Rates of in situ transcription and splicing in large human genes (original) (raw)

• Rasmussen, E.B. & Lis, J.T. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc. Natl. Acad. Sci. USA 90, 7923–7927 (1993).
  Article CAS Google Scholar
• Proudfoot, N.J., Furger, A. & Dye, M.J. Integrating mRNA processing with transcription. Cell 108, 501–512 (2002).
  Article CAS Google Scholar
• Neugebauer, K.M. On the importance of being co-transcriptional. J. Cell Sci. 115, 3865–3871 (2002).
  Article CAS Google Scholar
• Bentley, D.L. Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. Curr. Opin. Cell Biol. 17, 251–256 (2005).
  Article CAS Google Scholar
• Hirose, Y. & Manley, J.L. RNA polymerase II is an essential mRNA polyadenylation factor. Nature 395, 93–96 (1998).
  Article CAS Google Scholar
• Hirose, Y., Tacke, R. & Manley, J.L. Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev. 13, 1234–1239 (1999).
  Article CAS Google Scholar
• de la Mata, M. et al. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell 12, 525–532 (2003).
  Article CAS Google Scholar
• Cáceres, J.F. & Kornblihtt, A.R. Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet. 18, 186–193 (2002).
  Article Google Scholar
• Core, L.J. & Lis, J.T. Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 319, 1791–1792 (2008).
  Article CAS Google Scholar
• Batsché, E., Yaniv, M. & Muchardt, C. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat. Struct. Mol. Biol. 13, 22–29 (2006).
  Article Google Scholar
• Roberts, G.C., Gooding, C., Mak, H.Y., Proudfoot, N.J. & Smith, C.W. Co-transcriptional commitment to alternative splice site selection. Nucleic Acids Res. 26, 5568–5572 (1998).
  Article CAS Google Scholar
• Howe, K.J., Kane, C.M. & Ares, M. Jr. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA 9, 993–1006 (2003).
  Article CAS Google Scholar
• Kornblihtt, A.R. Chromatin, transcript elongation and alternative splicing. Nat. Struct. Mol. Biol. 13, 5–7 (2006).
  Article CAS Google Scholar
• Tennyson, C.N., Klamut, H.J. & Worton, R.G. The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced. Nat. Genet. 9, 184–190 (1995).
  Article CAS Google Scholar
• O'Brien, T. & Lis, J.T. Rapid changes in Drosophila transcription after an instantaneous heat shock. Mol. Cell. Biol. 13, 3456–3463 (1993).
  Article CAS Google Scholar
• Femino, A.M., Fogarty, K., Lifshitz, L.M., Carrington, W. & Singer, R.H. Visualization of single molecules of mRNA in situ. Methods Enzymol. 361, 245–304 (2003).
  Article CAS Google Scholar
• Darzacq, X. et al. In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 14, 796–806 (2007).
  Article CAS Google Scholar
• Boireau, S. et al. The transcriptional cycle of HIV-1 in real-time and live cells. J. Cell Biol. 179, 291–304 (2007).
  Article CAS Google Scholar
• Kessler, O., Jiang, Y. & Chasin, L.A. Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA. Mol. Cell. Biol. 13, 6211–6222 (1993).
  Article CAS Google Scholar
• Audibert, A., Weil, D. & Dautry, F. In vivo kinetics of mRNA splicing and transport in mammalian cells. Mol. Cell. Biol. 22, 6706–6718 (2002).
  Article CAS Google Scholar
• Das, R. et al. Functional coupling of RNAP II transcription to spliceosome assembly. Genes Dev. 20, 1100–1109 (2006).
  Article CAS Google Scholar
• Listerman, I., Sapra, A.K. & Neugebauer, K.M. Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nat. Struct. Mol. Biol. 13, 815–822 (2006).
  Article CAS Google Scholar
• Kornblihtt, A.R., de la Mata, M., Fededa, J.P., Munoz, M.J. & Nogues, G. Multiple links between transcription and splicing. RNA 10, 1489–1498 (2004).
  Article CAS Google Scholar
• König, H., Matter, N., Bader, R., Thiele, W. & Muller, F. Splicing segregation: the minor spliceosome acts outside the nucleus and controls cell proliferation. Cell 131, 718–729 (2007).
  Article Google Scholar
• Matera, A.G. & Ward, D.C. Nucleoplasmic organization of small nuclear ribonucleoproteins in cultured human cells. J. Cell Biol. 121, 715–727 (1993).
  Article CAS Google Scholar
• Pessa, H.K. et al. Minor spliceosome components are predominantly localized in the nucleus. Proc. Natl. Acad. Sci. USA 105, 8655–8660 (2008).
  Article CAS Google Scholar
• Friend, K., Kolev, N.G., Shu, M.D. & Steitz, J.A. Minor-class splicing occurs in the nucleus of the Xenopus oocyte. RNA 14, 1459–1462 (2008).
  Article CAS Google Scholar
• König, H. & Muller, F. Minor splicing: nuclear dogma still in question. Proc. Natl. Acad. Sci. USA 105, E37 (2008).
  Article Google Scholar
• Steitz, J.A. et al. Where in the cell is the minor spliceosome? Proc. Natl. Acad. Sci. USA 105, 8485–8486 (2008).
  Article CAS Google Scholar
• Marshall, N.F. & Price, D.H. Control of formation of two distinct classes of RNA polymerase II elongation complexes. Mol. Cell. Biol. 12, 2078–2090 (1992).
  Article CAS Google Scholar
• Price, D.H. P-TEFb, a cyclin-dependent kinase controlling elongation by RNA polymerase II. Mol. Cell. Biol. 20, 2629–2634 (2000).
  Article CAS Google Scholar
• Cheng, B. & Price, D.H. Properties of RNA polymerase II elongation complexes before and after the P-TEFb-mediated transition into productive elongation. J. Biol. Chem. 282, 21901–21912 (2007).
  Article CAS Google Scholar
• Chodosh, L.A., Fire, A., Samuels, M. & Sharp, P.A. 5,6-Dichloro-1-β-D-ribofuranosylbenzimidazole inhibits transcription elongation by RNA polymerase II in vitro. J. Biol. Chem. 264, 2250–2257 (1989).
  CAS PubMed Google Scholar
• Gomes, N.P. et al. Gene-specific requirement for P-TEFb activity and RNA polymerase II phosphorylation within the p53 transcriptional program. Genes Dev. 20, 601–612 (2006).
  Article CAS Google Scholar
• Capranico, G. et al. The effects of camptothecin on RNA polymerase II transcription: roles of DNA topoisomerase I. Biochimie 89, 482–489 (2007).
  Article CAS Google Scholar
• Mondal, N. & Parvin, J.D. DNA topoisomerase IIα is required for RNA polymerase II transcription on chromatin templates. Nature 413, 435–438 (2001).
  Article CAS Google Scholar
• Khobta, A. et al. Early effects of topoisomerase I inhibition on RNA polymerase II along transcribed genes in human cells. J. Mol. Biol. 357, 127–138 (2006).
  Article CAS Google Scholar
• Der, S.D., Zhou, A., Williams, B.R. & Silverman, R.H. Identification of genes differentially regulated by interferon α, β, or γ using oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 95, 15623–15628 (1998).
  Article CAS Google Scholar
• Patel, A.A., McCarthy, M. & Steitz, J.A. The splicing of U12-type introns can be a rate-limiting step in gene expression. EMBO J. 21, 3804–3815 (2002).
  Article CAS Google Scholar
• Ucker, D.S. & Yamamoto, K.R. Early events in the stimulation of mammary tumor virus RNA synthesis by glucocorticoids. Novel assays of transcription rates. J. Biol. Chem. 259, 7416–7420 (1984).
  CAS PubMed Google Scholar
• Burnette, J.M., Miyamoto-Sato, E., Schaub, M.A., Conklin, J. & Lopez, A.J. Subdivision of large introns in Drosophila by recursive splicing at nonexonic elements. Genetics 170, 661–674 (2005).
  Article CAS Google Scholar
• Fong, N., Bird, G., Vigneron, M. & Bentley, D.L. A 10 residue motif at the C-terminus of the RNA Pol II CTD is required for transcription, splicing and 3′ end processing. EMBO J. 22, 4274–4282 (2003).
  Article CAS Google Scholar
• Zeng, C. & Berget, S.M. Participation of the C-terminal domain of RNA polymerase II in exon definition during pre-mRNA splicing. Mol. Cell. Biol. 20, 8290–8301 (2000).
  Article CAS Google Scholar
• Hirose, Y. & Ohkuma, Y. Phosphorylation of the C-terminal domain of RNA polymerase II plays central roles in the integrated events of eucaryotic gene expression. J. Biochem. 141, 601–608 (2007).
  Article CAS Google Scholar
• Dye, M.J., Gromak, N. & Proudfoot, N.J. Exon tethering in transcription by RNA polymerase II. Mol. Cell 21, 849–859 (2006).
  Article CAS Google Scholar
• Rosonina, E. & Blencowe, B.J. Analysis of the requirement for RNA polymerase II CTD heptapeptide repeats in pre-mRNA splicing and 3′-end cleavage. RNA 10, 581–589 (2004).
  Article CAS Google Scholar
• West, A.B. et al. N-myc regulates parkin expression. J. Biol. Chem. 279, 28896–28902 (2004).
  Article CAS Google Scholar