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PMID: 23392244 Published · ppublish English Journal Article Review

Coupling pre-mRNA processing to transcription on the RNA factory assembly line.

RNA biology ·Vol. 10 ·No. 3 ·2013-03-00 ·Pages 380-90

Lee KM, Tarn WY

Abstract

It has been well-documented that nuclear processing of primary transcripts of RNA polymerase II occurs co-transcriptionally and is functionally coupled to transcription. Moreover, increasing evidence indicates that transcription influences pre-mRNA splicing and even several post-splicing RNA processing events. In this review, we discuss the issues of how RNA polymerase II modulates co-transcriptional RNA processing events via its carboxyl terminal domain, and the protein domains involved in coupling of transcription and RNA processing events. In addition, we describe how transcription influences the expression or stability of mRNAs through the formation of distinct mRNP complexes. Finally, we delineate emerging findings that chromatin modifications function in the regulation of RNA processing steps, especially splicing, in addition to transcription. Overall, we provide a comprehensive view that transcription could integrate different control systems, from epigenetic to post-transcriptional control, for efficient gene expression.

Keywords
CTD DNA methylation EJC FF domain SR proteins TREX WW domain chromatin modification splicing
MeSH Terms
Chromatin/metabolism Epigenesis, Genetic RNA Polymerase II/chemistry,metabolism RNA Precursors/genetics,metabolism RNA Processing, Post-Transcriptional RNA Stability Ribonucleoproteins/metabolism Transcription, Genetic
Chemicals
Chromatin RNA Precursors Ribonucleoproteins RNA Polymerase II
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Lee Kuo-Ming
Institute of Biomedical Sciences; Academia Sinica; Taipei, Taiwan.
Tarn Woan-Yuh
References (149)
149 references, click to expand
  1. The FF domain: a novel motif that often accompanies WW domains.
    Trends Biochem Sci. 1999 Jul;24(7):264-5 PMID: 10390614
  2. RS domains contact splicing signals and promote splicing by a common mechanism in yeast through humans.
    Genes Dev. 2006 Jul 1;20(13):1755-65 PMID: 16766678
  3. Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing.
    PLoS Genet. 2012;8(5):e1002717 PMID: 22615581
  4. Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm.
    Mol Cell. 2007 Sep 7;27(5):780-92 PMID: 17803942
  5. Human mRNA export machinery recruited to the 5' end of mRNA.
    Cell. 2006 Dec 29;127(7):1389-400 PMID: 17190602
  6. Separate domains of fission yeast Cdk9 (P-TEFb) are required for capping enzyme recruitment and primed (Ser7-phosphorylated) Rpb1 carboxyl-terminal domain substrate recognition.
    Mol Cell Biol. 2012 Jul;32(13):2372-83 PMID: 22508988
  7. Introns play an essential role in splicing-dependent formation of the exon junction complex.
    Genes Dev. 2007 Aug 15;21(16):1993-8 PMID: 17675447
  8. Biochemical analysis of TREX complex recruitment to intronless and intron-containing yeast genes.
    EMBO J. 2004 Jul 7;23(13):2620-31 PMID: 15192704
  9. Nucleosome positioning as a determinant of exon recognition.
    Nat Struct Mol Biol. 2009 Sep;16(9):996-1001 PMID: 19684599
  10. Exporting RNA from the nucleus to the cytoplasm.
    Nat Rev Mol Cell Biol. 2007 Oct;8(10):761-73 PMID: 17786152
  11. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus.
    Cell. 2012 Nov 9;151(4):750-764 PMID: 23084401
  12. Distinct roles for CTD Ser-2 and Ser-5 phosphorylation in the recruitment and allosteric activation of mammalian mRNA capping enzyme.
    Mol Cell. 1999 Mar;3(3):405-11 PMID: 10198643
  13. The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation.
    Genes Dev. 2008 Dec 15;22(24):3422-34 PMID: 19141475
  14. Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease.
    Nature. 2006 Dec 14;444(7121):953-6 PMID: 17128255
  15. Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36.
    Nat Struct Mol Biol. 2011 Jul 26;18(9):977-83 PMID: 21792193
  16. Ending the message: poly(A) signals then and now.
    Genes Dev. 2011 Sep 1;25(17):1770-82 PMID: 21896654
  17. The C-terminal domain of RNA polymerase II functions as a phosphorylation-dependent splicing activator in a heterologous protein.
    Mol Cell Biol. 2005 Jan;25(2):533-44 PMID: 15632056
  18. Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery.
    Cell. 2004 Jan 9;116(1):75-86 PMID: 14718168
  19. The role of Rat1 in coupling mRNA 3'-end processing to transcription termination: implications for a unified allosteric-torpedo model.
    Genes Dev. 2006 Apr 15;20(8):954-65 PMID: 16598041
  20. Transcription factor TFIID recruits factor CPSF for formation of 3' end of mRNA.
    Nature. 1997 Sep 25;389(6649):399-402 PMID: 9311784
  21. DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation.
    Nature. 2012 Mar 25;484(7394):386-9 PMID: 22446626
  22. Alternative splicing: decoding an expansive regulatory layer.
    Curr Opin Cell Biol. 2012 Jun;24(3):323-32 PMID: 22465326
  23. A conserved epitope on a subset of SR proteins defines a larger family of Pre-mRNA splicing factors.
    J Cell Biol. 1995 May;129(4):899-908 PMID: 7538140
  24. Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex.
    Genes Dev. 2011 May 15;25(10):1078-90 PMID: 21576267
  25. The multi-tasking P-TEFb complex.
    Curr Opin Cell Biol. 2008 Jun;20(3):334-40 PMID: 18513937
  26. WW domain-mediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif.
    Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10602-7 PMID: 9724750
  27. Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo.
    Mol Cell Biol. 2001 Oct;21(20):6782-95 PMID: 11564863
  28. The SR protein family of splicing factors: master regulators of gene expression.
    Biochem J. 2009 Jan 1;417(1):15-27 PMID: 19061484
  29. A molecular link between SR protein dephosphorylation and mRNA export.
    Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9666-70 PMID: 15210956
  30. Dynamic association of capping enzymes with transcribing RNA polymerase II.
    Genes Dev. 2000 Oct 1;14(19):2435-40 PMID: 11018011
  31. The WW domain-containing proteins interact with the early spliceosome and participate in pre-mRNA splicing in vivo.
    Mol Cell Biol. 2004 Oct;24(20):9176-85 PMID: 15456888
  32. Distinct activities of the DExD/H-box splicing factor hUAP56 facilitate stepwise assembly of the spliceosome.
    Genes Dev. 2008 Jul 1;22(13):1796-803 PMID: 18593880
  33. The dynamics of a pre-mRNA splicing factor in living cells.
    Nature. 1997 May 29;387(6632):523-7 PMID: 9168118
  34. Translation is required to remove Y14 from mRNAs in the cytoplasm.
    Curr Biol. 2002 Jul 9;12(13):1060-7 PMID: 12121612
  35. Structure of eukaryotic RNA polymerases.
    Annu Rev Biophys. 2008;37:337-52 PMID: 18573085
  36. When chromatin meets splicing.
    Nat Struct Mol Biol. 2009 Sep;16(9):902-3 PMID: 19739285
  37. CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II.
    Science. 2012 Jun 29;336(6089):1723-5 PMID: 22745433
  38. Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1.
    Genes Dev. 2012 Sep 1;26(17):1891-6 PMID: 22892239
  39. Posttranscriptional regulation in Drosophila oocytes and early embryos.
    Wiley Interdiscip Rev RNA. 2011 May-Jun;2(3):408-16 PMID: 21957026
  40. Genome-wide identification of miRNA targets by PAR-CLIP.
    Methods. 2012 Oct;58(2):94-105 PMID: 22926237
  41. mRNA export and the TREX complex.
    Biochim Biophys Acta. 2012 Jun;1819(6):507-13 PMID: 22178508
  42. Sus1, Cdc31, and the Sac3 CID region form a conserved interaction platform that promotes nuclear pore association and mRNA export.
    Mol Cell. 2009 Mar 27;33(6):727-37 PMID: 19328066
  43. Regulation of alternative splicing by histone modifications.
    Science. 2010 Feb 19;327(5968):996-1000 PMID: 20133523
  44. Phosphorylation-dephosphorylation differentially affects activities of splicing factor ASF/SF2.
    EMBO J. 1998 Nov 2;17(21):6359-67 PMID: 9799243
  45. Inducible gene expression: diverse regulatory mechanisms.
    Nat Rev Genet. 2010 Jun;11(6):426-37 PMID: 20421872
  46. The splicing factor SC35 has an active role in transcriptional elongation.
    Nat Struct Mol Biol. 2008 Aug;15(8):819-26 PMID: 18641664
  47. Splicing enhances translation in mammalian cells: an additional function of the exon junction complex.
    Genes Dev. 2004 Jan 15;18(2):210-22 PMID: 14752011
  48. Transcription elongation factor hSPT5 stimulates mRNA capping.
    Genes Dev. 1999 Jul 15;13(14):1774-9 PMID: 10421630
  49. Progression through the RNA polymerase II CTD cycle.
    Mol Cell. 2009 Nov 25;36(4):541-6 PMID: 19941815
  50. Functional interaction of yeast pre-mRNA 3' end processing factors with RNA polymerase II.
    Mol Cell. 2002 May;9(5):1101-11 PMID: 12049745
  51. The Glc7p nuclear phosphatase promotes mRNA export by facilitating association of Mex67p with mRNA.
    Mol Cell. 2004 Jan 30;13(2):201-12 PMID: 14759366
  52. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins.
    Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):6975-80 PMID: 8692929
  53. RNAP II CTD phosphorylated on threonine-4 is required for histone mRNA 3' end processing.
    Science. 2011 Nov 4;334(6056):683-6 PMID: 22053051
  54. REF1/Aly and the additional exon junction complex proteins are dispensable for nuclear mRNA export.
    J Cell Biol. 2002 Nov 25;159(4):579-88 PMID: 12438415
  55. Regulation of cytoplasmic mRNA decay.
    Nat Rev Genet. 2012 Mar 06;13(4):246-59 PMID: 22392217
  56. Evidence for a pioneer round of mRNA translation: mRNAs subject to nonsense-mediated decay in mammalian cells are bound by CBP80 and CBP20.
    Cell. 2001 Sep 7;106(5):607-17 PMID: 11551508
  57. UAP56- a key player with surprisingly diverse roles in pre-mRNA splicing and nuclear export.
    BMB Rep. 2009 Apr 30;42(4):185-8 PMID: 19403039
  58. First exon length controls active chromatin signatures and transcription.
    Cell Rep. 2012 Jul 26;2(1):62-8 PMID: 22840397
  59. Assembly, disassembly and recycling: the dynamics of exon junction complexes.
    RNA Biol. 2011 Jan-Feb;8(1):24-9 PMID: 21289489
  60. Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons.
    Nat Struct Mol Biol. 2011 Mar;18(3):337-44 PMID: 21358630
  61. The Prp19 complex is a novel transcription elongation factor required for TREX occupancy at transcribed genes.
    Genes Dev. 2011 Jun 1;25(11):1147-58 PMID: 21576257
  62. SAGA and a novel Drosophila export complex anchor efficient transcription and mRNA export to NPC.
    EMBO J. 2007 Dec 12;26(24):4956-65 PMID: 18034162
  63. The carboxy terminal domain of RNA polymerase II and alternative splicing.
    Trends Biochem Sci. 2010 Sep;35(9):497-504 PMID: 20418102
  64. Dynamics of human immunodeficiency virus transcription: P-TEFb phosphorylates RD and dissociates negative effectors from the transactivation response element.
    Mol Cell Biol. 2004 Jan;24(2):787-95 PMID: 14701750
  65. The human SWI/SNF subunit Brm is a regulator of alternative splicing.
    Nat Struct Mol Biol. 2006 Jan;13(1):22-9 PMID: 16341228
  66. The nonsense-mediated decay RNA surveillance pathway.
    Annu Rev Biochem. 2007;76:51-74 PMID: 17352659
  67. Epigenetics in alternative pre-mRNA splicing.
    Cell. 2011 Jan 7;144(1):16-26 PMID: 21215366
  68. Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay.
    Genes Dev. 2006 Feb 1;20(3):355-67 PMID: 16452507
  69. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions.
    EMBO J. 2000 Dec 15;19(24):6860-9 PMID: 11118221
  70. The spliceosome: design principles of a dynamic RNP machine.
    Cell. 2009 Feb 20;136(4):701-18 PMID: 19239890
  71. The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex.
    Genes Dev. 2011 May 1;25(9):972-83 PMID: 21536736
  72. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3' end processing.
    Mol Cell. 2004 Jan 16;13(1):67-76 PMID: 14731395
  73. The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression.
    Cell. 2007 Jul 13;130(1):179-91 PMID: 17632064
  74. Chromatin organization marks exon-intron structure.
    Nat Struct Mol Biol. 2009 Sep;16(9):990-5 PMID: 19684600
  75. In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei.
    RNA. 2004 Apr;10(4):622-33 PMID: 15037772
  76. Nucleosomes are well positioned in exons and carry characteristic histone modifications.
    Genome Res. 2009 Oct;19(10):1732-41 PMID: 19687145
  77. 7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development.
    Proc Natl Acad Sci U S A. 2009 May 12;106(19):7798-803 PMID: 19416841
  78. Transcription-independent phosphorylation of the RNA polymerase II C-terminal domain (CTD) involves ERK kinases (MEK1/2).
    Nucleic Acids Res. 1999 Nov 15;27(22):4399-404 PMID: 10536148
  79. Pre-mRNA processing reaches back to transcription and ahead to translation.
    Cell. 2009 Feb 20;136(4):688-700 PMID: 19239889
  80. Paraspeckle protein p54nrb links Sox9-mediated transcription with RNA processing during chondrogenesis in mice.
    J Clin Invest. 2008 Sep;118(9):3098-108 PMID: 18677406
  81. Shuttling SR proteins: more than splicing factors.
    FEBS J. 2011 Sep;278(18):3246-55 PMID: 21794093
  82. Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing.
    Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4325-30 PMID: 19251664
  83. TREX is a conserved complex coupling transcription with messenger RNA export.
    Nature. 2002 May 16;417(6886):304-8 PMID: 11979277
  84. The ever-increasing complexities of the exon junction complex.
    Curr Opin Cell Biol. 2004 Jun;16(3):279-84 PMID: 15145352
  85. The Ref/Aly proteins are dispensable for mRNA export and development in Caenorhabditis elegans.
    RNA. 2003 Jul;9(7):881-91 PMID: 12810921
  86. Advantages of next-generation sequencing versus the microarray in epigenetic research.
    Brief Funct Genomic Proteomic. 2009 May;8(3):174-83 PMID: 19535508
  87. Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II.
    Proc Natl Acad Sci U S A. 2004 May 18;101(20):7572-7 PMID: 15136722
  88. FBP WW domains and the Abl SH3 domain bind to a specific class of proline-rich ligands.
    EMBO J. 1997 May 1;16(9):2376-83 PMID: 9171351
  89. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals.
    Cell. 1997 May 2;89(3):403-12 PMID: 9150140
  90. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription.
    Nature. 1997 Jan 23;385(6614):357-61 PMID: 9002523
  91. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
    EMBO J. 2001 Sep 3;20(17):4987-97 PMID: 11532962
  92. Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation.
    Nucleic Acids Res. 2010 May;38(9):2757-74 PMID: 20044349
  93. Histone deacetylase activity modulates alternative splicing.
    PLoS One. 2011 Feb 02;6(2):e16727 PMID: 21311748
  94. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing.
    Genome Res. 2009 Sep;19(9):1593-605 PMID: 19581485
  95. Transitions in RNA polymerase II elongation complexes at the 3' ends of genes.
    EMBO J. 2004 Jan 28;23(2):354-64 PMID: 14739930
  96. A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly.
    Mol Cell. 2004 Nov 5;16(3):363-73 PMID: 15525510
  97. PP1/PP2A phosphatases are required for the second step of Pre-mRNA splicing and target specific snRNP proteins.
    Mol Cell. 2006 Sep 15;23(6):819-29 PMID: 16973434
  98. Connections between chromatin signatures and splicing.
    Wiley Interdiscip Rev RNA. 2013 Jan-Feb;4(1):77-91 PMID: 23074139
  99. Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner.
    Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):E627-35 PMID: 21808035
  100. The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II.
    J Biol Chem. 2000 Dec 22;275(51):39935-43 PMID: 10978320
  101. Nuclear speckles: a model for nuclear organelles.
    Nat Rev Mol Cell Biol. 2003 Aug;4(8):605-12 PMID: 12923522
  102. Differential chromatin marking of introns and expressed exons by H3K36me3.
    Nat Genet. 2009 Mar;41(3):376-81 PMID: 19182803
  103. Capping enzyme in eukaryotic mRNA synthesis.
    Prog Nucleic Acid Res Mol Biol. 1995;50:101-29 PMID: 7754031
  104. Functions of WW domains in the nucleus.
    FEBS Lett. 2001 Feb 16;490(3):190-5 PMID: 11223034
  105. TCERG1 regulates alternative splicing of the Bcl-x gene by modulating the rate of RNA polymerase II transcription.
    Mol Cell Biol. 2012 Feb;32(4):751-62 PMID: 22158966
  106. Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2.
    Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17551-8 PMID: 16251272
  107. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II.
    Nature. 2004 Nov 25;432(7016):517-22 PMID: 15565157
  108. Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation.
    Genome Res. 2011 Mar;21(3):390-401 PMID: 21163941
  109. Multifunctional factor ENY2 is associated with the THO complex and promotes its recruitment onto nascent mRNA.
    Genes Dev. 2010 Jan 1;24(1):86-96 PMID: 20048002
  110. A slow RNA polymerase II affects alternative splicing in vivo.
    Mol Cell. 2003 Aug;12(2):525-32 PMID: 14536091
  111. Structural insights to how mammalian capping enzyme reads the CTD code.
    Mol Cell. 2011 Jul 22;43(2):299-310 PMID: 21683636
  112. Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD.
    RNA. 2002 Sep;8(9):1102-11 PMID: 12358429
  113. P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation.
    Mol Cell. 2006 Jan 20;21(2):227-37 PMID: 16427012
  114. The structure of an FF domain from human HYPA/FBP11.
    J Mol Biol. 2002 Oct 25;323(3):411-6 PMID: 12381297
  115. SKAR links pre-mRNA splicing to mTOR/S6K1-mediated enhanced translation efficiency of spliced mRNAs.
    Cell. 2008 Apr 18;133(2):303-13 PMID: 18423201
  116. Interactions of Sen1, Nrd1, and Nab3 with multiple phosphorylated forms of the Rpb1 C-terminal domain in Saccharomyces cerevisiae.
    Eukaryot Cell. 2012 Apr;11(4):417-29 PMID: 22286094
  117. Hypophosphorylated ASF/SF2 binds TAP and is present in messenger ribonucleoproteins.
    J Biol Chem. 2004 Jul 23;279(30):31745-9 PMID: 15184380
  118. Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements.
    Mol Cell. 2005 Oct 7;20(1):65-75 PMID: 16209946
  119. mRNA export and gene expression: the SAGA-TREX-2 connection.
    Biochim Biophys Acta. 2012 Jun;1819(6):555-65 PMID: 22178374
  120. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.
    Nature. 2011 Nov 3;479(7371):74-9 PMID: 21964334
  121. Yra1p, a conserved nuclear RNA-binding protein, interacts directly with Mex67p and is required for mRNA export.
    EMBO J. 2000 Feb 1;19(3):410-20 PMID: 10722314
  122. Upf1 phosphorylation triggers translational repression during nonsense-mediated mRNA decay.
    Cell. 2008 Apr 18;133(2):314-27 PMID: 18423202
  123. The RNA-binding protein Y14 inhibits mRNA decapping and modulates processing body formation.
    Mol Biol Cell. 2013 Jan;24(1):1-13 PMID: 23115303
  124. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans.
    Nature. 2000 Sep 21;407(6802):401-5 PMID: 11014198
  125. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription.
    Genes Dev. 2000 Oct 1;14(19):2452-60 PMID: 11018013
  126. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing.
    Mol Cell. 2007 Jun 22;26(6):867-81 PMID: 17588520
  127. Control of alternative splicing through siRNA-mediated transcriptional gene silencing.
    Nat Struct Mol Biol. 2009 Jul;16(7):717-24 PMID: 19543290
  128. An intronic splicing silencer causes skipping of the IIIb exon of fibroblast growth factor receptor 2 through involvement of polypyrimidine tract binding protein.
    Mol Cell Biol. 2000 Oct;20(19):7388-400 PMID: 10982855
  129. TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II.
    Mol Cell. 2009 May 15;34(3):387-93 PMID: 19450536
  130. DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation.
    Cell. 2009 May 15;137(4):708-20 PMID: 19450518
  131. SRprises along a messenger's journey.
    Mol Cell. 2005 Mar 4;17(5):613-5 PMID: 15749011
  132. TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II.
    Mol Cell Biol. 2009 Oct;29(20):5455-64 PMID: 19667075
  133. The RNA polymerase II CTD coordinates transcription and RNA processing.
    Genes Dev. 2012 Oct 1;26(19):2119-37 PMID: 23028141
  134. Identification of Prp40, a novel essential yeast splicing factor associated with the U1 small nuclear ribonucleoprotein particle.
    Mol Cell Biol. 1996 Mar;16(3):960-7 PMID: 8622699
  135. RNA polymerase II elongation control.
    Annu Rev Biochem. 2012;81:119-43 PMID: 22404626
  136. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing.
    Mol Cell. 2007 Nov 30;28(4):665-76 PMID: 18042460
  137. Nucleosome positioning and gene regulation: advances through genomics.
    Nat Rev Genet. 2009 Mar;10(3):161-72 PMID: 19204718
  138. The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain.
    Nat Struct Mol Biol. 2008 Aug;15(8):795-804 PMID: 18660819
  139. A novel role for shuttling SR proteins in mRNA translation.
    Genes Dev. 2004 Apr 1;18(7):755-68 PMID: 15082528
  140. Arginine methylation facilitates the nuclear export of hnRNP proteins.
    Genes Dev. 1998 Mar 1;12(5):679-91 PMID: 9499403
  141. Sac3 is an mRNA export factor that localizes to cytoplasmic fibrils of nuclear pore complex.
    Mol Biol Cell. 2003 Mar;14(3):836-47 PMID: 12631707
  142. Distinct pathways for snoRNA and mRNA termination.
    Mol Cell. 2006 Dec 8;24(5):723-734 PMID: 17157255
  143. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
    Nat Struct Mol Biol. 2010 Jul;17(7):909-15 PMID: 20601959
  144. Pre-mRNA splicing is a determinant of histone H3K36 methylation.
    Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13564-9 PMID: 21807997
  145. Multiple links between transcription and splicing.
    RNA. 2004 Oct;10(10):1489-98 PMID: 15383674
  146. The type 2C Ser/Thr phosphatase PP2Cgamma is a pre-mRNA splicing factor.
    Genes Dev. 1999 Jan 1;13(1):87-97 PMID: 9887102
  147. The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1.
    Mol Cell Biol. 2001 Nov;21(22):7617-28 PMID: 11604498
  148. Transcriptional activators differ in their abilities to control alternative splicing.
    J Biol Chem. 2002 Nov 8;277(45):43110-4 PMID: 12221105
  149. Cotranscriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3' end processing factor Pcf11.
    Mol Cell. 2009 Jan 30;33(2):215-26 PMID: 19110458
Article Info
Journal
RNA biology
Abbr.
RNA Biol
ISSN
1555-8584
DOI
10.4161/rna.23697
Published
2013-03-00
Epub
2013-00-07
Pages
380-90
Language
English
Region
United States
NLM ID
101235328
PMCID
PMC3672281
Subset
IM
External Links
PubMed source DOI: 10.4161/rna.23697 PMC Full Text View journal details
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