Coupling between transcription and alternative splicing

Cancer Treatment and Research

Volumn , Issue , 2013, Pages 1-24

  Schor, Ignacio E ^a   Gómez Acuña, Luciana I ^a   Kornblihtt, Alberto R ^a  

^a INSTITUTO DE FISIOLOGÍA   (Argentina)

Author keywords

Alternative splicing; Chromatin; Co transcriptional splicing; Kinetic model; RNA polymerase II CTD; Transcription splicing coupling

Indexed keywords

MESSENGER RNA; RNA POLYMERASE II; CHROMATIN; RNA PRECURSOR;

ALTERNATIVE RNA SPLICING; ARTICLE; CARCINOGENESIS; CHROMATIN STRUCTURE; GENETIC TRANSCRIPTION; HUMAN; INTRON; KINETICS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; REGULATORY MECHANISM; RNA TRANSCRIPTION; SPLICEOSOME; TRANSCRIPTION REGULATION; CANCER GENETICS; CARBOXY TERMINAL SEQUENCE; CHEMICAL REACTION KINETICS; EXON; GENE EXPRESSION; HISTONE METHYLATION; INTRACELLULAR SIGNALING; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; PROTEIN SECONDARY STRUCTURE; RNA TRANSLATION; TRANSCRIPTION ELONGATION; CHROMATIN; RNA SPLICING;

ALTERNATIVE SPLICING; CHROMATIN; HUMANS; RNA POLYMERASE II; RNA PRECURSORS; RNA SPLICING; TRANSCRIPTION, GENETIC;

EID: 84891753215     PISSN: 09273042     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-642-31659-3_1     Document Type: Article

References (98)

1. Srebrow A, Kornblihtt AR (2006) The connection between splicing and cancer. J Cell Sci 119(13):2635-26411
2. Muñoz MJ, Perez Santángelo MS, Paronetto MP, de la Mata M, Pelisch F, Boireau S, Glover-Cutter K, Ben-Dov C, Blaustein M, Lozano JJ, Bird G, Bentley D, Bertrand E, Kornblihtt AR (2009) DNA damage regulates alternative splicing through inhibition of RNA Polymerase II elongation. Cell 137:708-7200
3. Berget SM (1995) Exon recognition in vertebrate splicing. J Biol Chem 270(6):2411-24144
4. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB (2008)Alternative isoformregulation in human tissue transcriptomes.Nature 456(27): 470-4766
5. Pan Q, Shai o, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high throughput sequencing. Nat Genet 40(12):1413-14155
6. Ermakova EO, Nurtdinov RN, Gelfand MS (2006) Fast rate of evolution in alternative spliced coding regions of mammalian genes. BMC Genomics 7:84-933
7. Smith CW, Valcárcel J (2000) Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem Sci 25(8):381-3888
8. Cáceres JF, Kornblihtt AR (2002) Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet 18:186-1933
9. Black DL (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 72:291-3366
10. Sharp PA (1994) Split genes and RNA splicing. Cell 77(6):805-8155
11. Kornblihtt AR, Pesce CG, Alonso CR et al (1996) The fibronectin gene as a model for splicing and transcription studies. FASEB J 10(2):248-2577
12. Fededa JP, Petrillo E, Gelfand MS et al (2005) A polar mechanism coordinates different regions of alternative splicing within a single gene. Mol Cell 19(3):393-4044
13. Lenasi T, Peterlin BM, Dovc P (2006) Distal regulation of alternative splicing by splicing enhancer in equine beta-casein intron 1. RNA 12(3):498-5077
14. Romano M, Marcucci R, Baralle FE (2001) Splicing of constitutive upstream introns is essential for the recognition of intra-exonic suboptimal splice sites in the thrombopoietin gene. Nucleic Acids Res 29(4):886-8944
15. Bentley D (2002) The mRNA assembly line: transcription and processing machines in the same factory. Curr Opin Cell Biol 14(3):336-3422
16. Bentley DL (2005) Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. Curr Opin Cell Biol 17(3):251-2566
17. Maniatis T, Reed R (2002) An extensive network of coupling among gene expression machines. Nature 416(6880):499-5066
18. Kornblihtt AR (2005) Promoter usage and alternative splicing. Curr Opin Cell Biol 17(3):262-2688
19. Zorio DA, Bentley DL (2004) The link between mRNA processing and transcription: communication works both ways. Exp Cell Res 296(1):91-977
20. Neugebauer KM (2002) On the importance of being co-transcriptional. J Cell Sci 115(Pt 20):3865-38711
21. Proudfoot NJ, Furger A, Dye MJ (2002) Integrating mRNA processing with transcription. Cell 108(4):501-5122
22. Beyer AL, Osheim YN (1988) Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev 2(6):754-7655
23. Tennyson CN, Klamut HJ, Worton RG (1995) The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced. Nat Genet 9(2):184-1900
24. Pandya-Jones A, Black DL (2009) Co-transcriptional splicing of constitutive and alternative exons. RNA 15:1896-19088
25. Bauren G, Wieslander L (1994) Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76(1):183-1922
26. de la Mata M, Lafaille C, Kornblihtt AR (2010) First come, first served revisited: Factors affecting the same alternative splicing events have different effects on the relative rates of intron removal. RNA 16:904-9122
27. Lazarev D, Manley JL (2007) Concurrent splicing and transcription are not sufficient to enhance splicing efficiency. RNA 13:1546-15577
28. Perales R, Bentley D (2009) "Cotranscriptionality": the transcription elongation complex as a Nexus for nuclear transactions. Mol Cell 36:178-1911
29. Alexander RD, Innocente SA, Barrass JD, Beggs JD (2010) Splicing-dependent RNA Polymerase pausing in yeast. Mol Cell 40:582-5933
30. Lin S, Coutinho-Mansfield G, Wang D, Pandit S, Fu XD (2008) The splicing factor SC35 has an active role in transcriptional elongation. Nat Struct Mol Biol 15(8):819-8266
31. Carrillo Oesterreich F, Preibisch S, Neugebauer KM (2010) Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol Cell 40:571-5811
32. Smale ST, Tjian R (1985) Transcription of herpes simplex virus tk sequences under the control of wild-type and mutant human RNA polymerase I promoters. Mol Cell Biol 5(2):352-3622
33. Sisodia SS, Sollner-Webb B, Cleveland DW (1987) Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation. Mol Cell Biol 7(10):3602-36122
34. McCracken S, Rosonina E, Fong N et al (1998) Role of RNA polymerase II carboxy-terminal domain in coordinating transcription with RNA processing. Cold Spring Harb Symp Quant Biol 63:301-3099
35. Dower K, Rosbash M (2002) T7 RNA polymerase-directed transcripts are processed in yeast and link 30 end formation to mRNA nuclear export. RNA 8(5):686-6977
36. Hicks MJ, Yang CR, Kotlajich MV, Hertel KJ (2006) Linking splicing to Pol II transcription stabilizes pre-mRNAs and influences splicing patterns. PLoS Biol 4(6):e1477
37. Das R, Dufu K, Romney B, Feldt M, Elenko M, Reed R (2006) Functional coupling of RNAP II transcription to spliceosome assembly. Genes Dev 20(9):1100-11099
38. Das R, Yu J, Zhang Z, Gygi MP, Krainer AR, Gygi SP, Reed R (2007) SR proteins function in coupling RNAP II trancription to pre-mRNA splicing. Mol Cell 26:867-8811
39. Misteli T, Spector DL (1999) RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo. Mol Cell 3(6):697-7055
40. McCracken S, Fong N, Yankulov K et al (1997) The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385(6614):357-3611
41. Zeng C, Berget SM (2000) Participation of the C-terminal domain of RNA polymerase II in exon definition during pre-mRNA splicing. Mol Cell Biol 20(21):8290-83011
42. Hirose Y, Tacke R, Manley JL (1999) Phosphorylated RNA polymerase II stimulates premRNA splicing. Genes Dev 13(10):1234-12399
43. Dye MJ, Gromak N, Proudfoot NJ (2006) Exon tethering in transcription by RNA polymerase II. Mol Cell 21(6):849-8599
44. Sims RJ 3rd, Belotserkovskaya R, Reinberg D (2004) Elongation by RNA polymerase II: the short and long of it. Genes Dev 18(20):2437-24688
45. Saunders A, Core LJ, Lis JT (2006) Breaking barriers to transcription elongation. Nat Rev Mol Cell Biol 7(8):557-5677
46. Muñoz MJ, de la Mata M, Kornblihtt AR (2010) The carboxy terminal domain of RNA polymerase II and alternative splicing. Trends Biochem Sci 35:497-5044
47. Xu YX, Hirose Y, Zhou XZ, Lu KP, Manley JL (2003) Pin1 modulates the structure and function of human RNA polymerase II. Genes Dev 17(22):2765-27766
48. Bird G, Zorio DA, Bentley DL (2004) RNA Polymerase II Carboxy-Terminal domain phosphorylation is required for Cotranscriptional Pre-mRNA Splicing and 30-End formation. Mol Cell Biol 24(20):8963-89699
49. de la Mata M, Kornblihtt AR (2006) Pol II CTD mediates SRp20 regulation of alternative splicing. Nat Struct Mol Biol 13(11):973-9800
50. Laurencikiene J, Kallman AM, Fong N, Bentley DL, Ohman M (2006) RNA editing and alternative splicing: the importance of co-transcriptional coordination. EMBO Rep 7(3): 303-3077
51. Rosonina E, Blencowe BJ (2004) Analysis of the requirement for RNA polymerase II CTD heptapeptide repeats in pre-mRNA splicing and 30-end cleavage. RNA 10(4):581-5899
52. Sims RJ III, Millhouse S, Chen CF, Lewis BA, Erdjument-Bromage H, Tempst P, Manley JL, Reinberg D (2007) Recognition of Trimethylated Histone H3 Lysine 4 facilitates the recruitment of transcription postinitiation factors and Pre-mRNA splicing. Mol Cell 28:665-6766
53. Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T (2010) Regulation of alternative splicing by histone modifications. Science 327:996-10000
54. Edmunds JW, Mahadevan LC, Clayton AL (2008) Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation. EMBO J 27:406-4200
55. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C, Shilatifard A, Buratowski S, Greenblatt J (2003) Methylation of Histone H3 by Set2 in Saccharomyces cerevisiae Is Linked to Transcriptional Elongation by RNA Polymerase II. Mol Cell Biol 23(12):4207-42188
56. Cramer P, Pesce CG, Baralle FE, Kornblihtt AR (1997) Functional association between promoter structure and transcript alternative splicing. Proc Natl Acad Sci U S A 94(21):11456-114600
57. Cramer P, Caceres JF, Cazalla D et al (1999) Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2/ASF and 9G8 effects on an exonic splicing enhancer. Mol Cell 4(2):251-2588
58. Auboeuf D, Honig A, Berget SM, O'Malley BW (2002) Coordinate regulation of transcription and splicing by steroid receptor coregulators. Science 298(5592):416-4199
59. Pagani F, Stuani C, Zuccato E, Kornblihtt AR, Baralle FE (2003) Promoter architecture modulates CFTR exon 9 skipping. J Biol Chem 278(3):1511-15177
60. Robson-Dixon ND, Garcia-Blanco MA (2004) MAZ elements alter transcription elongation and silencing of the fibroblast growth factor receptor 2 exon IIIb. J Biol Chem 279(28):29075-290844
61. Nogues G, Kadener S, Cramer P, Bentley D, Kornblihtt AR (2002) Transcriptional activators differ in their abilities to control alternative splicing. J Biol Chem 277(45):43110-431144
62. Rosonina E, Bakowski MA, McCracken S, Blencowe BJ (2003) Transcriptional activators control splicing and 30-end cleavage levels. J Biol Chem 278(44):43034-430400
63. Auboeuf D, Dowhan DH, Kang YK et al (2004) Differential recruitment of nuclear receptor coactivators may determine alternative RNA splice site choice in target genes. Proc Natl Acad Sci U S A 101(8):2270-22744
64. Auboeuf D, Dowhan DH, Li X et al (2004) CoAA, a nuclear receptor coactivator protein at the interface of transcriptional coactivation and RNA splicing. Mol Cell Biol 24(1):442-4533
65. Kotovic KM, Lockshon D, Boric L, Neugebauer KM (2003) Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast. Mol Cell Biol 23(16):5768-57799
66. Lacadie SA, Rosbash M (2005) Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:50ss base pairing in yeast. Mol Cell 19(1):65-755
67. Gornemann J, Kotovic KM, Hujer K, Neugebauer KM (2005) Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol Cell 19(1):53-633
68. Listerman I, Sapra AK, Neugebauer KM (2006) Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nat Struct Mol Biol 13(9):815-8222
69. Lai MC, Teh BH, Tarn WY (1999) A human papillomavirus E2 transcriptional activator. The interactions with cellular splicing factors and potential function in pre-mRNA processing. J Biol Chem 274(17):11832-118411
70. Monsalve M, Wu Z, Adelmant G, Puigserver P, Fan M, Spiegelman BM (2000) Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1. Mol Cell 6(2):307-3166
71. Guillouf C, Gallais I, Moreau-Gachelin F (2006) Spi-1/PU.1 oncoprotein affects splicing decisions in a promoter binding-dependent manner. J Biol Chem 281(28):19145-191555
72. Davies RC, Calvio C, Bratt E, Larsson SH, Lamond AI, Hastie ND (1998) WT1 interacts with the splicing factor U2AF65 in an isoform-dependent manner and can be incorporated into spliceosomes. Genes Dev 12(20):3217-32255
73. Nayler O, Stratling W, Bourquin JP et al (1998) SAF-B protein couples transcription and premRNA splicing to SAR/MAR elements. Nucleic Acids Res 26(15):3542-35499
74. Goldstrohm AC, Albrecht TR, Sune C, Bedford MT, Garcia-Blanco MA (2001) The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1. Mol Cell Biol 21(22):7617-76288
75. Lin KT, Lu RM, Tarn WY (2004) The WW domain-containing proteins interact with the early spliceosome and participate in pre-mRNA splicing in vivo. Mol Cell Biol 24(20): 9176-91855
76. Yuryev A, Patturajan M, Litingtung Y et al (1996) The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc Natl Acad Sci U S A 93(14):6975-69800
77. Young JI, Hong EP, Castle JC et al (2005) Regulation of RNA splicing by the methylationdependent transcriptional repressor methyl-CpG binding protein 2. Proc Natl Acad Sci U S A. 102(49):17551-175588
78. Millhouse S, Manley JL (2005) The C-terminal domain of RNA polymerase II functions as a phosphorylation-dependent splicing activator in a heterologous protein. Mol Cell Biol 25(2):533-5444
79. Sato S, Tomomori-Sato C, Parmely TJ et al (2004) A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. MolCell 14(5):685-6911
80. Eperon LP, Graham IR, Griffiths AD, Eperon IC (1988) Effects of RNA secondary structure on alternative splicing of pre-mRNA: is folding limited to a region behind the transcribing RNA polymerase? Cell 54(3):393-4011
81. Roberts GC, Gooding C, Mak HY, Proudfoot NJ, Smith CW (1998) Co-transcriptional commitment to alternative splice site selection. Nucleic Acids Res 26(24):5568-55722
82. Kadener S, Cramer P, Nogues G et al (2001) Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing. EMBO J 20(20):5759-57688
83. Kadener S, Fededa JP, Rosbash M, Kornblihtt AR (2002) Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. Proc Natl Acad Sci U S A 99(12):8185-81900
84. Nogues G, Munoz MJ, Kornblihtt AR (2003) Influence of polymerase II processivity on alternative splicing depends on splice site strength. J Biol Chem 278(52):52166-521711
85. de la Mata M, Alonso CR, Kadener S et al (2003) A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell 12(2):525-5322
86. Howe KJ, Kane CM, Ares M Jr (2003) Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA 9(8):993-10066
87. Lorincz MC, Dickerson DR, Schmitt M, Groudine M (2004) Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol 11(11):1068-10755
88. Batsche E, Yaniv M, Muchardt C (2006) The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat Struct Mol Biol 13(1):22-299
89. Kornblihtt AR (2006) Chromatin, transcript elongation and alternative splicing. Nat Struct Mol Biol 13(1):5-77
90. Schor IE, Rascovan N, Pelisch F, Alló M, Kornblihtt AR (2009) Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc Natl Acad Sci USA 106(11):4325-43300
91. Alló M, Buggiano V, Fededa JP, Petrillo E, Schor I, de la Mata M, Agirre E, Plass M, Eyras E, Elela SA, Klinck R, Chabot B, Kornblihtt AR (2009) Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat Struct Mol Biol 16(7):717-7244
92. Suzuki K, Juelich T, Lim H, Ishida T, Watanebe T, Cooper DA, Rao S, Kelleher AD (2008) Closed Chromatin architecture Is induced by an RNA Duplex targeting the HIV-1 promoter region. J Biol Chem 283:23353-233633
93. Kim DH, Villeneuve LM, Morris KV, Rossi JJ (2006) Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat Struct Mol Biol 13:793-7977
94. Morris KV, Chan SW, Jacobsen SE, Looney DJ (2004) Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305:1289-12922
95. Schwartz S, Meshorer E, Ast G (2009) Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 16(9):990-9955
96. Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, Valcárcel J, Guigó R (2009) Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol 16(9):996-10011
97. Kolosinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J (2009) Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41(3):376-3811
98. Yang L, Embree LJ, Hickstein DD (2000) TLS-ERG leukemia fusion protein inhibits RNA splicing mediated by serine-arginine proteins. Mol Cell Biol 20(10):3345-33544