim H, Fong N et al (2011) Pre-mRNA splicing is a determinant of histone H3K36 methylation. Proc Natl Acad Sci USA 108(33):13564–13569
de Almeida SF, Grosso AR, Koch F et al (2011) Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat Struct Mol Biol 18(9):977–983
Bieberstein NI, Carrillo Oesterreich F, Straube K et al (2012) First exon length controls active chromatin signatures and transcription. Cell Rep 2(1):62–68
Lopez-Bigas N, Audit B, Ouzounis C et al (2005) Are splicing mutations the most frequent cause of hereditary disease? FEBS lett 579(9):1900–1903
Cooper TA, Wan L, Dreyfuss G (2009) RNA and disease. Cell 136(4):777–793
Faustino NA, Cooper TA (2003) Pre-mRNA splicing and human disease. Genes Dev 17(4): 419–437
Zumer K, Plemenitas A, Saksela K et al (2011) Patient mutation in AIRE disrupts P-TEFb binding and target gene transcription. Nucleic Acids Res 39(18):7908–7919
Pramono ZA, Wee KB, Wang JL et al (2012) A prospective study in the rational design of efficient antisense oligonucleotides for exon skipping in the DMD gene. Hum Gene Ther 23(7):781–790
Nilsen TW (2005) Spliceosome assembly in yeast: one ChIP at a time? Nat Struct Mol Biol 12(7):571–573
Gunderson FQ, Merkhofer EC, Johnson TL (2011) Dynamic histone acetylation is critical for cotranscriptional spliceosome assembly and spliceosomal rearrangements. Proc Natl Acad Sci USA 108(5):2004–2009
Schmidt U, Basyuk E, Robert MC et al (2011) Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation. J Cell Biol 193(5):819–829
Huranova M, Ivani I, Benda A et al (2010) The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells. J Cell Biol 191(1):75–86
Rino J, Carvalho T, Braga J et al (2007) A stochastic view of spliceosome assembly and recycling in the nucleus. PLoS Comput Biol 3(10):2019–2031
Yu Y, Das R, Folco EG et al (2010) A model in vitro system for co-transcriptional splicing. Nucleic Acids Res 38(21):7570–7578
Hicks MJ, Yang CR, Kotlajich MV et al (2006) Linking splicing to Pol II transcription stabilizes pre-mRNAs and influences splicing patterns. PLoS Biol 4(6):e147
Brugiolo M, Herzel L, Neugebauer KM (2013) Counting on co-transcriptional splicing. F1000Prime Rep 5:9
Wilmes GM, Bergkessel M, Bandyopadhyay S et al (2008) A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell 32(5):735–746
Moehle EA, Ryan CJ, Krogan NJ et al (2012) The yeast SR-like protein Npl3 links chromatin modification to mRNA processing. PLoS Genet 8(11):e1003101
Acknowledgments
We would like to thank members of the Johnson Lab for critical reading of the manuscript and apologize to any colleagues whose work is not referenced due to unintentional oversight or space constraints. Funding was provided by the National Institutes of General Medical Sciences (GM085474), the National Science Foundation (MCB-1051921), and an IRACDA fellowship to E.C.M. (K12 GM068524).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Merkhofer, E.C., Hu, P., Johnson, T.L. (2014). Introduction to Cotranscriptional RNA Splicing. In: Hertel, K. (eds) Spliceosomal Pre-mRNA Splicing. Methods in Molecular Biology, vol 1126. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-980-2_6
Download citation
DOI: https://doi.org/10.1007/978-1-62703-980-2_6
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-979-6
Online ISBN: 978-1-62703-980-2
eBook Packages: Springer Protocols