Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control

Advanced Review

Sarah A. Peck, Katlyn D. Hughes, Jose F. Victorino, Amber L. Mosley

Published Online: Mar 07 2019

DOI: 10.1002/wrna.1529

Full article on Wiley Online Library: HTML PDF

Can't access this content? Tell your librarian.

Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co‐transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3′ end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health. These critical quality control pathways are regulated by the highly dynamic protein–protein interaction network at the site of transcription. Recent work has further revealed the extent to which the processes of transcription and RNA processing and quality control are integrated, and how critically their coupling relies upon the dynamic protein interactions that take place co‐transcriptionally. This review focuses specifically on the intricate balance between 3′ end processing and RNA decay during transcription termination. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Processing > 3' End Processing RNA Processing > Splicing Mechanisms RNA Processing > Capping and 5' End Modifications

Cleavage and polyadenylation: Cap binding complex (CBC) binds 5′ guanosine cap. Cleavage factor 1A (CF1A) is recruited to Ser2 phosphorylated CTD of RNAPII. Cleavage and polyadenylation factor (CPF) is recruited and cleaves RNA after polyadenylation signal. Poly(A) polymerase polyadenylates 3′ end of RNA following cleavage. Xrn2 degrades 5′ end of uncapped RNA and removes RNAPII from the DNA template

[ Normal View | Magnified View ]

RNA processing and degradation: Processing and degradation factors are recruited to the site of transcription. Shown are two polymerases moving in opposite directions demonstrating each of the major RNA processing pathways (as described in the key)

[ Normal View | Magnified View ]

Nrd1‐Nab3‐Sen1 termination: Nrd1 is recruited to the site of transcription by Ser5 phosphorylated CTD. Nab3 and Nrd1 form a heterodimer and bind to RNA via their RNA recognition motif domains. Nab3 and Nrd1 are thought to be able to recruit Sen1, which then catches RNAPII and unwinds the DNA/RNA hybrid (also known as R‐loop). TRAMP unwinds RNA and its subunit Trf4 polyadenylates the 3′ end of RNA for processing and/or degradation. The exosome complex then degrades the RNA 3′–5′

[ Normal View | Magnified View ]

References

Adelman,, K., & Lis,, J. T. (2012). Promoter‐proximal pausing of RNA polymerase II: Emerging roles in metazoans. Nature Reviews Genetics, 13(10), 720–731. https://doi.org/10.1038/nrg3293
Agafonov,, D. E., Kastner,, B., Dybkov,, O., Hofele,, R. V., Liu,, W. T., Urlaub,, H., … Stark,, H. (2016). Molecular architecture of the human U4/U6.U5 tri‐snRNP. Science, 351(6280), 1416–1420. https://doi.org/10.1126/science.aad2085
Ahearn,, J. M., Jr., Bartolomei,, M. S., West,, M. L., Cisek,, L. J., & Corden,, J. L. (1987). Cloning and sequence analysis of the mouse genomic locus encoding the largest subunit of RNA polymerase II. Journal of Biological Chemistry, 262(22), 10695–10705.
Ahn,, S. H., Kim,, M., & Buratowski,, S. (2004). Phosphorylation of serine 2 within the RNA polymerase II C‐terminal domain couples transcription and 3′ end processing. Molecular Cell, 13(1), 67–76.
Alexander,, R. D., Innocente,, S. A., Barrass,, J. D., & Beggs,, J. D. (2010). Splicing‐dependent RNA polymerase pausing in yeast. Molecular Cell, 40(4), 582–593. https://doi.org/10.1016/j.molcel.2010.11.005
Allmang,, C., Kufel,, J., Chanfreau,, G., Mitchell,, P., Petfalski,, E., & Tollervey,, D. (1999). Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO Journal, 18(19), 5399–5410. https://doi.org/10.1093/emboj/18.19.5399
Amberg,, D. C., Goldstein,, A. L., & Cole,, C. N. (1992). Isolation and characterization of RAT1: An essential gene of Saccharomyces cerevisiae required for the efficient nucleocytoplasmic trafficking of mRNA. Genes %26 Development, 6(7), 1173–1189.
Ameur,, A., Zaghlool,, A., Halvardson,, J., Wetterbom,, A., Gyllensten,, U., Cavelier,, L., & Feuk,, L. (2011). Total RNA sequencing reveals nascent transcription and widespread co‐transcriptional splicing in the human brain. Nature Structural %26 Molecular Biology, 18(12), 1435–1440. https://doi.org/10.1038/nsmb.2143
Andersen,, P. R., Domanski,, M., Kristiansen,, M. S., Storvall,, H., Ntini,, E., Verheggen,, C., … Jensen,, T. H. (2013). The human cap‐binding complex is functionally connected to the nuclear RNA exosome. Nature Structural %26 Molecular Biology, 20(12), 1367–1376. https://doi.org/10.1038/nsmb.2703
Andreassi,, C., & Riccio,, A. (2009). To localize or not to localize: mRNA fate is in 3′UTR ends. Trends in Cell Biology, 19(9), 465–474. https://doi.org/10.1016/j.tcb.2009.06.001
Andrulis,, E. D., Werner,, J., Nazarian,, A., Erdjument‐Bromage,, H., Tempst,, P., & Lis,, J. T. (2002). The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature, 420(6917), 837–841. https://doi.org/10.1038/nature01181
Arigo,, J. T., Eyler,, D. E., Carroll,, K. L., & Corden,, J. L. (2006). Termination of cryptic unstable transcripts is directed by yeast RNA‐binding proteins Nrd1 and Nab3. Molecular Cell, 23(6), 841–851. https://doi.org/10.1016/j.molcel.2006.07.024
Arndt,, K. M., & Reines,, D. (2015). Termination of transcription of short noncoding RNAs by RNA polymerase II. Annual Review of Biochemistry, 84, 381–404. https://doi.org/10.1146/annurev-biochem-060614-034457
Baejen,, C., Andreani,, J., Torkler,, P., Battaglia,, S., Schwalb,, B., Lidschreiber,, M., … Cramer,, P. (2017). Genome‐wide analysis of RNA polymerase II termination at protein‐coding genes. Molecular Cell, 66(1), 38–49 .e36. https://doi.org/10.1016/j.molcel.2017.02.009
Baejen,, C., Torkler,, P., Gressel,, S., Essig,, K., Soding,, J., & Cramer,, P. (2014). Transcriptome maps of mRNP biogenesis factors define pre‐mRNA recognition. Molecular Cell, 55(5), 745–757. https://doi.org/10.1016/j.molcel.2014.08.005
Baillat,, D., Hakimi,, M. A., Naar,, A. M., Shilatifard,, A., Cooch,, N., & Shiekhattar,, R. (2005). Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C‐terminal repeat of RNA polymerase II. Cell, 123(2), 265–276. https://doi.org/10.1016/j.cell.2005.08.019
Bauren,, G., & Wieslander,, L. (1994). Splicing of Balbiani ring 1 gene pre‐mRNA occurs simultaneously with transcription. Cell, 76(1), 183–192.
Beaulieu,, Y. B., Kleinman,, C. L., Landry‐Voyer,, A. M., Majewski,, J., & Bachand,, F. (2012). Polyadenylation‐dependent control of long noncoding RNA expression by the poly(A)‐binding protein nuclear 1. PLoS Genetics, 8(11), e1003078. https://doi.org/10.1371/journal.pgen.1003078
Bentley,, D. L. (2014). Coupling mRNA processing with transcription in time and space. Nature Reviews Genetics, 15(3), 163–175. https://doi.org/10.1038/nrg3662
Bertram,, K., Agafonov,, D. E., Dybkov,, O., Haselbach,, D., Leelaram,, M. N., Will,, C. L., … Stark,, H. (2017). Cryo‐EM structure of a pre‐catalytic human spliceosome primed for activation. Cell, 170(4), 701–713. https://doi.org/10.1016/j.cell.2017.07.011
Bertram,, K., Agafonov,, D. E., Liu,, W. T., Dybkov,, O., Will,, C. L., Hartmuth,, K., … Luhrmann,, R. (2017). Cryo‐EM structure of a human spliceosome activated for step 2 of splicing. Nature, 542(7641), 318–323. https://doi.org/10.1038/nature21079
Beyer,, A. L., & Osheim,, Y. N. (1988). Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes %26 Development, 2(6), 754–765.
Bitton,, D. A., Atkinson,, S. R., Rallis,, C., Smith,, G. C., Ellis,, D. A., Chen,, Y. Y., … Bahler,, J. (2015). Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast. Genome Research, 25(6), 884–896. https://doi.org/10.1101/gr.185371.114
Boczonadi,, V., Muller,, J. S., Pyle,, A., Munkley,, J., Dor,, T., Quartararo,, J., … Horvath,, R. (2014). EXOSC8 mutations alter mRNA metabolism and cause hypomyelination with spinal muscular atrophy and cerebellar hypoplasia. Nature Communications, 5, 4287. https://doi.org/10.1038/ncomms5287
Booth,, G. T., Parua,, P. K., Sansó,, M., Fisher,, R. P., & Lis,, J. T. (2018). Cdk9 regulates a promoter‐proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast. Nature Communications, 9, 543. https://doi.org/10.1038/s41467-018-03006-4
Bousquet‐Antonelli,, C., Presutti,, C., & Tollervey,, D. (2000). Identification of a regulated pathway for nuclear pre‐mRNA turnover. Cell, 102(6), 765–775. https://doi.org/10.1016/S0092-8674(00)00065-9
Brannan,, K., Kim,, H., Erickson,, B., Glover‐Cutter,, K., Kim,, S., Fong,, N., … Bentley,, D. L. (2012). mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Molecular Cell, 46(3), 311–324. https://doi.org/10.1016/j.molcel.2012.03.006
Bresson,, S. M., & Tollervey,, D. (2018). Surveillance‐ready transcription: Nuclear RNA decay as a default fate. Open Biology, 8(3), e170270. https://doi.org/10.1098/rsob.170270
Bresson,, S. M., Tuck,, A., Staneva,, D., & Tollervey,, D. (2017). Nuclear RNA decay pathways aid rapid remodeling of gene expression in yeast. Molecular Cell, 65(5), 787–800 .e785. https://doi.org/10.1016/j.molcel.2017.01.005
Bresson,, S. M., & Conrad,, N. K. (2013). The human nuclear poly(A)‐binding protein promotes RNA hyperadenylation and decay. PLoS Genetics, 9(10), e1003893. https://doi.org/10.1371/journal.pgen.1003893
Bresson,, S. M., Hunter,, O. V., Hunter,, A. C., & Conrad,, N. K. (2015). Canonical poly(A) polymerase activity promotes the decay of a wide variety of mammalian nuclear RNAs. PLoS Genetics, 11(10), e1005610. https://doi.org/10.1271/journal.pgen.1005610
Buhler,, M., Haas,, W., Gygi,, S. P., & Moazed,, D. (2007). RNAi‐dependent and ‐independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell, 129(4), 707–721. https://doi.org/10.1016/j.cell.2007.03.038
Buratowski,, S. (2003). The CTD code. Nature Structural Biology, 10(9), 679–680. https://doi.org/10.1038/nsb0903-679
Buratowski,, S. (2009). Progression through the RNA polymerase II CTD cycle. Molecular Cell, 36(4), 541–546. https://doi.org/10.1016/j.molcel.2009.10.019
Burkard,, K. T. D., & Butler,, J. S. (2000). A nuclear 3′–5′ exonuclease involved in mRNA degradation interacts with poly(A) polymerase and the hnRNA protein Npl3p. Molecular and Cellular Biology, 20(2), 604–616. https://doi.org/10.1128/Mcb.20.2.604-616.2000
Burke,, J. E., Longhurst,, A. D., Merkurjev,, D., Sales‐Lee,, J., Rao,, B., Moresco,, J. J., … Madhani,, H. D. (2018). Spliceosome profiling visualizes operations of a dynamic RNP at nucleotide resolution. Cell, 173(4), 1014–1030. https://doi.org/10.1016/j.cell.2018.03.020
Cakiroglu,, S. A., Zaugg,, J. B., & Luscombe,, N. M. (2016). Backmasking in the yeast genome: Encoding overlapping information for protein‐coding and RNA degradation. Nucleic Acids Research, 44(17), 8065–8072. https://doi.org/10.1093/nar/gkw683
Callahan,, K. P., & Butler,, J. S. (2010). TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6. Journal of Biological Chemistry, 285(6), 3540–3547. https://doi.org/10.1074/jbc.M109.058396
Carrillo Oesterreich,, F., Herzel,, L., Straube,, K., Hujer,, K., Howard,, J., & Neugebauer,, K. M. (2016). Splicing of nascent RNA coincides with intron exit from RNA polymerase II. Cell, 165, 372–381. https://doi.org/10.1016/j.cell.2016.02.045
Carrillo Oesterreich,, F., Preibisch,, S., & Neugebauer,, K. M. (2010). Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Molecular Cell, 40(4), 571–581. https://doi.org/10.1016/j.molcel.2010.11.004
Carroll,, K. L., Ghirlando,, R., Ames,, J. M., & Corden,, J. L. (2007). Interaction of yeast RNA‐binding proteins Nrd1 and Nab3 with RNA polymerase II terminator elements. RNA, 13(3), 361–373. https://doi.org/10.1261/rna.338407
Carroll,, K. L., Pradhan,, D. A., Granek,, J. A., Clarke,, N. D., & Corden,, J. L. (2004). Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. Molecular and Cellular Biology, 24(14), 6241–6252. https://doi.org/10.1128/MCB.24.14.6241-6252.2004
Casanal,, A., Kumar,, A., Hill,, C. H., Easter,, A. D., Emsley,, P., Degliesposti,, G., … Passmore,, L. A. (2017). Architecture of eukaryotic mRNA 3′‐end processing machinery. Science, 358(6366), 1056–1059. https://doi.org/10.1126/science.aao6535
Chang,, J. H., Jiao,, X. F., Chiba,, K., Oh,, C., Martin,, C. E., Kiledjian,, M., & Tong,, L. (2012). Dxo1 is a new type of eukaryotic enzyme with both decapping and 5′–3′ exoribonuclease activity. Nature Structural and Molecular Biology, 19(10), 1011–1017. https://doi.org/10.1038/nsmb.2381
Chédin,, F. (2016). Nascent connections: R‐loops and chromatin patterning. Trends in Genetics, 32(12), 828–838. https://doi.org/10.1016/j.tig.2016.10.002
Chen,, F. X., Smith,, E. R., & Shilatifard,, A. (2018). Born to run: Control of transcription elongation by RNA polymerase II. Nature Reviews Molecular Cell Biology, 19(7), 464–478. https://doi.org/10.1038/s41580-018-0010-5
Chlebowski,, A., Lubas,, M., Jensen,, T. H., & Dziembowski,, A. (2013). RNA decay machines: The exosome. Biochimica et Biophysica Acta, 1829(6–7), 552–560. https://doi.org/10.1016/j.bbagrm.2013.01.006
Cho,, E. J., Takagi,, T., Moore,, C. R., & Buratowski,, S. (1997). mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy‐terminal domain. Genes %26 Development, 11(24), 3319–3326.
Coller,, J., & Parker,, R. (2004). Eukaryotic mRNA decapping. Annual Review of Biochemistry, 73(1), 861–890. https://doi.org/10.1146/annurev.biochem.73.011303.074032
Conn,, V. M., Hugouvieux,, V., Nayak,, A., Conos,, S. A., Capovilla,, G., Cildir,, G., … Conn,, S. J. (2017). A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R‐loop formation. Nature Plants, 3, 17053. https://doi.org/10.1038/nplants.2017.53
Cougot,, N., van Dijk,, E., Babajko,, S., & Seraphin,, B. (2004). Cap‐tabolism. Trends in Biochemical Sciences, 29(8), 436–444. https://doi.org/10.1016/j.tibs.2004.06.008
Coy,, S., Volanakis,, A., Shah,, S., & Vasiljeva,, L. (2013). The Sm complex is required for the processing of non‐coding RNAs by the exosome. PLoS One, 8(6), e65606. https://doi.org/10.1371/journal.pone.0065606
Creamer,, T. J., Darby,, M. M., Jamonnak,, N., Schaughency,, P., Hao,, H., Wheelan,, S. J., & Corden,, J. L. (2011). Transcriptome‐wide binding sites for components of the Saccharomyces cerevisiae non‐poly(A) termination pathway: Nrd1, Nab3, and Sen1. PLoS Genetics, 7(10), e1002329. https://doi.org/10.1371/journal.pgen.1002329
Damgaard,, C. K., Kahns,, S., Lykke‐Andersen,, S., Nielsen,, A. L., Jensen,, T. H., & Kjems,, J. (2008). A 5′ splice site enhances the recruitment of basal transcription initiation factors in vivo. Molecular Cell, 29(2), 271–278. https://doi.org/10.1016/j.molcel.2007.11.035
Danin‐Kreiselman,, M., Lee,, C. Y., & Chanfreau,, G. (2003). RNAse III‐mediated degradation of unspliced pre‐mRNAs and lariat introns. Molecular Cell, 11(5), 1279–1289.
Davidson,, L., Muniz,, L., & West,, S. (2014). 3′ end formation of pre‐mRNA and phosphorylation of Ser2 on the RNA polymerase II CTD are reciprocally coupled in human cells. Genes %26 Development, 28(4), 342–356. https://doi.org/10.1101/gad.231274.113
Davis,, C. A., & Ares,, M., Jr. (2006). Accumulation of unstable promoter‐associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America, 103(9), 3262–3267. https://doi.org/10.1073/pnas.0507783103
de Almeida,, S. F., Garcia‐Sacristan,, A., Custodio,, N., & Carmo‐Fonseca,, M. (2010). A link between nuclear RNA surveillance, the human exosome and RNA polymerase II transcriptional termination. Nucleic Acids Research, 38(22), 8015–8026. https://doi.org/10.1093/nar/gkq703
Dengl,, S., & Cramer,, P. (2009). Torpedo nuclease Rat1 is insufficient to terminate RNA polymerase II in vitro. Journal of Biological Chemistry, 284(32), 21270–21279. https://doi.org/10.1074/jbc.M109.013847
Di Giammartino,, D. C., Nishida,, K., & Manley,, J. L. (2011). Mechanisms and consequences of alternative polyadenylation. Molecular Cell, 43(6), 853–866. https://doi.org/10.1016/j.molcel.2011.08.017
Dichtl,, B., Blank,, D., Ohnacker,, M., Friedlein,, A., Roeder,, D., Langen,, H., & Keller,, W. (2002). A role for SSU72 in balancing RNA polymerase II transcription elongation and termination. Molecular Cell, 10(5), 1139–1150.
Dujardin,, G., Lafaille,, C., Petrillo,, E., Buggiano,, V., Gomez Acuña,, L. I., Fiszbein,, A., … Kornblihtt,, A. R. (2013). Transcriptional elongation and alternative splicing. Biochimica et Biophysica Acta, 1829(1), 134–140. https://doi.org/10.1016/j.bbagrm.2012.08.005
Eaton,, J. D., Davidson,, L., Bauer,, D. L. V., Natsume,, T., Kanemaki,, M. T., & West,, S. (2018). Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity. Genes %26 Development, 32(2), 127–139. https://doi.org/10.1101/gad.308528.117
Eberle,, A. B., Hessle,, V., Helbig,, R., Dantoft,, W., Gimber,, N., & Visa,, N. (2010). Splice‐site mutations cause Rrp6‐mediated nuclear retention of the unspliced RNAs and transcriptional down‐regulation of the splicing‐defective genes. PLoS One, 5(7), e11540. https://doi.org/10.1371/journal.pone.0011540
Eckard,, S. C., Rice,, G. I., Fabre,, A., Badens,, C., Gray,, E. E., Hartley,, J. L., … Stetson,, D. B. (2014). The SKIV2L RNA exosome limits activation of the RIG‐I‐like receptors. Nature Immunology, 15(9), 839–845. https://doi.org/10.1038/ni.2948
Egloff,, S., O`Reilly,, D., Chapman,, R. D., Taylor,, A., Tanzhaus,, K., Pitts,, L., … Murphy,, S. (2007). Serine‐7 of the RNA polymerase II CTD is specifically required for snRNA gene expression. Science, 318(5857), 1777–1779. https://doi.org/10.1126/science.1145989
Egloff,, S., Szczepaniak,, S. A., Dienstbier,, M., Taylor,, A., Knight,, S., & Murphy,, S. (2010). The integrator complex recognizes a new double mark on the RNA polymerase II carboxyl‐terminal domain. Journal of Biological Chemistry, 285(27), 20564–20569. https://doi.org/10.1074/jbc.M110.132530
Egloff,, S., Zaborowska,, J., Laitem,, C., Kiss,, T., & Murphy,, S. (2012). Ser7 phosphorylation of the CTD recruits the RPAP2 Ser5 phosphatase to snRNA genes. Molecular Cell, 45(1), 111–122. https://doi.org/10.1016/j.molcel.2011.11.006
Eick,, D., & Geyer,, M. (2013). The RNA polymerase II carboxy‐terminal domain (CTD) code. Chemical Reviews, 113(11), 8456–8490. https://doi.org/10.1021/cr400071f
Elkon,, R., Ugalde,, A. P., & Agami,, R. (2013). Alternative cleavage and polyadenylation: Extent, regulation and function. Nature Reviews Genetics, 14(7), 496–506. https://doi.org/10.1038/nrg3482
Erickson,, B., Sheridan,, R. M., Cortazar,, M., & Bentley,, D. L. (2018). Dynamic turnover of paused Pol II complexes at human promoters. Genes %26 Development, 32(17–18), 1215–1225. https://doi.org/10.1101/gad.316810.118
Fabian,, M. R., Sonenberg,, N., & Filipowicz,, W. (2010). Regulation of mRNA translation and stability by microRNAs. Annual Review of Biochemistry, 79, 351–379. https://doi.org/10.1146/annurev-biochem-060308-103103
Fica,, S. M., & Nagai,, K. (2017). Cryo‐electron microscopy snapshots of the spliceosome: Structural insights into a dynamic ribonucleoprotein machine. Nature Structural %26 Molecular Biology, 24(10), 791–799. https://doi.org/10.1038/nsmb.3463
Finci,, L. I., Zhang,, X., Huang,, X., Zhou,, Q., Tsai,, J., Teng,, T., … Larsen,, N. A. (2018). The cryo‐EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre‐mRNA substrate competitive mechanism of action. Genes %26 Development, 32(3–4), 309–320. https://doi.org/10.1101/gad.311043.117
Flaherty,, S. M., Fortes,, P., Izaurralde,, E., Mattaj,, I. W., & Gilmartin,, G. M. (1997). Participation of the nuclear cap binding complex in pre‐mRNA 3′ processing. Proceedings of the National Academy of Sciences of the United States of America, 94(22), 11893–11898. https://doi.org/10.1073/pnas.94.22.11893
Fong,, N., & Bentley,, D. L. (2001). Capping, splicing, and 3′ processing are independently stimulated by RNA polymerase II: Different functions for different segments of the CTD. Genes %26 Development, 15(14), 1783–1795.
Fong,, N., Brannan,, K., Erickson,, B., Kim,, H., Cortazar,, M. A., Sheridan,, R. M., … Bentley,, D. L. (2015). Effects of transcription elongation rate and Xrn2 exonuclease activity on RNA polymerase II termination suggest widespread kinetic competition. Molecular Cell, 60(2), 256–267. https://doi.org/10.1016/j.molcel.2015.09.026
Fox,, M. J., Gao,, H., Smith‐Kinnaman,, W. R., Liu,, Y., & Mosley,, A. L. (2015). The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1‐Nab3 pathway. PLoS Genetics, 11(2), e1004999. https://doi.org/10.1371/journal.pgen.1004999
Franks,, T. M., & Lykke‐Andersen,, J. (2008). The control of mRNA decapping and P‐body formation. Molecular Cell, 32(5), 605–615. https://doi.org/10.1016/j.molcel.2008.11.001
Furuichi,, Y., & Shatkin,, A. J. (2000). Viral and cellular mRNA capping: Past and prospects. Advances in Virus Research, 55, 135–184.
Fusby,, B., Kim,, S., Erickson,, B., Kim,, H., Peterson,, M. L., & Bentley,, D. L. (2016). Coordination of RNA polymerase II pausing and 3′ end processing factor recruitment with alternative polyadenylation. Molecular and Cellular Biology, 36(2), 295–303. https://doi.org/10.1128/MCB.00898-15
Galej,, W. P., Wilkinson,, M. E., Fica,, S. M., Oubridge,, C., Newman,, A. J., & Nagai,, K. (2016). Cryo‐EM structure of the spliceosome immediately after branching. Nature, 537(7619), 197–201. https://doi.org/10.1038/nature19316
Galy,, V., Gadal,, O., Fromont‐Racine,, M., Romano,, A., Jacquier,, A., & Nehrbass,, U. (2004). Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1. Cell, 116(1), 63–73.
Ghaemmaghami,, S., Huh,, W., Bower,, K., Howson,, R. W., Belle,, A., Dephoure,, N., … Weissman,, J. S. (2003). Global analysis of protein expression in yeast. Nature, 425(6959), 737–741. https://doi.org/10.1038/nature02046
Ghosh,, A., Shuman,, S., & Lima,, C. D. (2011). Structural insights to how mammalian capping enzyme reads the CTD code. Molecular Cell, 43(2), 299–310. https://doi.org/10.1016/j.molcel.2011.06.001
Gilbert,, W., & Guthrie,, C. (2004). The Glc7p nuclear phosphatase promotes mRNA export by facilitating association of Mex67p with mRNA. Molecular Cell, 13(2), 201–212.
Girard,, C., Will,, C. L., Peng,, J., Makarov,, E. M., Kastner,, B., Lemm,, I., … Luhrmann,, R. (2012). Post‐transcriptional spliceosomes are retained in nuclear speckles until splicing completion. Nature Communications, 3, 994. https://doi.org/10.1038/ncomms1998
Glover‐Cutter,, K., Kim,, S., Espinosa,, J., & Bentley,, D. L. (2008). RNA polymerase II pauses and associates with pre‐mRNA processing factors at both ends of genes. Nature Structural %26 Molecular Biology, 15(1), 71–78. https://doi.org/10.1038/nsmb1352
Greenleaf,, A. L. (1993). Positive patches and negative noodles: Linking RNA processing to transcription? Trends in Biochemical Sciences, 18(4), 117–119.
Gromak,, N., West,, S., & Proudfoot,, N. J. (2006). Pause sites promote transcriptional termination of mammalian RNA polymerase II. Molecular and Cellular Biology, 26(10), 3986–3996. https://doi.org/10.1128/MCB.26.10.3986-3996.2006
Grudzien‐Nogalska,, E., & Kiledjian,, M. (2017). New insights into decapping enzymes and selective mRNA decay. WIREs RNA, 8(1), e1379. https://doi.org/10.1002/wrna.1379
Grzechnik,, P., Gdula,, M. R., & Proudfoot,, N. J. (2015). Pcf11 orchestrates transcription termination pathways in yeast. Genes %26 Development, 29(8), 849–861. https://doi.org/10.1101/gad.251470.114
Gudipati,, R. K., Villa,, T., Boulay,, J., & Libri,, D. (2008). Phosphorylation of the RNA polymerase II C‐terminal domain dictates transcription termination choice. Nature Structural %26 Molecular Biology, 15(8), 786–794. https://doi.org/10.1038/nsmb.1460
Gudipati,, R. K., Xu,, Z., Lebreton,, A., Seraphin,, B., Steinmetz,, L. M., Jacquier,, A., & Libri,, D. (2012). Extensive degradation of RNA precursors by the exosome in wild‐type cells. Molecular Cell, 48(3), 409–421. https://doi.org/10.1016/j.molcel.2012.08.018
Gusarov,, I., & Nudler,, E. (1999). The mechanism of intrinsic transcription termination. Molecular Cell, 3(4), 495–504.
Haag,, J. R., & Pikaard,, C. S. (2011). Multisubunit RNA polymerases IV and V: Purveyors of non‐coding RNA for plant gene silencing. Nature Reviews Molecular Cell Biology, 12(8), 483–492. https://doi.org/10.1038/nrm3152
Halbeisen,, R. E., Galgano,, A., Scherrer,, T., & Gerber,, A. P. (2008). Post‐transcriptional gene regulation: From genome‐wide studies to principles. Cellular and Molecular Life Sciences, 65(5), 798–813. https://doi.org/10.1007/s00018-007-7447-6
Hammell,, C. M., Gross,, S., Zenklusen,, D., Heath,, C. V., Stutz,, F., Moore,, C., & Cole,, C. N. (2002). Coupling of termination, 3′ processing, and mRNA export. Molecular and Cellular Biology, 22(18), 6441–6457.
Han,, Z., Libri,, D., & Porrua,, O. (2017). Biochemical characterization of the helicase Sen1 provides new insights into the mechanisms of non‐coding transcription termination. Nucleic Acids Research, 45(3), 1355–1370. https://doi.org/10.1093/nar/gkw1230
Harlen,, K. M., Trotta,, K. L., Smith,, E. E., Mosaheb,, M. M., Fuchs,, S. M., & Churchman,, L. S. (2016). Comprehensive RNA polymerase II interactomes reveal distinct and varied roles for each phospho‐CTD residue. Cell Reports, 15(10), 2147–2158. https://doi.org/10.1016/j.celrep.2016.05.010
Hazelbaker,, D. Z., Marquardt,, S., Wlotzka,, W., & Buratowski,, S. (2013). Kinetic competition between RNA polymerase II and Sen1‐dependent transcription termination. Molecular Cell, 49(1), 55–66. https://doi.org/10.1016/j.molcel.2012.10.014
Henriques,, T., Gilchrist,, D. A., Nechaev,, S., Bern,, M., Muse,, G. W., Burkholder,, A., … Adelman,, K. (2013). Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals. Molecular Cell, 52(4), 517–528. https://doi.org/10.1016/j.molcel.2013.10.001
Heo,, D. H., Yoo,, I., Kong,, J., Lidschreiber,, M., Mayer,, A., Choi,, B. Y., … Kim,, M. (2013). The RNA polymerase II C‐terminal domain‐interacting domain of yeast Nrd1 contributes to the choice of termination pathway and couples to RNA processing by the nuclear exosome. Journal of Biological Chemistry, 288(51), 36676–36690. https://doi.org/10.1074/jbc.M113.508267
Hernández,, H., & Robinson,, C. V. (2007). Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry. Nature Protocols, 2(3), 715–726. https://doi.org/10.1038/nprot.2007.73
Herzel,, L., Ottoz,, D. S. M., Alpert,, T., & Neugebauer,, K. M. (2017). Splicing and transcription touch base: Co‐transcriptional spliceosome assembly and function. Nature Reviews Molecular Cell Biology, 18(10), 637–650. https://doi.org/10.1038/nrm.2017.63
Hessle,, V., von Euler,, A., Gonzalez de Valdivia,, E., & Visa,, N. (2012). Rrp6 is recruited to transcribed genes and accompanies the spliced mRNA to the nuclear pore. RNA, 18(8), 1466–1474. https://doi.org/10.1261/rna.032045.111
Hieronymus,, H., Yu,, M. C., & Silver,, P. A. (2004). Genome‐wide mRNA surveillance is coupled to mRNA export. Genes %26 Development, 18(21), 2652–2662. https://doi.org/10.1101/gad.1241204
Hilleren,, P., & Parker,, R. (2001). Defects in the mRNA export factors Rat7p, Gle1p, Mex67p, and Rat8p cause hyperadenylation during 3′‐end formation of nascent transcripts. RNA, 7(5), 753–764. https://doi.org/10.1017/S1355838201010147
Honorine,, R., Mosrin‐Huaman,, C., Hervouet‐Coste,, N., Libri,, D., & Rahmouni,, A. R. (2011). Nuclear mRNA quality control in yeast is mediated by Nrd1 co‐transcriptional recruitment, as revealed by the targeting of rho‐induced aberrant transcripts. Nucleic Acids Research, 39(7), 2809–2820. https://doi.org/10.1093/nar/gkq1192
Houseley,, J., Kotovic,, K., El Hage,, A., & Tollervey,, D. (2007). Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control. EMBO Journal, 26(24), 4996–5006. https://doi.org/10.1038/sj.emboj.7601921
Hrossova,, D., Sikorsky,, T., Potesil,, D., Bartosovic,, M., Pasulka,, J., Zdrahal,, Z., … Vanacova,, S. (2015). RBM7 subunit of the NEXT complex binds U‐rich sequences and targets 3′‐end extended forms of snRNAs. Nucleic Acids Research, 43(8), 4236–4248. https://doi.org/10.1093/nar/gkv240
Hsin,, J. P., Sheth,, A., & Manley,, J. L. (2011). RNAP II CTD phosphorylated on threonine‐4 is required for histone mRNA 3′ end processing. Science, 334(6056), 683–686. https://doi.org/10.1126/science.1206034
Hunter,, G. O., Fox,, M. J., Smith‐Kinnaman,, W. R., Gogol,, M., Fleharty,, B., & Mosley,, A. L. (2016). Phosphatase Rtr1 regulates global levels of serine 5 RNA polymerase II C‐terminal domain phosphorylation and cotranscriptional histone methylation. Molecular and Cellular Biology, 36(17), 2236–2245. https://doi.org/10.1128/MCB.00870-15
Inada,, T. (2013). Quality control systems for aberrant mRNAs induced by aberrant translation elongation and termination. Biochimica et Biophysica Acta, 1829(6–7), 634–642. https://doi.org/10.1016/j.bbagrm.2013.02.004
Itoh,, N., Yamada,, H., Kaziro,, Y., & Mizumoto,, K. (1987). Messenger‐RNA guanylyltransferase from Saccharomyces cerevisiae—Large‐scale purification, subunit functions, and subcellular‐localization. Journal of Biological Chemistry, 262(5), 1989–1995.
Izaurralde,, E., Lewis,, J., Gamberi,, C., Jarmolowski,, A., McGuigan,, C., & Mattaj,, I. W. (1995). A cap‐binding protein complex mediating U snRNA export. Nature, 376(6542), 709–712. https://doi.org/10.1038/376709a0
Izaurralde,, E., Lewis,, J., McGuigan,, C., Jankowska,, M., Darzynkiewicz,, E., & Mattaj,, I. W. (1994). A nuclear cap binding protein complex involved in pre‐mRNA splicing. Cell, 78(4), 657–668.
Jamonnak,, N., Creamer,, T. J., Darby,, M. M., Schaughency,, P., Wheelan,, S. J., & Corden,, J. L. (2011). Yeast Nrd1, Nab3, and Sen1 transcriptome‐wide binding maps suggest multiple roles in post‐transcriptional RNA processing. RNA, 17(11), 2011–2025. https://doi.org/10.1261/rna.2840711
Jenal,, M., Elkon,, R., Loayza‐Puch,, F., van Haaften,, G., Kühn,, U., Menzies,, F. M., … Agami,, R. (2012). The poly(A)‐binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites. Cell, 149(3), 538–553. https://doi.org/10.1016/j.cell.2012.03.022
Jiao,, X., Chang,, J. H., Kilic,, T., Tong,, L., & Kiledjian,, M. (2013). A mammalian pre‐mRNA 5′ end capping quality control mechanism and an unexpected link of capping to pre‐mRNA processing. Molecular Cell, 50(1), 104–115. https://doi.org/10.1016/j.molcel.2013.02.017
Jiao,, X., Xiang,, S., Oh,, C., Martin,, C. E., Tong,, L., & Kiledjian,, M. (2010). Identification of a quality‐control mechanism for mRNA 5′‐end capping. Nature, 467(7315), 608–611. https://doi.org/10.1038/nature09338
Jimeno‐Gonzalez,, S., Haaning,, L. L., Malagon,, F., & Jensen,, T. H. (2010). The yeast 5′–3′ exonuclease Rat1p functions during transcription elongation by RNA polymerase II. Molecular Cell, 37(4), 580–587. https://doi.org/10.1016/j.molcel.2010.01.019
Johnson,, S. A., Cubberley,, G., & Bentley,, D. L. (2009). Cotranscriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3′ end processing factor Pcf11. Molecular Cell, 33(2), 215–226. https://doi.org/10.1016/j.molcel.2008.12.007
Kaida,, D. (2016). The reciprocal regulation between splicing and 3′‐end processing. WIREs RNA, 7(4), 499–511. https://doi.org/10.1002/wrna.1348
Karousis,, E. D., Nasif,, S., & Muhlemann,, O. (2016). Nonsense‐mediated mRNA decay: Novel mechanistic insights and biological impact. WIREs RNA, 7(5), 661–682. https://doi.org/10.1002/wrna.1357
Kawauchi,, J., Mischo,, H., Braglia,, P., Rondon,, A., & Proudfoot,, N. J. (2008). Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination. Genes %26 Development, 22(8), 1082–1092. https://doi.org/10.1101/gad.463408
Kerwitz,, Y., Kuhn,, U., Lilie,, H., Knoth,, A., Scheuermann,, T., Friedrich,, H., … Wahle,, E. (2003). Stimulation of poly(A) polymerase through a direct interaction with the nuclear poly(A) binding protein allosterically regulated by RNA. EMBO Journal, 22(14), 3705–3714. https://doi.org/10.1093/emboj/cdg347
Khodor,, Y. L., Menet,, J. S., Tolan,, M., & Rosbash,, M. (2012). Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse. RNA, 18(12), 2174–2186. https://doi.org/10.1261/rna.034090.112
Khodor,, Y. L., Rodriguez,, J., Abruzzi,, K. C., Tang,, C. H., Marr,, M. T., 2nd, & Rosbash,, M. (2011). Nascent‐seq indicates widespread cotranscriptional pre‐mRNA splicing in Drosophila. Genes %26 Development, 25(23), 2502–2512. https://doi.org/10.1101/gad.178962.111
Kilchert,, C., Wittmann,, S., Passoni,, M., Shah,, S., Granneman,, S., & Vasiljeva,, L. (2015). Regulation of mRNA levels by decay‐promoting introns that recruit the exosome specificity factor Mmi1. Cell Reports, 13(11), 2504–2515. https://doi.org/10.1016/j.celrep.2015.11.026
Kim,, M., Ahn,, S. H., Krogan,, N. J., Greenblatt,, J. F., & Buratowski,, S. (2004). Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes. EMBO Journal, 23(2), 354–364. https://doi.org/10.1038/sj.emboj.7600053
Kim,, M., Krogan,, N. J., Vasiljeva,, L., Rando,, O. J., Nedea,, E., Greenblatt,, J. F., & Buratowski,, S. (2004). The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature, 432(7016), 517–522. https://doi.org/10.1038/nature03041
Kim,, W., Bennett,, E. J., Huttlin,, E. L., Guo,, A., Li,, J., Possemato,, A., … Gygi,, S. P. (2011). Systematic and quantitative assessment of the ubiquitin‐modified proteome. Molecular Cell, 44(2), 325–340. https://doi.org/10.1016/j.molcel.2011.08.025
Kireeva,, M. L., Nedialkov,, Y. A., Cremona,, G. H., Purtov,, Y. A., Lubkowska,, L., Malagon,, F., … Kashlev,, M. (2008). Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Molecular Cell, 30(5), 557–566. https://doi.org/10.1016/j.molcel.2008.04.017
Komarnitsky,, P., Cho,, E. J., & Buratowski,, S. (2000). Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes %26 Development, 14(19), 2452–2460.
Kubicek,, K., Cerna,, H., Holub,, P., Pasulka,, J., Hrossova,, D., Loehr,, F., … Stefl,, R. (2012). Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1. Genes %26 Development, 26(17), 1891–1896. https://doi.org/10.1101/gad.192781.112
Kuehner,, J. N., Pearson,, E., & Moore,, C. (2011). Unravelling the means to an end: RNA polymerase II transcription termination. Nature Reviews Molecular Cell Biology, 12(5), 283–294. https://doi.org/10.1038/nrm3098
Kufel,, J., Bousquet‐Antonelli,, C., Beggs,, J. D., & Tollervey,, D. (2004). Nuclear pre‐mRNA decapping and 5′ degradation in yeast require the Lsm2‐8p complex. Molecular and Cellular Biology, 24(21), 9646–9657. https://doi.org/10.1128/MCB.24.21.9646-9657.2004
Kwak,, H., Fuda,, N. J., Core,, L. J., & Lis,, J. T. (2013). Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science, 339, 950–953.
Lai,, F., Gardini,, A., Zhang,, A., & Shiekhattar,, R. (2015). Integrator mediates the biogenesis of enhancer RNAs. Nature, 525(7569), 399–403. https://doi.org/10.1038/nature14906
Lee,, Y. J., & Glaunsinger,, B. A. (2009). Aberrant herpesvirus‐induced polyadenylation correlates with cellular messenger RNA destruction. PLoS Biology, 7(5), e1000107. https://doi.org/10.1371/journal.pbio.1000107
Lemay,, J. F., Larochelle,, M., Marguerat,, S., Atkinson,, S., Bahler,, J., & Bachand,, F. (2014). The RNA exosome promotes transcription termination of backtracked RNA polymerase II. Nature Structural %26 Molecular Biology, 21(10), 919–926. https://doi.org/10.1038/nsmb.2893
Lemieux,, C., Marguerat,, S., Lafontaine,, J., Barbezier,, N., Bahler,, J., & Bachand,, F. (2011). A pre‐mRNA degradation pathway that selectively targets intron‐containing genes requires the nuclear poly(A)‐binding protein. Molecular Cell, 44(1), 108–119. https://doi.org/10.1016/j.molcel.2011.06.035
Leonaite,, B., Han,, Z., Basquin,, J., Bonneau,, F., Libri,, D., Porrua,, O., & Conti,, E. (2017). Sen1 has unique structural features grafted on the architecture of the Upf1‐like helicase family. EMBO Journal, 36(11), 1590–1604. https://doi.org/10.15252/embj.201696174
Liang,, D., Tatomer,, D. C., Luo,, Z., Wu,, H., Yang,, L., Chen,, L. L., … Wilusz,, J. E. (2017). The output of protein‐coding genes shifts to circular RNAs when the pre‐mRNA processing machinery is limiting. Molecular Cell, 68(5), 940–954 .e943. https://doi.org/10.1016/j.molcel.2017.10.034
Libri,, D., Dower,, K., Boulay,, J., Thomsen,, R., Rosbash,, M., & Jensen,, T. H. (2002). Interactions between mRNA export commitment, 3′‐end quality control, and nuclear degradation. Molecular and Cellular Biology, 22(23), 8254–8266. https://doi.org/10.1128/mcb.22.23.8254-8266.2002
Licatalosi,, D. D., Geiger,, G., Minet,, M., Schroeder,, S., Cilli,, K., McNeil,, J. B., & Bentley,, D. L. (2002). Functional interaction of yeast pre‐mRNA 3′ end processing factors with RNA polymerase II. Molecular Cell, 9(5), 1101–1111.
Lim,, S. J., Boyle,, P. J., Chinen,, M., Dale,, R. K., & Lei,, E. P. (2013). Genome‐wide localization of exosome components to active promoters and chromatin insulators in Drosophila. Nucleic Acids Research, 41(5), 2963–2980. https://doi.org/10.1093/nar/gkt037
Loya,, T. J., O`Rourke,, T. W., & Reines,, D. (2012). A genetic screen for terminator function in yeast identifies a role for a new functional domain in termination factor Nab3. Nucleic Acids Research, 40(15), 7476–7491. https://doi.org/10.1093/nar/gks377
Lubas,, M., Andersen,, P. R., Schein,, A., Dziembowski,, A., Kudla,, G., & Jensen,, T. H. (2015). The human nuclear exosome targeting complex is loaded onto newly synthesized RNA to direct early ribonucleolysis. Cell Reports, 10(2), 178–192. https://doi.org/10.1016/j.celrep.2014.12.026
Lubas,, M., Christensen,, M. S., Kristiansen,, M. S., Domanski,, M., Falkenby,, L. G., Lykke‐Andersen,, S., … Jensen,, T. H. (2011). Interaction profiling identifies the human nuclear exosome targeting complex. Molecular Cell, 43(4), 624–637. https://doi.org/10.1016/j.molcel.2011.06.028
Lunde,, B. M., Reichow,, S. L., Kim,, M., Suh,, H., Leeper,, T. C., Yang,, F., … Varani,, G. (2010). Cooperative interaction of transcription termination factors with the RNA polymerase II C‐terminal domain. Nature Structural %26 Molecular Biology, 17(10), 1195–1201. https://doi.org/10.1038/nsmb.1893
Luo,, M. J., & Reed,, R. (1999). Splicing is required for rapid and efficient mRNA export in metazoans. Proceedings of the National Academy of Sciences of the United States of America, 96(26), 14937–14942. https://doi.org/10.1073/pnas.96.26.14937
Luo,, W., Johnson,, A. W., & Bentley,, D. L. (2006). The role of Rat1 in coupling mRNA 3′‐end processing to transcription termination: Implications for a unified allosteric‐torpedo model. Genes %26 Development, 20(8), 954–965. https://doi.org/10.1101/gad.1409106
Lutz,, C. S., & Moreira,, A. (2011). Alternative mRNA polyadenylation in eukaryotes: An effective regulator of gene expression. WIREs RNA, 2(1), 22–31. https://doi.org/10.1002/wrna.47
Malagon,, F., Kireeva,, M. L., Shafer,, B. K., Lubkowska,, L., Kashlev,, M., & Strathern,, J. N. (2006). Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6‐azauracil. Genetics, 172(4), 2201–2209. https://doi.org/10.1534/genetics.105.052415
Mandal,, S. S., Chu,, C., Wada,, T., Handa,, H., Shatkin,, A. J., & Reinberg,, D. (2004). Functional interactions of RNA‐capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proceedings of the National Academy of Sciences of the United States of America, 101(20), 7572–7577. https://doi.org/10.1073/pnas.0401493101
Martinez‐Rucobo,, F. W., Kohler,, R., van de Waterbeemd,, M., Heck,, A. J. R., Hemann,, M., Herzog,, F., … Cramer,, P. (2015). Molecular basis of transcription‐coupled pre‐mRNA capping. Molecular Cell, 58(6), 1079–1089. https://doi.org/10.1016/j.molcel.2015.04.004
Mayer,, A., di Iulio,, J., Maleri,, S., Eser,, U., Vierstra,, J., Reynolds,, A., … Churchman,, L. S. (2015). Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell, 161(3), 541–554. https://doi.org/10.1016/j.cell.2015.03.010
Mayer,, A., Heidemann,, M., Lidschreiber,, M., Schreieck,, A., Sun,, M., Hintermair,, C., … Cramer,, P. (2012). CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science, 336(6089), 1723–1725. https://doi.org/10.1126/science.1219651
Mayer,, A., Landry,, H. M., & Churchman,, L. S. (2017). Pause %26 go: From the discovery of RNA polymerase pausing to its functional implications. Current Opinion in Cell Biology, 46, 72–80. https://doi.org/10.1016/j.ceb.2017.03.002
Mayer,, A., Lidschreiber,, M., Siebert,, M., Leike,, K., Soding,, J., & Cramer,, P. (2010). Uniform transitions of the general RNA polymerase II transcription complex. Nature Structural %26 Molecular Biology, 17(10), 1272–1278. https://doi.org/10.1038/nsmb.1903
McCracken,, S., Fong,, N., Rosonina,, E., Yankulov,, K., Brothers,, G., Siderovski,, D., … Bentley,, D. L. (1997). 5′‐Capping enzymes are targeted to pre‐mRNA by binding to the phosphorylated carboxy‐terminal domain of RNA polymerase II. Genes %26 Development, 11(24), 3306–3318.
McCracken,, S., Fong,, N., Yankulov,, K., Ballantyne,, S., Pan,, G., Greenblatt,, J., … Bentley,, D. L. (1997). The C‐terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature, 385(6614), 357–361. https://doi.org/10.1038/385357a0
Meola,, N., Domanski,, M., Karadoulama,, E., Chen,, Y., Gentil,, C., Pultz,, D., … Jensen,, T. H. (2016). Identification of a nuclear exosome decay pathway for processed transcripts. Molecular Cell, 64(3), 520–533. https://doi.org/10.1016/j.molcel.2016.09.025
Milligan,, L., Torchet,, C., Allmang,, C., Shipman,, T., & Tollervey,, D. (2005). A nuclear surveillance pathway for mRNAs with defective polyadenylation. Molecular and Cellular Biology, 25(22), 9996–10004. https://doi.org/10.1128/MCB.25.22.9996-10004.2005
Mischo,, H. E., Chun,, Y., Harlen,, K. M., Smalec,, B. M., Dhir,, S., Churchman,, L. S., & Buratowski,, S. (2018). Cell‐cycle modulation of transcription termination factor Sen1. Molecular Cell, 70(2), 312–326. https://doi.org/10.1016/j.molcel.2018.03.010
Mischo,, H. E., Gomez‐Gonzalez,, B., Grzechnik,, P., Rondon,, A. G., Wei,, W., Steinmetz,, L., … Proudfoot,, N. J. (2011). Yeast Sen1 helicase protects the genome from transcription‐associated instability. Molecular Cell, 41(1), 21–32. https://doi.org/10.1016/j.molcel.2010.12.007
Mischo,, H. E., & Proudfoot,, N. J. (2013). Disengaging polymerase: Terminating RNA polymerase II transcription in budding yeast. Biochimica et Biophysica Acta, 1829(1), 174–185. https://doi.org/10.1016/j.bbagrm.2012.10.003
Misteli,, T., & Spector,, D. L. (1999). RNA polymerase II targets pre‐mRNA splicing factors to transcription sites in vivo. Molecular Cell, 3(6), 697–705.
Mitchell,, P., Petfalski,, E., Shevchenko,, A., Mann,, M., & Tollervey,, D. (1997). The exosome: A conserved eukaryotic RNA processing complex containing multiple 3′→5′ exoribonucleases. Cell, 91(4), 457–466.
Moore,, M. J., Schwartzfarb,, E. M., Silver,, P. A., & Yu,, M. C. (2006). Differential recruitment of the splicing machinery during transcription predicts genome‐wide patterns of mRNA splicing. Molecular Cell, 24(6), 903–915. https://doi.org/10.1016/j.molcel.2006.12.006
Morales,, J. C., Richard,, P., Rommel,, A., Fattah,, F. J., Motea,, E. A., Patidar,, P. L., … Boothman,, D. A. (2014). Kub5‐Hera, the human Rtt103 homolog, plays dual functional roles in transcription termination and DNA repair. Nucleic Acids Research, 42(8), 4996–5006. https://doi.org/10.1093/nar/gku160
Mosley,, A. L., Pattenden,, S. G., Carey,, M., Venkatesh,, S., Gilmore,, J. M., Florens,, L., … Washburn,, M. P. (2009). Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation. Molecular Cell, 34(2), 168–178. https://doi.org/10.1016/j.molcel.2009.02.025
Mouaikel,, J., Causse,, S. Z., Rougemaille,, M., Daubenton‐Carafa,, Y., Blugeon,, C., Lemoine,, S., … Libri,, D. (2013). High‐frequency promoter firing links THO complex function to heavy chromatin formation. Cell Reports, 5(4), 1082–1094. https://doi.org/10.1016/j.celrep.2013.10.013
Muse,, G. W., Gilchrist,, D. A., Nechaev,, S., Shah,, R., Parker,, J. S., Grissom,, S. F., … Adelman,, K. (2007). RNA polymerase is poised for activation across the genome. Nature Genetics, 39(12), 1507–1511. https://doi.org/10.1038/ng.2007.21
Nechaev,, S., Fargo,, D. C., dos Santos,, G., Liu,, L., Gao,, Y., & Adelman,, K. (2010). Global analysis of short RNAs reveals widespread promoter‐proximal stalling and arrest of Pol II in Drosophila. Science, 327(5963), 335–338. https://doi.org/10.1126/science.1181421
Nemec,, C. M., Yang,, F., Gilmore,, J. M., Hintermair,, C., Ho,, Y. H., Tseng,, S. C., … Ansari,, A. Z. (2017). Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner. Proceedings of the National Academy of Sciences of the United States of America, 114(20), E3944–E3953. https://doi.org/10.1073/pnas.1700128114
Nguyen,, T. H., Galej,, W. P., Bai,, X. C., Savva,, C. G., Newman,, A. J., Scheres,, S. H., & Nagai,, K. (2015). The architecture of the spliceosomal U4/U6.U5 tri‐snRNP. Nature, 523(7558), 47–52. https://doi.org/10.1038/nature14548
Nguyen,, T. H., Galej,, W. P., Fica,, S. M., Lin,, P. C., Newman,, A. J., & Nagai,, K. (2016). CryoEM structures of two spliceosomal complexes: Starter and dessert at the spliceosome feast. Current Opinion in Structural Biology, 36, 48–57. https://doi.org/10.1016/j.sbi.2015.12.005
Nguyen,, T. H., Galej,, W. P., Bai,, X. C., Oubridge,, C., Newman,, A. J., Scheres,, S. H. W., & Nagai,, K. (2016). Cryo‐EM structure of the yeast U4/U6.U5 tri‐snRNP at 3.7 A resolution. Nature, 530(7590), 298–302. https://doi.org/10.1038/nature16940
Ni,, Z., Xu,, C., Guo,, X., Hunter,, G. O., Kuznetsova,, O. V., Tempel,, W., … Greenblatt,, J. F. (2014). RPRD1A and RPRD1B are human RNA polymerase II C‐terminal domain scaffolds for Ser5 dephosphorylation. Nature Structural %26 Molecular Biology, 21(8), 686–695. https://doi.org/10.1038/nsmb.2853
Nilsen,, T. W., & Graveley,, B. R. (2010). Expansion of the eukaryotic proteome by alternative splicing. Nature, 463(7280), 457–463. https://doi.org/10.1038/nature08909
Nojima,, T., Gomes,, T., Grosso,, A. R. F., Kimura,, H., Dye,, M. J., Dhir,, S., … Proudfoot,, N. J. (2015). Mammalian NET‐Seq reveals genome‐wide nascent transcription coupled to RNA processing. Cell, 161(3), 526–540. https://doi.org/10.1016/j.cell.2015.03.027
Nojima,, T., Rebelo,, K., Gomes,, T., Grosso,, A. R., Proudfoot,, N. J., & Carmo‐Fonseca,, M. (2018). RNA polymerase II phosphorylated on CTD serine 5 interacts with the spliceosome during co‐transcriptional splicing. Molecular Cell, 72(2), 369–379. https://doi.org/10.1016/j.molcel.2018.09.004
Nudler,, E. (2012). RNA polymerase backtracking in gene regulation and genome instability. Cell, 149(7), 1438–1445. https://doi.org/10.1016/j.cell.2012.06.003
Ohi,, M. D., Ren,, L., Wall,, J. S., Gould,, K. L., & Walz,, T. (2007). Structural characterization of the fission yeast U5.U2/U6 spliceosome complex. Proceedings of the National Academy of Sciences of the United States of America, 104(9), 3195–3200. https://doi.org/10.1073/pnas.0611591104
Ohle,, C., Tesorero,, R., Schermann,, G., Dobrev,, N., Sinning,, I., & Fischer,, T. (2016). Transient RNA–DNA hybrids are required for efficient double‐strand break repair. Cell, 167(4), 1001–1013. https://doi.org/10.1016/j.cell.2016.10.001
O`Reilly,, D., Kuznetsova,, O. V., Laitem,, C., Zaborowska,, J., Dienstbier,, M., & Murphy,, S. (2014). Human snRNA genes use polyadenylation factors to promote efficient transcription termination. Nucleic Acids Research, 42(1), 264–275. https://doi.org/10.1093/nar/gkt892
Palumbo,, M. C., Farina,, L., & Paci,, P. (2015). Kinetics effects and modeling of mRNA turnover. WIREs RNA, 6(3), 327–336. https://doi.org/10.1002/wrna.1277
Pandya‐Jones,, A., & Black,, D. L. (2009). Co‐transcriptional splicing of constitutive and alternative exons. RNA, 15(10), 1896–1908. https://doi.org/10.1261/rna.1714509
Park,, J., Kang,, M., & Kim,, M. (2015). Unraveling the mechanistic features of RNA polymerase II termination by the 5′–3′ exoribonuclease Rat1. Nucleic Acids Research, 43(5), 2625–2637. https://doi.org/10.1093/nar/gkv133
Pearson,, E., & Moore,, C. (2014). The evolutionarily conserved Pol II flap loop contributes to proper transcription termination on short yeast genes. Cell Reports, 9(3), 821–828. https://doi.org/10.1016/j.celrep.2014.10.007
Pearson,, E., & Moore,, C. L. (2013). Dismantling promoter‐driven RNA polymerase II transcription complexes in vitro by the termination factor Rat1. Journal of Biological Chemistry, 288(27), 19750–19759. https://doi.org/10.1074/jbc.M112.434985
Pefanis,, E., Wang,, J., Rothschild,, G., Lim,, J., Chao,, J., Rabadan,, R., … Basu,, U. (2014). Noncoding RNA transcription targets AID to divergently transcribed loci in B cells. Nature, 514(7522), 389–393. https://doi.org/10.1038/nature13580
Pefanis,, E., Wang,, J., Rothschild,, G., Lim,, J., Kazadi,, D., Sun,, J., … Basu,, U. (2015). RNA exosome‐regulated long non‐coding RNA transcription controls super‐enhancer activity. Cell, 161(4), 774–789. https://doi.org/10.1016/j.cell.2015.04.034
Pei,, Y., Schwer,, B., & Shuman,, S. (2003). Interactions between fission yeast Cdk9, its cyclin partner Pch1, and mRNA capping enzyme Pct1 suggest an elongation checkpoint for mRNA quality control. Journal of Biological Chemistry, 278, 7180–7188. https://doi.org/10.1074/jbc.M211713200
Perales,, R., & Bentley,, D. (2009). "Cotranscriptionality": The transcription elongation complex as a nexus for nuclear transactions. Molecular Cell, 36(2), 178–191. https://doi.org/10.1016/j.molcel.2009.09.018
Pomeranz Krummel,, D. A., Oubridge,, C., Leung,, A. K., Li,, J., & Nagai,, K. (2009). Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. Nature, 458(7237), 475–480. https://doi.org/10.1038/nature07851
Porrua,, O., Boudvillain,, M., & Libri,, D. (2016). Transcription termination: Variations on common themes. Trends in Genetics, 32(8), 508–522. https://doi.org/10.1016/j.tig.2016.05.007
Porrua,, O., Hobor,, F., Boulay,, J., Kubicek,, K., D`Aubenton‐Carafa,, Y., Gudipati,, R. K., … Libri,, D. (2012). In vivo SELEX reveals novel sequence and structural determinants of Nrd1‐Nab3‐Sen1‐dependent transcription termination. EMBO Journal, 31(19), 3935–3948. https://doi.org/10.1038/emboj.2012.237
Porrua,, O., & Libri,, D. (2013). A bacterial‐like mechanism for transcription termination by the Sen1p helicase in budding yeast. Nature Structural %26 Molecular Biology, 20(7), 884–891. https://doi.org/10.1038/nsmb.2592
Porrua,, O., & Libri,, D. (2015). Transcription termination and the control of the transcriptome: Why, where and how to stop. Nature Reviews Molecular Cell Biology, 16(3), 190–202. https://doi.org/10.1038/nrm3943
Preker,, P., Almvig,, K., Christensen,, M. S., Valen,, E., Mapendano,, C. K., Sandelin,, A., & Jensen,, T. H. (2011). PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters. Nucleic Acids Research, 39(16), 7179–7193. https://doi.org/10.1093/nar/gkr370
Preker,, P., Nielsen,, J., Kammler,, S., Lykke‐Andersen,, S., Christensen,, M. S., Mapendano,, C. K., … Jensen,, T. H. (2008). RNA exosome depletion reveals transcription upstream of active human promoters. Science, 322(5909), 1851–1854. https://doi.org/10.1126/science.1164096
Proudfoot,, N. J. (2016). Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut. Science, 352(6291), aad9926. https://doi.org/10.1126/science.aad9926
Rasmussen,, E. B., & Lis,, J. T. (1993). In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proceedings of the National Academy of Sciences of the United States of America, 90(17), 7923–7927.
Reed,, R., & Hurt,, E. (2002). A conserved mRNA export machinery coupled to pre‐mRNA splicing. Cell, 108(4), 523–531.
Richard,, P., & Manley,, J. L. (2009). Transcription termination by nuclear RNA polymerases. Genes %26 Development, 23(11), 1247–1269. https://doi.org/10.1101/gad.1792809
Roberts,, G. C., Gooding,, C., Mak,, H. Y., Proudfoot,, N. J., & Smith,, C. W. (1998). Co‐transcriptional commitment to alternative splice site selection. Nucleic Acids Research, 26(24), 5568–5572.
Rondon,, A. G., Mischo,, H. E., Kawauchi,, J., & Proudfoot,, N. J. (2009). Fail‐safe transcriptional termination for protein‐coding genes in S. cerevisiae. Molecular Cell, 36(1), 88–98. https://doi.org/10.1016/j.molcel.2009.07.028
Sadowski,, M., Dichtl,, B., Hubner,, W., & Keller,, W. (2003). Independent functions of yeast Pcf11p in pre‐mRNA 3′ end processing and in transcription termination. EMBO Journal, 22(9), 2167–2177. https://doi.org/10.1093/emboj/cdg200
Saguez,, C., Schmid,, M., Olesen,, J. R., Ghazy,, M. A., Qu,, X., Poulsen,, M. B., … Jensen,, T. H. (2008). Nuclear mRNA surveillance in THO/sub2 mutants is triggered by inefficient polyadenylation. Molecular Cell, 31(1), 91–103. https://doi.org/10.1016/j.molcel.2008.04.030
Santos‐Pereira,, J. M., & Aguilera,, A. (2015). R loops: New modulators of genome dynamics and function. Nature Reviews Genetics, 16(10), 583–597. https://doi.org/10.1038/nrg3961
Schaefke,, B., Sun,, W., Li,, Y. S., Fang,, L., & Chen,, W. (2018). The evolution of posttranscriptional regulation. WIREs RNA, 9, e1485. https://doi.org/10.1002/wrna.1485
Schaughency,, P., Merran,, J., & Corden,, J. L. (2014). Genome‐wide mapping of yeast RNA polymerase II termination. PLoS Genetics, 10(10), e1004632. https://doi.org/10.1371/journal.pgen.1004632
Schmid,, M., & Jensen,, T. H. (2018). Controlling nuclear RNA levels. Nature Reviews Genetics, 19, 518–529. https://doi.org/10.1038/s41576-018-0013-2
Schmidt,, K., & Butler,, J. S. (2013). Nuclear RNA surveillance: Role of TRAMP in controlling exosome specificity. WIREs RNA, 4(2), 217–231. https://doi.org/10.1002/wrna.1155
Schneider,, C., Kudla,, G., Wlotzka,, W., Tuck,, A., & Tollervey,, D. (2012). Transcriptome‐wide analysis of exosome targets. Molecular Cell, 48(3), 422–433. https://doi.org/10.1016/j.molcel.2012.08.013
Schonemann,, L., Kuhn,, U., Martin,, G., Schafer,, P., Gruber,, A. R., Keller,, W., … Wahle,, E. (2014). Reconstitution of CPSF active in polyadenylation: Recognition of the polyadenylation signal by WDR33. Genes %26 Development, 28(21), 2381–2393. https://doi.org/10.1101/gad.250985.114
Schreieck,, A., Easter,, A. D., Etzold,, S., Wiederhold,, K., Lidschreiber,, M., Cramer,, P., & Passmore,, L. A. (2014). RNA polymerase II termination involves C‐terminal‐domain tyrosine dephosphorylation by CPF subunit Glc7. Nature Structural %26 Molecular Biology, 21(2), 175–179. https://doi.org/10.1038/nsmb.2753
Schulz,, D., Schwalb,, B., Kiesel,, A., Baejen,, C., Torkler,, P., Gagneur,, J., … Cramer,, P. (2013). Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell, 155(5), 1075–1087. https://doi.org/10.1016/j.cell.2013.10.024
Shi,, Y., Di Giammartino,, D. C., Taylor,, D., Sarkeshik,, A., Rice,, W. J., Yates,, J. R., 3rd, … Manley,, J. L. (2009). Molecular architecture of the human pre‐mRNA 3′ processing complex. Molecular Cell, 33(3), 365–376. https://doi.org/10.1016/j.molcel.2008.12.028
Shukla,, S., & Parker,, R. (2014). Quality control of assembly‐defective U1 snRNAs by decapping and 5′‐to‐3′ exonucleolytic digestion. Proceedings of the National Academy of Sciences of the United States of America, 111(32), E3277–E3286. https://doi.org/10.1073/pnas.1412614111
Shuman,, S. (1995). Capping enzyme in eukaryotic mRNA synthesis. Progress in Nucleic Acid Research and Molecular Biology, 50, 101–129.
Skaar,, J. R., Ferris,, A. L., Wu,, X., Saraf,, A., Khanna,, K. K., Florens,, L., … Pagano,, M. (2015). The integrator complex controls the termination of transcription at diverse classes of gene targets. Cell Research, 25(3), 288–305. https://doi.org/10.1038/cr.2015.19
Skourti‐Stathaki,, K., Kamieniarz‐Gdula,, K., & Proudfoot,, N. J. (2014). R‐loops induce repressive chromatin marks over mammalian gene terminators. Nature, 516(7531), 436–439. https://doi.org/10.1038/nature13787
Skourti‐Stathaki,, K., Proudfoot,, N. J., & Gromak,, N. (2011). Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2‐dependent termination. Molecular Cell, 42(6), 794–805. https://doi.org/10.1016/j.molcel.2011.04.026
Skruzny,, M., Schneider,, C., Racz,, A., Weng,, J., Tollervey,, D., & Hurt,, E. (2009). An endoribonuclease functionally linked to perinuclear mRNP quality control associates with the nuclear pore complexes. PLoS Biology, 7(1), e8. https://doi.org/10.1371/journal.pbio.1000008
Song,, M. G., Li,, Y., & Kiledjian,, M. (2010). Multiple mRNA decapping enzymes in mammalian cells. Molecular Cell, 40(3), 423–432. https://doi.org/10.1016/j.molcel.2010.10.010
Sperling,, R. (2017). The nuts and bolts of the endogenous spliceosome. WIREs RNA, 8(1), e1377. https://doi.org/10.1002/wrna.1377
Steinmetz,, E. J., Conrad,, N. K., Brow,, D. A., & Corden,, J. L. (2001). RNA‐binding protein Nrd1 directs poly(A)‐independent 3′‐end formation of RNA polymerase II transcripts. Nature, 413(6853), 327–331. https://doi.org/10.1038/35095090
Steurer,, B., Janssens,, R. C., Geverts,, B., Geijer,, M. E., Wienholz,, F., Theil,, A. F., … Marteijn,, J. A. (2018). Live‐cell analysis of endogenous GFP‐RPB1 uncovers rapid turnover of initiating and promoter‐paused RNA polymerase II. Proceedings of the National Academy of Sciences of the United States of America, 115(19), E4368–E4376. https://doi.org/10.1073/pnas.1717920115
Stiller,, J. W., & Hall,, B. D. (2002). Evolution of the RNA polymerase II C‐terminal domain. Proceedings of the National Academy of Sciences of the United States of America, 99(9), 6091–6096. https://doi.org/10.1073/pnas.082646199
Svejstrup,, J. Q. (2007). Contending with transcriptional arrest during RNAPII transcript elongation. Trends in Biochemical Sciences, 32(4), 165–171. https://doi.org/10.1016/j.tibs.2007.02.005
Szczepinska,, T., Kalisiak,, K., Tomecki,, R., Labno,, A., Borowski,, L. S., Kulinski,, T. M., … Dziembowski,, A. (2015). DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts. Genome Research, 25(11), 1622–1633. https://doi.org/10.1101/gr.189597.115
Tan‐Wong,, S. M., Zaugg,, J. B., Camblong,, J., Xu,, Z., Zhang,, D. W., Mischo,, H. E., … Proudfoot,, N. J. (2012). Gene loops enhance transcriptional directionality. Science, 338(6107), 671–675. https://doi.org/10.1126/science.1224350
Thiebaut,, M., Kisseleva‐Romanova,, E., Rougemaille,, M., Boulay,, J., & Libri,, D. (2006). Transcription termination and nuclear degradation of cryptic unstable transcripts: A role for the nrd1‐nab3 pathway in genome surveillance. Molecular Cell, 23(6), 853–864. https://doi.org/10.1016/j.molcel.2006.07.029
Tian,, B., Hu,, J., Zhang,, H., & Lutz,, C. S. (2005). A large‐scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Research, 33(1), 201–212. https://doi.org/10.1093/nar/gki158
Tian,, B., & Manley,, J. L. (2013). Alternative cleavage and polyadenylation: The long and short of it. Trends in Biochemical Sciences, 38(6), 312–320. https://doi.org/10.1016/j.tibs.2013.03.005
Tietjen,, J. R., Zhang,, D. W., Rodriguez‐Molina,, J. B., White,, B. E., Akhtar,, M. S., Heidemann,, M., … Ansari,, A. Z. (2010). Chemical‐genomic dissection of the CTD code. Nature Structural %26 Molecular Biology, 17(9), 1154–1161. https://doi.org/10.1038/nsmb.1900
Tilgner,, H., Knowles,, D. G., Johnson,, R., Davis,, C. A., Chakrabortty,, S., Djebali,, S., … Guigo,, R. (2012). Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co‐transcriptional in the human genome but inefficient for lncRNAs. Genome Research, 22(9), 1616–1625. https://doi.org/10.1101/gr.134445.111
Topisirovic,, I., Svitkin,, Y. V., Sonenberg,, N., & Shatkin,, A. J. (2011). Cap and cap‐binding proteins in the control of gene expression. WIREs RNA, 2(2), 277–298. https://doi.org/10.1002/wrna.52
Torchet,, C., Bousquet‐Antonelli,, C., Milligan,, L., Thompson,, E., Kufel,, J., & Tollervey,, D. (2002). Processing of 3′‐extended read‐through transcripts by the exosome can generate functional mRNAs. Molecular Cell, 9(6), 1285–1296.
Tudek,, A., Porrua,, O., Kabzinski,, T., Lidschreiber,, M., Kubicek,, K., Fortova,, A., … Libri,, D. (2014). Molecular basis for coordinating transcription termination with noncoding RNA degradation. Molecular Cell, 55(3), 467–481. https://doi.org/10.1016/j.molcel.2014.05.031
Valen,, E., Preker,, P., Andersen,, P. R., Zhao,, X., Chen,, Y., Ender,, C., … Jensen,, T. H. (2011). Biogenic mechanisms and utilization of small RNAs derived from human protein‐coding genes. Nature Structural %26 Molecular Biology, 18(9), 1075–1082. https://doi.org/10.1038/nsmb.2091
van Hoof,, A., Lennertz,, P., & Parker,, R. (2000). Yeast exosome mutants accumulate 3′‐extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Molecular and Cellular Biology, 20(2), 441–452.
Vasiljeva,, L., & Buratowski,, S. (2006). Nrd1 interacts with the nuclear exosome for 3′ processing of RNA polymerase II transcripts. Molecular Cell, 21(2), 239–248. https://doi.org/10.1016/j.molcel.2005.11.028
Vasiljeva,, L., Kim,, M., Mutschler,, H., Buratowski,, S., & Meinhart,, A. (2008). The Nrd1‐Nab3‐Sen1 termination complex interacts with the Ser5‐phosphorylated RNA polymerase II C‐terminal domain. Nature Structural %26 Molecular Biology, 15(8), 795–804. https://doi.org/10.1038/nsmb.1468
Vasiljeva,, L., Kim,, M., Terzi,, N., Soares,, L. M., & Buratowski,, S. (2008). Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Molecular Cell, 29(3), 313–323. https://doi.org/10.1016/j.molcel.2008.01.011
Viladevall,, L., St Amour,, C. V., Rosebrock,, A., Schneider,, S., Zhang,, C., Allen,, J. J., … Fisher,, R. P. (2009). TFIIH and P‐TEFb coordinate transcription with capping enzyme recruitment at specific genes in fission yeast. Molecular Cell, 33(6), 738–751. https://doi.org/10.1016/j.molcel.2009.01.029
Wagschal,, A., Rousset,, E., Basavarajaiah,, P., Contreras,, X., Harwig,, A., Laurent‐Chabalier,, S., … Kiernan,, R. (2012). Microprocessor, Setx, Xrn2, and Rrp6 co‐operate to induce premature termination of transcription by RNAPII. Cell, 150(6), 1147–1157. https://doi.org/10.1016/j.cell.2012.08.004
Wahba,, L., Gore,, S. K., & Koshland,, D. (2013). The homologous recombination machinery modulates the formation of RNA–DNA hybrids and associated chromosome instability. eLife, 2, e00505. https://doi.org/10.7554/eLife.00505
Wan,, J., Yourshaw,, M., Mamsa,, H., Rudnik‐Schoneborn,, S., Menezes,, M. P., Hong,, J. E., … Jen,, J. C. (2012). Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration. Nature Genetics, 44(6), 704–708. https://doi.org/10.1038/ng.2254
Wan,, R., Yan,, C., Bai,, R., Wang,, L., Huang,, M., Wong,, C. C., & Shi,, Y. (2016). The 3.8 A structure of the U4/U6.U5 tri‐snRNP: Insights into spliceosome assembly and catalysis. Science, 351(6272), 466–475. https://doi.org/10.1126/science.aad6466
Wang,, S. W., Stevenson,, A. L., Kearsey,, S. E., Watt,, S., & Bahler,, J. (2008). Global role for polyadenylation‐assisted nuclear RNA degradation in posttranscriptional gene silencing. Molecular and Cellular Biology, 28(2), 656–665. https://doi.org/10.1128/MCB.01531-07
Wani,, S., Yuda,, M., Fujiwara,, Y., Yamamoto,, M., Harada,, F., Ohkuma,, Y., & Hirose,, Y. (2014). Vertebrate Ssu72 regulates and coordinates 3′‐end formation of RNAs transcribed by RNA polymerase II. PLoS One, 9(8), e106040. https://doi.org/10.1371/journal.pone.0106040
West,, S., Gromak,, N., & Proudfoot,, N. J. (2004). Human 5′→3′ exonuclease Xrn2 promotes transcription termination at co‐transcriptional cleavage sites. Nature, 432(7016), 522–525. https://doi.org/10.1038/nature03035
Wilusz,, C. J., Wormington,, M., & Peltz,, S. W. (2001). The cap‐to‐tail guide to mRNA turnover. Nature Reviews Molecular Cell Biology, 2(4), 237–246. https://doi.org/10.1038/35067025
Wilusz,, J. E. (2018). A 360° view of circular RNAs: From biogenesis to functions. WIREs RNA, 9, e1478. https://doi.org/10.1002/wrna.1478
Windhager,, L., Bonfert,, T., Burger,, K., Ruzsics,, Z., Krebs,, S., Kaufmann,, S., … Dolken,, L. (2012). Ultrashort and progressive 4sU‐tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Research, 22(10), 2031–2042. https://doi.org/10.1101/gr.131847.111
Wlotzka,, W., Kudla,, G., Granneman,, S., & Tollervey,, D. (2011). The nuclear RNA polymerase II surveillance system targets polymerase III transcripts. EMBO Journal, 30(9), 1790–1803. https://doi.org/10.1038/emboj.2011.97
Woodward,, L. A., Mabin,, J. W., Gangras,, P., & Singh,, G. (2017). The exon junction complex: A lifelong guardian of mRNA fate. WIREs RNA, 8(3), e1477. https://doi.org/10.1002/wrna.1411
Wyers,, F., Rougemaille,, M., Badis,, G., Rousselle,, J. C., Dufour,, M. E., Boulay,, J., … Jacquier,, A. (2005). Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell, 121(5), 725–737. https://doi.org/10.1016/j.cell.2005.04.030
Xiang,, K., Tong,, L., & Manley,, J. L. (2014). Delineating the structural blueprint of the pre‐mRNA 3′‐end processing machinery. Molecular and Cellular Biology, 34(11), 1894–1910. https://doi.org/10.1128/MCB.00084-14
Xiang,, S., Cooper‐Morgan,, A., Jiao,, X. F., Kiledjian,, M., Manley,, J. L., & Tong,, L. (2009). Structure and function of the 5′→3′ exoribonuclease Rat1 and its activating partner Rai1. Nature, 458(7239), 784–788. https://doi.org/10.1038/nature07731
Xue,, Y., Bai,, X. X., Lee,, I., Kallstrom,, G., Ho,, J., Brown,, J., … Johnson,, A. W. (2000). Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. Molecular and Cellular Biology, 20(11), 4006–4015. https://doi.org/10.1128/Mcb.20.11.4006-4015.2000
Yan,, C. Y., Hang,, J., Wan,, R. X., Huang,, M., Wong,, C. C. L., & Shi,, Y. G. (2015). Structure of a yeast spliceosome at 3.6 Å resolution. Science, 349(6253), 1182–1191. https://doi.org/10.1126/science.aac7629
Yang,, C., Hager,, P. W., & Stiller,, J. W. (2014). The identification of putative RNA polymerase II C‐terminal domain associated proteins in red and green algae. Transcription, 5(5), e970944. https://doi.org/10.4161/21541264.2014.970944
Yue,, Z., Maldonado,, E., Pillutla,, R., Cho,, H., Reinberg,, D., & Shatkin,, A. J. (1997). Mammalian capping enzyme complements mutant Saccharomyces cerevisiae lacking mRNA guanylyltransferase and selectively binds the elongating form of RNA polymerase II. Proceedings of the National Academy of Sciences of the United States of America, 94(24), 12898–12903.
Zaborowska,, J., Egloff,, S., & Murphy,, S. (2016). The pol II CTD: New twists in the tail. Nature Structural %26 Molecular Biology, 23(9), 771–777. https://doi.org/10.1038/nsmb.3285
Zenklusen,, D., Larson,, D. R., & Singer,, R. H. (2008). Single‐RNA counting reveals alternative modes of gene expression in yeast. Nature Structural %26 Molecular Biology, 15(12), 1263–1271. https://doi.org/10.1038/nsmb.1514
Zhai,, L. T., & Xiang,, S. (2014). mRNA quality control at the 5′ end. Journal of Zhejiang University. Science. B, 15(5), 438–443. https://doi.org/10.1631/jzus.B1400070
Zhang,, H., Rigo,, F., & Martinson,, H. G. (2015). Poly(A) signal‐dependent transcription termination occurs through a conformational change mechanism that does not require cleavage at the poly(A) site. Molecular Cell, 59(3), 437–448. https://doi.org/10.1016/j.molcel.2015.06.008
Zhao,, D. Y., Gish,, G., Braunschweig,, U., Li,, Y., Ni,, Z., Schmitges,, F. W., … Greenblatt,, J. F. (2016). SMN and symmetric arginine dimethylation of RNA polymerase II C‐terminal domain control termination. Nature, 529(7584), 48–53. https://doi.org/10.1038/nature16469
Zhou,, M., & Law,, J. A. (2015). RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II`s rules. Current Opinion in Plant Biology, 27, 154–164. https://doi.org/10.1016/j.pbi.2015.07.005
Zinder,, J. C., & Lima,, C. D. (2017). Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors. Genes %26 Development, 31(2), 88–100. https://doi.org/10.1101/gad.294769.116

Access to this WIREs title is by subscription only.

Recommend to Your
Librarian Now!

Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control

Browse by Topic

Access to this WIREs title is by subscription only.

The latest WIREs articles in your inbox