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Genetics Research International
Volume 2011, Article ID 623718, 16 pages
http://dx.doi.org/10.4061/2011/623718
Review Article

Updating the CTD Story: From Tail to Epic

Department of Biochemistry and Center for RNA Biology, Duke University Medical Center, Durham, NC 27710, USA

Received 27 June 2011; Accepted 10 August 2011

Academic Editor: Carles Sune

Copyright © 2011 Bartlomiej Bartkowiak et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. E. H. Fischer and E. G. Krebs, “Conversion of phosphorylase b to phosphorylase a in muscle extracts,” Journal of Biological Chemistry, vol. 216, no. 1, pp. 121–132, 1955. View at Google Scholar · View at Scopus
  2. H. P. Phatnani and A. L. Greenleaf, “Phosphorylation and functions of the RNA polymerase II CTD,” Genes and Development, vol. 20, no. 21, pp. 2922–2936, 2006. View at Publisher · View at Google Scholar · View at Scopus
  3. L. A. Allison, J. K. Wong, V. D. Fitzpatrick, M. Moyle, and C. J. Ingles, “The C-terminal domain of the largest subunit of RNA polymerase II of Saccharomyces cerevisiae, Drosophila melanogaster, and mammals: a conserved structure with an essential function,” Molecular and Cellular Biology, vol. 8, no. 1, pp. 321–329, 1988. View at Google Scholar · View at Scopus
  4. J. L. Corden, “Tails of RNA polymerase II,” Trends in Biochemical Sciences, vol. 15, no. 10, pp. 383–387, 1990. View at Google Scholar · View at Scopus
  5. M. Nonet, D. Sweetser, and R. A. Young, “Functional redundancy and structural polymorphism in the large subunit of RNA polymerase II,” Cell, vol. 50, no. 6, pp. 909–915, 1987. View at Google Scholar · View at Scopus
  6. W. A. Zehring, J. M. Lee, J. R. Weeks, R. S. Jokerst, and A. L. Greenleaf, “The C-terminal repeat domain of RNA polymerase II largest subunit is essential in vivo but is not required for accurate transcription initiation in vitro,” Proceedings of the National Academy of Sciences of the United States of America, vol. 85, no. 11, pp. 3698–3702, 1988. View at Google Scholar · View at Scopus
  7. A. Meinhart, T. Kamenski, S. Hoeppner, S. Baumli, and P. Cramer, “A structural perspective of CTD function,” Genes and Development, vol. 19, no. 12, pp. 1401–1415, 2005. View at Publisher · View at Google Scholar · View at Scopus
  8. S. Egloff and S. Murphy, “Cracking the RNA polymerase II CTD code,” Trends in Genetics, vol. 24, no. 6, pp. 280–288, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. S. Buratowski, “Progression through the RNA Polymerase II CTD Cycle,” Molecular Cell, vol. 36, no. 4, pp. 541–546, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. C. J. Hengartner, V. E. Myer, S. M. Liao, C. J. Wilson, S. S. Koh, and R. A. Young, “Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases,” Molecular Cell, vol. 2, no. 1, pp. 43–53, 1998. View at Google Scholar · View at Scopus
  11. P. Komarnitsky, E. J. Cho, and S. Buratowski, “Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription,” Genes and Development, vol. 14, no. 19, pp. 2452–2460, 2000. View at Publisher · View at Google Scholar · View at Scopus
  12. R. Tietjen, D. W. Zhang, J. B. Rodríguez-Molina et al., “Chemical-genomic dissection of the CTD code,” Nature Structural and Molecular Biology, vol. 17, no. 9, pp. 1154–1161, 2010. View at Publisher · View at Google Scholar · View at Scopus
  13. M. Kim, H. Suh, E. J. Cho, and S. Buratowski, “Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7,” Journal of Biological Chemistry, vol. 284, no. 39, pp. 26421–26426, 2009. View at Publisher · View at Google Scholar · View at Scopus
  14. M. Patturajan, R. J. Schulte, B. M. Sefton et al., “Growth-related changes in phosphorylation of yeast RNA polymerase II,” Journal of Biological Chemistry, vol. 273, no. 8, pp. 4689–4694, 1998. View at Publisher · View at Google Scholar · View at Scopus
  15. R. D. Chapman, M. Heidemann, T. K. Albert et al., “Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7,” Science, vol. 318, no. 5857, pp. 1780–1782, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. J. C. Jones, H. P. Phatnani, T. A. Haystead, J. A. MacDonald, S. M. Alam, and A. L. Greenleaf, “C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats,” Journal of Biological Chemistry, vol. 279, no. 24, pp. 24957–24964, 2004. View at Publisher · View at Google Scholar · View at Scopus
  17. P. Liu, J. M. Kenney, J. W. Stiller, and A. L. Greenleaf, “Genetic organization, length conservation, and evolution of RNA polymerase II carboxyl-terminal domain,” Molecular Biology and Evolution, vol. 27, no. 11, pp. 2628–2641, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. J. W. Stiller and M. S. Cook, “Functional unit of the RNA polymerase II C-terminal domain lies within heptapeptide pairs,” Eukaryotic Cell, vol. 3, no. 3, pp. 735–740, 2004. View at Publisher · View at Google Scholar · View at Scopus
  19. H. Kim, B. Erickson, W. Luo et al., “Gene-specific RNA polymerase II phosphorylation and the CTD code,” Nature Structural and Molecular Biology, vol. 17, no. 10, pp. 1279–1286, 2010. View at Publisher · View at Google Scholar · View at Scopus
  20. A. Mayer, M. Lidschreiber, M. Siebert, K. Leike, J. Söding, and P. Cramer, “Uniform transitions of the general RNA polymerase II transcription complex,” Nature Structural and Molecular Biology, vol. 17, no. 10, pp. 1272–1278, 2010. View at Publisher · View at Google Scholar · View at Scopus
  21. R. Baskaran, M. E. Dahmus, and J. Y. J. Wang, “Tyrosine phosphorylation of mammalian RNA polymerase II carboxyl-terminal domain,” Proceedings of the National Academy of Sciences of the United States of America, vol. 90, no. 23, pp. 11167–11171, 1993. View at Publisher · View at Google Scholar · View at Scopus
  22. J. Zhang and J. L. Corden, “Identification of phosphorylation sites in the repetitive carboxyl-terminal domain of the mouse RNA polymerase II largest subunit,” Journal of Biological Chemistry, vol. 266, no. 4, pp. 2290–2296, 1991. View at Google Scholar · View at Scopus
  23. W. G. Kelly, M. E. Dahmus, and G. W. Hart, “RNA polymerase II is a glycoprotein. Modification of the COOH-terminal domain by O-GlcNAc,” Journal of Biological Chemistry, vol. 268, no. 14, pp. 10416–10424, 1993. View at Google Scholar · View at Scopus
  24. S. Krishnamurthy, M. A. Ghazy, C. Moore, and M. Hampsey, “Functional interaction of the Ess1 prolyl isomerase with components of the RNA polymerase II initiation and termination machineries,” Molecular and Cellular Biology, vol. 29, no. 11, pp. 2925–2934, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. Y. X. Xu and J. L. Manley, “Pin1 modulates RNA polymerase II activity during the transcription cycle,” Genes and Development, vol. 21, no. 22, pp. 2950–2962, 2007. View at Publisher · View at Google Scholar · View at Scopus
  26. C. B. Wilcox, A. Rossettini, and S. D. Hanes, “Genetic interactions with C-terminal domain (CTD) kinases and the CTD of RNA Pol II suggest a role for ESS1 in transcription initiation and elongation in Saccharomyces cerevisiae,” Genetics, vol. 167, no. 1, pp. 93–105, 2004. View at Publisher · View at Google Scholar · View at Scopus
  27. J. W. Werner-Allen, C. J. Lee, P. Liu et al., “cis-Proline-mediated Ser(P)5 dephosphorylation by the RNA polymerase II C-terminal domain phosphatase Ssu72,” Journal of Biological Chemistry, vol. 286, pp. 5717–5726, 2011. View at Google Scholar
  28. K. Xiang, T. Nagaike, S. Xiang et al., “Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex,” Nature, vol. 467, no. 7316, pp. 729–733, 2010. View at Publisher · View at Google Scholar · View at Scopus
  29. R. J. Sims III, L. A. Rojas, D. Beck et al., “The C-terminal domain of RNA polymerase II is modified by site-specific methylation,” Science, vol. 332, pp. 99–103, 2011. View at Google Scholar
  30. R. D. Chapman, M. Heidemann, C. Hintermair, and D. Eick, “Molecular evolution of the RNA polymerase II CTD,” Trends in Genetics, vol. 24, no. 6, pp. 289–296, 2008. View at Publisher · View at Google Scholar · View at Scopus
  31. N. Fong and D. L. Bentley, “Capping, splicing, and 3′ processing are independently stimulated by RNA polymerase II: different functions for different segments of the CTD,” Genes and Development, vol. 15, no. 14, pp. 1783–1795, 2001. View at Publisher · View at Google Scholar · View at Scopus
  32. S. Egloff, D. O'Reilly, R. D. Chapman et al., “Serine-7 of the RNA polymerase II CTD is specifically required for snRNA gene expression,” Science, vol. 318, no. 5857, pp. 1777–1779, 2007. View at Publisher · View at Google Scholar · View at Scopus
  33. E. J. Cho, M. S. Kobor, M. Kim, J. Greenblatt, and S. Buratowski, “Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain,” Genes and Development, vol. 15, no. 24, pp. 3319–3329, 2001. View at Publisher · View at Google Scholar · View at Scopus
  34. S. Krishnamurthy, X. He, M. Reyes-Reyes, C. Moore, and M. Hampsey, “Ssu72 Is an RNA polymerase II CTD phosphatase,” Molecular Cell, vol. 14, no. 3, pp. 387–394, 2004. View at Publisher · View at Google Scholar · View at Scopus
  35. M. Reyes-Reyes and M. Hampsey, “Role for the Ssu72 C-terminal domain phosphatase in RNA polymerase II transcription elongation,” Molecular and Cellular Biology, vol. 27, no. 3, pp. 926–936, 2007. View at Publisher · View at Google Scholar · View at Scopus
  36. A. L. Mosley, S. G. Pattenden, M. Carey et al., “Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation,” Molecular Cell, vol. 34, no. 2, pp. 168–178, 2009. View at Publisher · View at Google Scholar · View at Scopus
  37. S. C. Schroeder, B. Schwer, S. Shuman, and D. Bentley, “Dynamic association of capping enzymes with transcribing RNA polymerase II,” Genes and Development, vol. 14, no. 19, pp. 2435–2440, 2000. View at Publisher · View at Google Scholar · View at Scopus
  38. M. S. Akhtar, M. Heidemann, J. R. Tietjen et al., “TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II,” Molecular Cell, vol. 34, no. 3, pp. 387–393, 2009. View at Publisher · View at Google Scholar · View at Scopus
  39. K. Glover-Cutter, S. Larochelle, B. Erickson et al., “TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II,” Molecular and Cellular Biology, vol. 29, no. 20, pp. 5455–5464, 2009. View at Publisher · View at Google Scholar · View at Scopus
  40. B. W. Guidi, G. Bjornsdottir, D. C. Hopkins et al., “Mutual targeting of mediator and the TFIIH kinase Kin28,” Journal of Biological Chemistry, vol. 279, no. 28, pp. 29114–29120, 2004. View at Publisher · View at Google Scholar · View at Scopus
  41. T. Max, M. Søgaard, and J. Q. Svejstrup, “Hyperphosphorylation of the C-terminal repeat domain of RNA polymerase II facilitates dissociation of its complex with mediator,” Journal of Biological Chemistry, vol. 282, no. 19, pp. 14113–14120, 2007. View at Publisher · View at Google Scholar · View at Scopus
  42. S. M. Liao, J. Zhang, D. A. Jeffery et al., “A kinase-cyclin pair in the RNA polymerase II holoenzyme,” Nature, vol. 374, no. 6518, pp. 193–196, 1995. View at Google Scholar · View at Scopus
  43. S. Akoulitchev, S. Chuikov, and D. Reinberg, “TFIIH is negatively regulated by cdk8-containing mediator complexes,” Nature, vol. 407, no. 6800, pp. 102–106, 2000. View at Publisher · View at Google Scholar · View at Scopus
  44. M. D. Galbraith, A. J. Donner, and J. M. Espinosa, “CDK8: a positive regulator of transcription,” Transcription, vol. 1, no. 1, pp. 4–12, 2010. View at Publisher · View at Google Scholar
  45. S. W. Hong, S. M. Hong, J. W. Yoo et al., “Phosphorylation of the RNA polymerase II C-terminal domain by TFIIH kinase is not essential for transcription of Saccharomyces cerevisiae genome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 34, pp. 14276–14280, 2009. View at Publisher · View at Google Scholar · View at Scopus
  46. E. I. Kanin, R. T. Kipp, C. Kung et al., “Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does not impair global mRNA synthesis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 14, pp. 5812–5817, 2007. View at Publisher · View at Google Scholar · View at Scopus
  47. R. P. Fisher, “Secrets of a double agent: CDK7 in cell-cycle control and transcription,” Journal of Cell Science, vol. 118, no. 22, pp. 5171–5180, 2005. View at Publisher · View at Google Scholar · View at Scopus
  48. Y. Pei, H. Du, J. Singer et al., “Cyclin-dependent kinase 9 (Cdk9) of fission yeast is activated by the CDK-activating kinase Csk1, overlaps functionally with the TFIIH-associated kinase Mcs6, and associates with the mRNA cap methyltransferase Pcm1 in vivo,” Molecular and Cellular Biology, vol. 26, no. 3, pp. 777–788, 2006. View at Publisher · View at Google Scholar · View at Scopus
  49. H. Qiu, C. Hu, and A. G. Hinnebusch, “Phosphorylation of the Pol II CTD by KIN28 enhances BUR1/BUR2 recruitment and Ser2 CTD phosphorylation near promoters,” Molecular Cell, vol. 33, no. 6, pp. 752–762, 2009. View at Publisher · View at Google Scholar · View at Scopus
  50. L. Viladevall, C. V. S. Amour, A. Rosebrock et al., “TFIIH and P-TEFb coordinate transcription with capping enzyme recruitment at specific genes in fission yeast,” Molecular Cell, vol. 33, no. 6, pp. 738–751, 2009. View at Publisher · View at Google Scholar · View at Scopus
  51. J. M. Lee and A. L. Greenleaf, “CTD kinase large subunit is encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae,” Gene Expression, vol. 1, no. 2, pp. 149–167, 1991. View at Google Scholar · View at Scopus
  52. D. E. Sterner, Jae Moon Lee, S. E. Hardin, and A. L. Greenleaf, “The yeast carboxyl-terminal repeat domain kinase CTDK-I is a divergent cyclin-cyclin-dependent kinase complex,” Molecular and Cellular Biology, vol. 15, no. 10, pp. 5716–5724, 1995. View at Google Scholar · View at Scopus
  53. T. Xiao, H. Hall, K. O. Kizer et al., “Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast,” Genes and Development, vol. 17, no. 5, pp. 654–663, 2003. View at Publisher · View at Google Scholar · View at Scopus
  54. M. L. Youdell, K. O. Kizer, E. Kisseleva-Romanova et al., “Roles for Ctk1 and Spt6 in regulating the different methylation states of histone H3 lysine 36,” Molecular and Cellular Biology, vol. 28, no. 16, pp. 4915–4926, 2008. View at Publisher · View at Google Scholar · View at Scopus
  55. S. H. Ahn, M. Kim, and S. Buratowski, “Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end processing,” Molecular Cell, vol. 13, no. 1, pp. 67–76, 2004. View at Publisher · View at Google Scholar · View at Scopus
  56. D. A. Skaar and A. L. Greenleaf, “The RNA polymerase II CTD kinase CTDK-I affects pre-mRNA 3′ cleavage/polyadenylation through the processing component Pti1p,” Molecular Cell, vol. 10, no. 6, pp. 1429–1439, 2002. View at Publisher · View at Google Scholar · View at Scopus
  57. S. H. Ahn, M. C. Keogh, and S. Buratowski, “Ctk1 promotes dissociation of basal transcription factors from elongating RNA polymerase II,” EMBO Journal, vol. 28, no. 3, pp. 205–212, 2009. View at Publisher · View at Google Scholar · View at Scopus
  58. S. Yao, A. Neiman, and G. Prelich, “BUR1 and BUR2 encode a divergent cyclin-dependent kinase-cyclin complex important for transcription in vivo,” Molecular and Cellular Biology, vol. 20, no. 19, pp. 7080–7087, 2000. View at Publisher · View at Google Scholar · View at Scopus
  59. M. C. Keogh, V. Podolny, and S. Buratowski, “Bur1 kinase is required for efficient transcription elongation by RNA polymerase II,” Molecular and Cellular Biology, vol. 23, no. 19, pp. 7005–7018, 2003. View at Publisher · View at Google Scholar · View at Scopus
  60. Y. Pei and S. Shuman, “Characterization of the Schizosaccharomyces pombe Cdk9/Pch1 protein kinase: Spt5 phosphorylation, autophosphorylation, and mutational analysis,” Journal of Biological Chemistry, vol. 278, no. 44, pp. 43346–43356, 2003. View at Publisher · View at Google Scholar · View at Scopus
  61. Y. Liu, L. Warfield, C. Zhang et al., “Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex,” Molecular and Cellular Biology, vol. 29, no. 17, pp. 4852–4863, 2009. View at Publisher · View at Google Scholar · View at Scopus
  62. J. Karagiannis and M. K. Balasubramanian, “A cyclin-dependent kinase that promotes cytokinesis through modulating phosphorylation of the carboxy terminal domain of the RNA Pol II Rpb1p sub-unit,” PLoS One, vol. 2, no. 5, article e433, 2007. View at Publisher · View at Google Scholar · View at Scopus
  63. N. F. Marshall, J. Peng, Z. Xie, and D. H. Price, “Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase,” Journal of Biological Chemistry, vol. 271, no. 43, pp. 27176–27183, 1996. View at Publisher · View at Google Scholar · View at Scopus
  64. N. F. Marshall and D. H. Price, “Control of formation of two distinct classes of RNA polymerase II elongation complexes,” Molecular and Cellular Biology, vol. 12, no. 5, pp. 2078–2090, 1992. View at Google Scholar · View at Scopus
  65. N. F. Marshall and D. H. Price, “Purification of P-TEFb, a transcription factor required for the transition into productive elongation,” Journal of Biological Chemistry, vol. 270, no. 21, pp. 12335–12338, 1995. View at Publisher · View at Google Scholar · View at Scopus
  66. T. Lenasi and M. Barboric, “P-TEFb stimulates transcription elongation and pre-mRNA splicing through multilateral mechanisms,” RNA Biology, vol. 7, no. 2, pp. 145–150, 2010. View at Publisher · View at Google Scholar · View at Scopus
  67. B. M. Peterlin and D. H. Price, “Controlling the elongation phase of transcription with P-TEFb,” Molecular Cell, vol. 23, no. 3, pp. 297–305, 2006. View at Publisher · View at Google Scholar · View at Scopus
  68. S. Nechaev and K. Adelman, “Pol II waiting in the starting gates: regulating the transition from transcription initiation into productive elongation,” Biochimica et Biophysica Acta, vol. 1809, pp. 34–45, 2011. View at Google Scholar
  69. A. Wood and A. Shilatifard, “Bur1/Bur2 and the Ctk complex in yeast: the split personality of mammalian P-TEFb,” Cell Cycle, vol. 5, no. 10, pp. 1066–1068, 2006. View at Google Scholar · View at Scopus
  70. Z. Guo and J. W. Stiller, “Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs,” BMC Genomics, vol. 5, article 69, 2004. View at Publisher · View at Google Scholar · View at Scopus
  71. J. Liu and E. T. Kipreos, “Evolution of cyclin-dependent kinases (CDKs) and CDK-activating kinases (CAKs): differential conservation of CAKs in yeast and metazoa,” Molecular Biology and Evolution, vol. 17, no. 7, pp. 1061–1074, 2000. View at Google Scholar · View at Scopus
  72. B. Bartkowiak, P. Liu, H. P. Phatnani et al., “CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1,” Genes and Development, vol. 24, no. 20, pp. 2303–2316, 2010. View at Publisher · View at Google Scholar · View at Scopus
  73. R. Berro, C. Pedati, K. Kehn-Hall et al., “CDK13, a new potential human immunodeficiency virus type 1 inhibitory factor regulating viral mRNA splicing,” Journal of Virology, vol. 82, no. 14, pp. 7155–7166, 2008. View at Publisher · View at Google Scholar · View at Scopus
  74. H. H. Chen, Y. C. Wang, and M. J. Fann, “Identification and characterization of the CDK12/cyclin L1 complex involved in alternative splicing regulation,” Molecular and Cellular Biology, vol. 26, no. 7, pp. 2736–2745, 2006. View at Publisher · View at Google Scholar · View at Scopus
  75. H. H. Chen, Y. H. Wong, A. M. Geneviere, and M. J. Fann, “CDK13/CDC2L5 interacts with L-type cyclins and regulates alternative splicing,” Biochemical and Biophysical Research Communications, vol. 354, no. 3, pp. 735–740, 2007. View at Publisher · View at Google Scholar · View at Scopus
  76. T. K. Ko, E. Kelly, and J. Pines, “CrkRS: a novel conserved Cdc2-related protein kinase that colocalises with SC35 speckles,” Journal of Cell Science, vol. 114, no. 14, pp. 2591–2603, 2001. View at Google Scholar · View at Scopus
  77. Y. Even, S. Durieux, M. L. Escande et al., “CDC2L5, a Cdk-like kinase with RS domain, interacts with the ASF/SF2-associated protein p32 and affects splicing in vivo,” Journal of Cellular Biochemistry, vol. 99, no. 3, pp. 890–904, 2006. View at Publisher · View at Google Scholar · View at Scopus
  78. T. J. Fu, J. Peng, G. Lee, D. H. Price, and O. Flores, “Cyclin K functions as a CDK9 regulatory subunit and participates in RNA polymerase II transcription,” Journal of Biological Chemistry, vol. 274, no. 49, pp. 34527–34530, 1999. View at Publisher · View at Google Scholar · View at Scopus
  79. D. J. Matthews and M. E. Gerritsen, Targeting Protein Kinases for Cancer Therapy, John Wiley & Sons, Hoboken, NJ, USA, 2010.
  80. H. S. Y. Mancebo, G. Lee, J. Flygare et al., “P-TEFb kinase is required for HIV Tat transcriptional activation in vivo and in vitro,” Genes and Development, vol. 11, no. 20, pp. 2633–2644, 1997. View at Google Scholar · View at Scopus
  81. Y. Zhu, T. Pe'ery, J. Peng et al., “Transcription elongation factor P-TEFb is required for HIV-1 tat transactivation in vitro,” Genes and Development, vol. 11, no. 20, pp. 2622–2632, 1997. View at Google Scholar · View at Scopus
  82. A. V. Philips and T. A. Cooper, “RNA processing and human disease,” Cellular and Molecular Life Sciences, vol. 57, no. 2, pp. 235–249, 2000. View at Google Scholar · View at Scopus
  83. K. Inoue, M. Ohno, H. Sakamoto, and Y. Shimura, “Effect of the cap structure on pre-mRNA splicing in Xenopus oocyte nuclei,” Genes and Development, vol. 3, no. 9, pp. 1472–1479, 1989. View at Google Scholar · View at Scopus
  84. J. D. Lewis, E. Izaurralde, A. Jarmolowski, C. McGuigan, and L. W. Mattaj, “A nuclear cap-binding complex facilitates association of U1 snRNP with the cap-proximal 5' splice site,” Genes and Development, vol. 10, no. 13, pp. 1683–1698, 1996. View at Google Scholar · View at Scopus
  85. C. Cooke and J. C. Alwine, “The cap and the 3′ splice site similarly affect polyadenylation efficiency,” Molecular and Cellular Biology, vol. 16, no. 6, pp. 2579–2584, 1996. View at Google Scholar · View at Scopus
  86. S. M. Flaherty, P. Fortes, E. Izaurralde, I. W. Mattaj, and G. M. Gilmartin, “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, vol. 94, no. 22, pp. 11893–11898, 1997. View at Google Scholar · View at Scopus
  87. R. P. Hart, M. A. McDevitt, and J. R. Nevins, “Poly(A) site cleavage in a HeLa nuclear extract is dependent on downstream sequences,” Cell, vol. 43, no. 3, pp. 677–683, 1985. View at Google Scholar · View at Scopus
  88. G. Baurén, S. Belikov, and L. Wieslander, “Transcriptional termination in the Balbiani ring 1 gene is closely coupled to 3'-end formation and excision of the 3'-terminal intron,” Genes and Development, vol. 12, no. 17, pp. 2759–2769, 1998. View at Google Scholar · View at Scopus
  89. M. Niwa and S. M. Berget, “Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns,” Genes and Development, vol. 5, no. 11, pp. 2086–2095, 1991. View at Google Scholar · View at Scopus
  90. S. Vagner, C. Vagner, and I. W. Mattaj, “The carboxyl terminus of vertebrate poly(A) polymerase interacts with U2AF 65 to couple 3'-end processing and splicing,” Genes and Development, vol. 14, no. 4, pp. 403–413, 2000. View at Google Scholar · View at Scopus
  91. M. Alló, V. Buggiano, J. P. Fededa et al., “Control of alternative splicing through siRNA-mediated transcriptional gene silencing,” Nature Structural and Molecular Biology, vol. 16, no. 7, pp. 717–724, 2009. View at Publisher · View at Google Scholar · View at Scopus
  92. R. F. Luco, Q. Pan, K. Tominaga, B. J. Blencowe, O. M. Pereira-Smith, and T. Misteli, “Regulation of alternative splicing by histone modifications,” Science, vol. 327, no. 5968, pp. 996–1000, 2010. View at Publisher · View at Google Scholar · View at Scopus
  93. I. E. Schor, N. Rascovan, F. Pelisch, M. Alió, and A. R. Kornblihtt, “Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 11, pp. 4325–4330, 2009. View at Publisher · View at Google Scholar · View at Scopus
  94. R. Jove and J. L. Manley, “In vitro transcription from the adenovirus 2 major late promoter utilizing templates truncated at promoter-proximal sites,” Journal of Biological Chemistry, vol. 259, no. 13, pp. 8513–8521, 1984. View at Google Scholar · View at Scopus
  95. E. B. Rasmussen and J. T. Lis, “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, vol. 90, no. 17, pp. 7923–7927, 1993. View at Google Scholar · View at Scopus
  96. E. J. Cho, T. Takagi, C. R. Moore, and S. Buratowski, “mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain,” Genes and Development, vol. 11, no. 24, pp. 3319–3326, 1997. View at Google Scholar · View at Scopus
  97. S. McCracken, N. Fong, E. Rosonina et al., “5'-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II,” Genes and Development, vol. 11, no. 24, pp. 3306–3318, 1997. View at Google Scholar · View at Scopus
  98. Z. Yue, E. Maldonado, R. Pillutla, H. Cho, D. Reinberg, and A. J. Shatkin, “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, vol. 94, no. 24, pp. 12898–12903, 1997. View at Publisher · View at Google Scholar · View at Scopus
  99. C. K. Ho and S. Shuman, “Distinct roles for CTD Ser-2 and Ser-5 phosphorylation in the recruitment and allosteric activation of mammalian mRNA capping enzyme,” Molecular Cell, vol. 3, no. 3, pp. 405–411, 1999. View at Publisher · View at Google Scholar · View at Scopus
  100. C. Fabrega, V. Shen, S. Shuman, and C. D. Lima, “Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II,” Molecular Cell, vol. 11, no. 6, pp. 1549–1561, 2003. View at Publisher · View at Google Scholar · View at Scopus
  101. B. M. Lunde, S. L. Reichow, M. Kim et al., “Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain,” Nature Structural and Molecular Biology, vol. 17, no. 10, pp. 1195–1201, 2010. View at Publisher · View at Google Scholar · View at Scopus
  102. N. Proudfoot, “New perspectives on connecting messenger RNA 3′ end formation to transcription,” Current Opinion in Cell Biology, vol. 16, no. 3, pp. 272–278, 2004. View at Publisher · View at Google Scholar · View at Scopus
  103. S. Buratowski, “Connections between mRNA 3′ end processing and transcription termination,” Current Opinion in Cell Biology, vol. 17, no. 3, pp. 257–261, 2005. View at Publisher · View at Google Scholar · View at Scopus
  104. D. Barilla, B. A. Lee, and N. J. Proudfoot, “Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, pp. 445–450, 2001. View at Google Scholar
  105. A. Kyburz, M. Sadowski, B. Dichtl, and W. Keller, “The role of the yeast cleavage and polyadenylation factor subunit Ydh1p/Cft2p in pre-mRNA 3′-end formation,” Nucleic Acids Research, vol. 31, no. 14, pp. 3936–3945, 2003. View at Publisher · View at Google Scholar · View at Scopus
  106. D. D. Licatalosi, G. Geiger, M. Minet et al., “Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II,” Molecular Cell, vol. 9, no. 5, pp. 1101–1111, 2002. View at Publisher · View at Google Scholar · View at Scopus
  107. T. Maniatis and R. Reed, “An extensive network of coupling among gene expression machines,” Nature, vol. 416, no. 6880, pp. 499–506, 2002. View at Publisher · View at Google Scholar · View at Scopus
  108. S. McCracken, N. Fong, K. Yankulov et al., “The C-terminal domain of RNA polymerase II couples mRNA processing to transcription,” Nature, vol. 385, no. 6614, pp. 357–361, 1997. View at Publisher · View at Google Scholar · View at Scopus
  109. N. J. Proudfoot, A. Furger, and M. J. Dye, “Integrating mRNA processing with transcription,” Cell, vol. 108, no. 4, pp. 501–512, 2002. View at Publisher · View at Google Scholar · View at Scopus
  110. Y. Hirose and J. L. Manley, “RNA polymerase II is an essential mRNA polyadenylation factor,” Nature, vol. 395, no. 6697, pp. 93–96, 1998. View at Publisher · View at Google Scholar · View at Scopus
  111. M. Kim, N. J. Krogan, L. Vasiljeva et al., “The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II,” Nature, vol. 432, no. 7016, pp. 517–522, 2004. View at Publisher · View at Google Scholar · View at Scopus
  112. J. N. Kuehner, E. L. Pearson, and C. Moore, “Unravelling the means to an end: RNA polymerase II transcription termination,” Nature Reviews Molecular Cell Biology, vol. 12, pp. 283–294, 2011. View at Google Scholar
  113. C. G. Noble, D. Hollingworth, S. R. Martin et al., “Key features of the interaction between Pcf11 CID and RNA polymerase II CTD,” Nature Structural and Molecular Biology, vol. 12, no. 2, pp. 144–151, 2005. View at Publisher · View at Google Scholar · View at Scopus
  114. E. Y. Jacobs, I. Ogiwara, and A. Weiner, “Role of the C-terminal domain of RNA polymerase II in U2 snRNA transcription and 3′ processing,” Molecular and Cellular Biology, vol. 24, no. 2, pp. 846–855, 2004. View at Publisher · View at Google Scholar · View at Scopus
  115. J. E. Medlin, P. Uguen, A. Taylor, D. L. Bentley, and S. Murphy, “The C-terminal domain of pol II and a DRB-sensitive kinase are required for 3′ processing of U2 snRNA,” EMBO Journal, vol. 22, no. 4, pp. 925–934, 2003. View at Publisher · View at Google Scholar · View at Scopus
  116. S. Egloff, D. O'Reilly, and S. Murphy, “Expression of human snRNA genes from beginning to end,” Biochemical Society Transactions, vol. 36, no. 4, pp. 590–594, 2008. View at Publisher · View at Google Scholar · View at Scopus
  117. D. Baillat, M. A. Hakimi, A. M. Naar, A. Shilatifard, N. Cooch, and R. Shiekhattar, “Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II,” Cell, vol. 123, no. 2, pp. 265–276, 2005. View at Publisher · View at Google Scholar · View at Scopus
  118. S. Egloff, S. A. Szczepaniak, M. Dienstbier, A. Taylor, S. Knight, and S. Murphy, “The integrator complex recognizes a new double mark on the RNA polymerase II carboxyl-terminal domain,” Journal of Biological Chemistry, vol. 285, no. 27, pp. 20564–20569, 2010. View at Publisher · View at Google Scholar · View at Scopus
  119. B. Li, M. Carey, and J. L. Workman, “The role of chromatin during transcription,” Cell, vol. 128, no. 4, pp. 707–719, 2007. View at Publisher · View at Google Scholar · View at Scopus
  120. K. O. Kizer, H. P. Phatnani, Y. Shibata, H. Hall, A. L. Greenleaf, and B. D. Strahl, “A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation,” Molecular and Cellular Biology, vol. 25, no. 8, pp. 3305–3316, 2005. View at Publisher · View at Google Scholar · View at Scopus
  121. N. J. Krogan, M. Kim, A. Tong et al., “Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II,” Molecular and Cellular Biology, vol. 23, no. 12, pp. 4207–4218, 2003. View at Publisher · View at Google Scholar · View at Scopus
  122. N. J. Krogan, J. Dover, A. Wood et al., “The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation,” Molecular Cell, vol. 11, no. 3, pp. 721–729, 2003. View at Publisher · View at Google Scholar · View at Scopus
  123. H. H. Ng, F. Robert, R. A. Young, and K. Struhl, “Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity,” Molecular Cell, vol. 11, no. 3, pp. 709–719, 2003. View at Publisher · View at Google Scholar · View at Scopus
  124. M. Hampsey and D. Reinberg, “Tails of intrigue: phosphorylation of RNA polymerase II mediates histone methylation,” Cell, vol. 113, no. 4, pp. 429–432, 2003. View at Publisher · View at Google Scholar · View at Scopus
  125. A. A. Joshi and K. Struhl, “Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation,” Molecular Cell, vol. 20, no. 6, pp. 971–978, 2005. View at Publisher · View at Google Scholar · View at Scopus
  126. M. C. Keogh, S. K. Kurdistani, S. A. Morris et al., “Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex,” Cell, vol. 123, no. 4, pp. 593–605, 2005. View at Publisher · View at Google Scholar · View at Scopus
  127. S. Drouin, L. Laramee, P. E. Jacques, A. Forest, M. Bergeron, and F. Robert, “DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genes,” PLoS Genet, vol. 6, Article ID e1001173, 2010. View at Google Scholar
  128. C. K. Govind, H. Qiu, D. S. Ginsburg et al., “Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes,” Molecular Cell, vol. 39, no. 2, pp. 234–246, 2010. View at Publisher · View at Google Scholar · View at Scopus
  129. S. M. Yoh, H. Cho, L. Pickle, R. M. Evans, and K. A. Jones, “The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export,” Genes and Development, vol. 21, no. 2, pp. 160–174, 2007. View at Publisher · View at Google Scholar · View at Scopus
  130. M. Sun, L. Larivière, S. Dengl, A. Mayer, and P. Cramer, “A tandem SH2 domain in transcription elongation factor Spt6 binds the phosphorylated RNA polymerase II C-terminal repeat domain (CTD),” Journal of Biological Chemistry, vol. 285, no. 53, pp. 41597–41603, 2010. View at Publisher · View at Google Scholar · View at Scopus
  131. S. M. Yoh, J. S. Lucas, and K. A. Jones, “The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation,” Genes and Development, vol. 22, no. 24, pp. 3422–3434, 2008. View at Publisher · View at Google Scholar · View at Scopus
  132. M. Rodriguez-Paredes, M. Ceballos-Chavez, M. Esteller, M. Garcia-Dominguez, and J. C. Reyes, “The chromatin remodeling factor CHD8 interacts with elongating RNA polymerase II and controls expression of the cyclin E2 gene,” Nucleic Acids Research, vol. 37, pp. 2449–2460, 2009. View at Google Scholar
  133. S. H. Kwon, L. Florens, S. K. Swanson, M. P. Washburn, S. M. Abmayr, and J. L. Workman, “Heterochromatin protein 1 (HP1) connects the FACT histone chaperone complex to the phosphorylated CTD of RNA polymerase II,” Genes and Development, vol. 24, no. 19, pp. 2133–2145, 2010. View at Publisher · View at Google Scholar · View at Scopus
  134. M. J. Munoz, M. de la Mata, and A. R. Kornblihtt, “The carboxy terminal domain of RNA polymerase II and alternative splicing,” Trends in Biochemical Sciences, vol. 35, no. 9, pp. 497–504, 2010. View at Publisher · View at Google Scholar · View at Scopus
  135. A. C. Goldstrohm, A. L. Greenleaf, and M. A. Garcia-Blanco, “Co-transcriptional splicing of pre-messenger RNAs: considerations for the mechanism of alternative splicing,” Gene, vol. 277, no. 1-2, pp. 31–47, 2001. View at Publisher · View at Google Scholar · View at Scopus
  136. G. Bird, D. A. R. Zorio, and D. L. Bentley, “RNA polymerase II carboxy-terminal domain phosphorylation is required for cotranscriptional pre-mRNA splicing and 3′-end formation,” Molecular and Cellular Biology, vol. 24, no. 20, pp. 8963–8969, 2004. View at Publisher · View at Google Scholar · View at Scopus
  137. A. L. Greenleaf, “Positive patches and negative noodles: linking RNA processing to transcription?” Trends in Biochemical Sciences, vol. 18, no. 4, pp. 117–119, 1993. View at Publisher · View at Google Scholar · View at Scopus
  138. E. Kim, L. Du, D. B. Bregman, and S. L. Warren, “Splicing factors associate with hyperphosphorylated RNA polymerase II in the absence of pre-mRNA,” Journal of Cell Biology, vol. 136, no. 1, pp. 19–28, 1997. View at Publisher · View at Google Scholar · View at Scopus
  139. M. J. Mortillaro, B. J. Blencowe, X. Wei et al., “A hyperphosphorylated form of the large subunit of RNA polymerase II is associated with splicing complexes and the nuclear matrix,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 16, pp. 8253–8257, 1996. View at Publisher · View at Google Scholar · View at Scopus
  140. A. Yuryev, M. Patturajan, Y. Litingtung et al., “The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 14, pp. 6975–6980, 1996. View at Publisher · View at Google Scholar · View at Scopus
  141. L. Du and S. L. Warren, “A functional interaction between the carboxy-terminal domain of RNA polymerase II and pre-mRNA splicing,” Journal of Cell Biology, vol. 136, no. 1, pp. 5–18, 1997. View at Publisher · View at Google Scholar · View at Scopus
  142. Y. Hirose, R. Tacke, and J. L. Manley, “Phosphorylated RNA polymerase II stimulates pre-mRNA splicing,” Genes and Development, vol. 13, no. 10, pp. 1234–1239, 1999. View at Google Scholar · View at Scopus
  143. C. Zeng and S. M. Berget, “Participation of the C-terminal domain of RNA polymerase II in exon definition during pre-mRNA splicing,” Molecular and Cellular Biology, vol. 20, no. 21, pp. 8290–8301, 2000. View at Publisher · View at Google Scholar · View at Scopus
  144. M. Patturajan, X. Wei, R. Berezney, and J. L. Corden, “A nuclear matrix protein interacts with the phosphorylated C-terminal domain of RNA polymerase II,” Molecular and Cellular Biology, vol. 18, no. 4, pp. 2406–2415, 1998. View at Google Scholar · View at Scopus
  145. D. P. Morris and A. L. Greenleaf, “The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II,” Journal of Biological Chemistry, vol. 275, no. 51, pp. 39935–39943, 2000. View at Publisher · View at Google Scholar · View at Scopus
  146. S. M. Carty, A. C. Goldstrohm, C. Suñé, M. A. Garcia-Blanco, and A. L. Greenleaf, “Protein-interaction modules that organize nuclear function: FF domains of CA150 bind the phosphoCTD of RNA polymerase II,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 16, pp. 9015–9020, 2000. View at Publisher · View at Google Scholar · View at Scopus
  147. A. Emili, M. Shales, S. McCracken et al., “Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD,” RNA, vol. 8, no. 9, pp. 1102–1111, 2002. View at Publisher · View at Google Scholar · View at Scopus
  148. C. J. David, A. R. Boyne, S. R. Millhouse, and J. L. Manley, “The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex,” Genes and Development, vol. 25, pp. 972–983, 2011. View at Google Scholar
  149. M. de la Mata and A. R. Kornblihtt, “RNA polymerase II C-terminal domain mediates regulation of alternative splicing by SRp20,” Nature Structural and Molecular Biology, vol. 13, no. 11, pp. 973–980, 2006. View at Publisher · View at Google Scholar · View at Scopus
  150. M. de la Mata, C. R. Alonso, S. Kadener et al., “A slow RNA polymerase II affects alternative splicing in vivo,” Molecular Cell, vol. 12, no. 2, pp. 525–532, 2003. View at Publisher · View at Google Scholar · View at Scopus
  151. S. Kadener, P. Cramer, G. Nogués et al., “Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing,” EMBO Journal, vol. 20, no. 20, pp. 5759–5768, 2001. View at Publisher · View at Google Scholar · View at Scopus
  152. E. Batsche, M. Yaniv, and C. Muchardt, “The human SWI/SNF subunit Brm is a regulator of alternative splicing,” Nature Structural & Molecular Biology, vol. 13, pp. 22–29, 2006. View at Google Scholar
  153. M. J. Dye, N. Gromak, and N. J. Proudfoot, “Exon tethering in transcription by RNA polymerase II,” Molecular Cell, vol. 21, no. 6, pp. 849–859, 2006. View at Publisher · View at Google Scholar · View at Scopus
  154. P. Loyer, J. H. Trembley, J. A. Grenet et al., “Characterization of cyclin L1 and L2 interactions with CDK11 and splicing factors: influence of cyclin L isoforms on splice site selection,” Journal of Biological Chemistry, vol. 283, no. 12, pp. 7721–7732, 2008. View at Publisher · View at Google Scholar · View at Scopus
  155. J. H. Trembley, D. Hu, L. C. Hsu et al., “PITSLRE p110 protein kinases associate with transcription complexes and affect their activity,” Journal of Biological Chemistry, vol. 277, no. 4, pp. 2589–2596, 2002. View at Publisher · View at Google Scholar · View at Scopus
  156. S. Lin and X. D. Fu, “SR proteins and related factors in alternative splicing,” Advances in Experimental Medicine and Biology, vol. 623, pp. 107–122, 2007. View at Google Scholar · View at Scopus
  157. J. C. Long and J. F. Caceres, “The SR protein family of splicing factors: master regulators of gene expression,” Biochemical Journal, vol. 417, no. 1, pp. 15–27, 2009. View at Publisher · View at Google Scholar · View at Scopus
  158. X. Y. Zhong, P. Wang, J. Han, M. G. Rosenfeld, and X. D. Fu, “SR proteins in vertical integration of gene expression from transcription to RNA processing to translation,” Molecular Cell, vol. 35, no. 1, pp. 1–10, 2009. View at Publisher · View at Google Scholar · View at Scopus
  159. S. Rodriguez-Navarro, “Insights into SAGA function during gene expression,” EMBO Reports, vol. 10, pp. 843–850, 2009. View at Google Scholar
  160. P. Pascual-Garcia and S. Rodriguez-Navarro, “A tale of coupling, Sus1 function in transcription and mRNA export,” RNA Biology, vol. 6, no. 2, pp. 141–144, 2009. View at Google Scholar · View at Scopus
  161. K. Strasser, S. Masuda, P. Mason et al., “TREX is a conserved complex coupling transcription with messenger RNA export,” Nature, vol. 417, pp. 304–308, 2002. View at Google Scholar
  162. K. Strasser and E. Hurt, “Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p,” Nature, vol. 413, no. 6856, pp. 648–652, 2001. View at Publisher · View at Google Scholar · View at Scopus
  163. F. Stutz, A. Bachi, T. Doerks et al., “REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export,” RNA, vol. 6, pp. 638–650, 2000. View at Google Scholar
  164. S. A. Johnson, G. Cubberley, and D. L. Bentley, “Cotranscriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3′ end processing factor Pcf11,” Molecular Cell, vol. 33, no. 2, pp. 215–226, 2009. View at Publisher · View at Google Scholar · View at Scopus
  165. H. Le Hir, E. Izaurralde, L. E. Maquat, and M. J. Moore, “The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions,” EMBO Journal, vol. 19, no. 24, pp. 6860–6869, 2000. View at Publisher · View at Google Scholar · View at Scopus
  166. T. Ø. Tange, T. Shibuya, M. S. Jurica, and M. J. Moore, “Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core,” RNA, vol. 11, no. 12, pp. 1869–1883, 2005. View at Publisher · View at Google Scholar · View at Scopus
  167. F. Lejeune, Y. Ishigaki, X. Li, and L. E. Maquat, “The exon junction complex is detected on CBP80-bound but not eIF4E-bound mRNA in mammalian cells: dynamics of mRNP remodeling,” EMBO Journal, vol. 21, no. 13, pp. 3536–3545, 2002. View at Publisher · View at Google Scholar · View at Scopus
  168. D. Zenklusen, P. Vinciguerra, Y. Strahm, and F. Stutz, “The yeast hnRNP-Like proteins Yra1p and Yra2p participate in mRNA export through interaction with Mex67p,” Molecular and Cellular Biology, vol. 21, no. 13, pp. 4219–4232, 2001. View at Publisher · View at Google Scholar · View at Scopus
  169. A. G. Rondon, S. Jimeno, M. Garcia-Rubio, and A. Aguilera, “Molecular evidence that the eukaryotic THO/TREX complex is required for efficient transcription elongation,” Journal of Biological Chemistry, vol. 278, pp. 39037–39043, 2003. View at Google Scholar
  170. H. P. Phatnani, J. C. Jones, and A. L. Greenleaf, “Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome,” Biochemistry, vol. 43, no. 50, pp. 15702–15719, 2004. View at Publisher · View at Google Scholar · View at Scopus
  171. C. Maris, C. Dominguez, and F. H. T. Allain, “The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression,” FEBS Journal, vol. 272, no. 9, pp. 2118–2131, 2005. View at Publisher · View at Google Scholar · View at Scopus
  172. A. Clery, M. Blatter, and F. H. Allain, “RNA recognition motifs: boring? Not quite,” Current Opinion in Structural Biology, vol. 18, pp. 290–298, 2008. View at Google Scholar
  173. A. Aguilera, “The connection between transcription and genomic instability,” EMBO Journal, vol. 21, no. 3, pp. 195–201, 2002. View at Publisher · View at Google Scholar · View at Scopus
  174. X. Li and J. L. Manley, “Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability,” Cell, vol. 122, no. 3, pp. 365–378, 2005. View at Publisher · View at Google Scholar · View at Scopus
  175. C. Gonzalez-Aguilera, C. Tous, B. Gomez-Gonzalez, P. Huertas, R. Luna, and A. Aguilera, “The THP1-SAC3-SUS1-CDC31 complex works in transcription elongation-mRNA export preventing RNA-mediated genome instability,” Molecular Biology of the Cell, vol. 19, pp. 4310–4318, 2008. View at Google Scholar
  176. S. Jimeno, A. G. Rondán, R. Luna, and A. Aguilera, “The yeast THO complex and mRNA export factors link RNA metabolism with transcription and genome instability,” EMBO Journal, vol. 21, no. 13, pp. 3526–3535, 2002. View at Publisher · View at Google Scholar · View at Scopus
  177. D. Ostapenko and M. J. Solomon, “Budding yeast CTDK-I is required for DNA damage-induced transcription,” Eukaryotic Cell, vol. 2, no. 2, pp. 274–283, 2003. View at Publisher · View at Google Scholar · View at Scopus
  178. C. B. Bennett, L. K. Lewis, G. Karthikeyan et al., “Genes required for ionizing radiation resistance in yeast,” Nature Genetics, vol. 29, no. 4, pp. 426–434, 2001. View at Publisher · View at Google Scholar · View at Scopus
  179. T. J. Westmoreland, J. R. Marks, J. A. Olson Jr., E. M. Thompson, M. A. Resnick, and C. B. Bennett, “Cell cycle progression in G1 and S phases is CCR4 dependent following ionizing radiation or replication stress in Saccharomyces cerevisiae,” Eukaryotic Cell, vol. 3, no. 2, pp. 430–446, 2004. View at Publisher · View at Google Scholar · View at Scopus
  180. O. Aygun, J. Svejstrup, and Y. Liu, “A RECQ5-RNA polymerase II association identified by targeted proteomic analysis of human chromatin,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 25, pp. 8580–8584, 2008. View at Publisher · View at Google Scholar · View at Scopus
  181. K. Izumikawa, M. Yanagida, T. Hayano et al., “Association of human DNA helicase RecQ5β with RNA polymerase II and its possible role in transcription,” Biochemical Journal, vol. 413, no. 3, pp. 505–516, 2008. View at Publisher · View at Google Scholar · View at Scopus
  182. R. Kanagaraj, D. Huehn, A. MacKellar et al., “RECQ5 helicase associates with the C-terminal repeat domain of RNA polymerase II during productive elongation phase of transcription,” Nucleic Acids Research, vol. 38, no. 22, pp. 8131–8140, 2010. View at Publisher · View at Google Scholar · View at Scopus