Making ends meet: Coordination between RNA 3′-end processing and transcription initiation

Wiley Interdisciplinary Reviews: RNA

Volumn 4, Issue 3, 2013, Pages 233-246

  Andersen, Pia K ^a   Jensen, Torben Heick ^a   Lykke Andersen, Søren ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

GENERAL TRANSCRIPTION FACTOR; MESSENGER RNA; RNA POLYMERASE II; SMALL NUCLEAR RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; BINDING KINETICS; CARBOXY TERMINAL SEQUENCE; CHEMICAL REACTION; CHROMATIN IMMUNOPRECIPITATION; CONFORMATIONAL TRANSITION; DNA TEMPLATE; GENE LOCUS; GENE REPLICATION; GENOME ANALYSIS; HELA CELL; OPEN READING FRAME; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; REVIEW; RNA PROCESSING; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE;

ANIMALS; HUMANS; RNA 3' END PROCESSING; RNA POLYMERASE II; TRANSCRIPTION INITIATION, GENETIC;

EID: 84876441383     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.1156     Document Type: Review

References (144)

1. Vannini A, Cramer P. Conservation between the RNA polymerase I, II, and III transcription initiation machineries. Mol Cell 2012, 45:439-446.
2. Haag JR, Pikaard CS. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol 2011, 12: 483-492.
3. Kuehner JN, Pearson EL, Moore C. Unravelling the means to an end: RNA polymerase II transcription termination. Nat Rev Mol Cell Biol 2011, 12: 283-294.
4. Proudfoot NJ. Ending the message: poly(A) signals then and now. Genes Dev 2011, 25:1770-1782.
5. Richard P, Manley JL. Transcription termination by nuclear RNA polymerases. Genes Dev 2009, 23:1247-1269.
6. Andersen PK, Lykke-Andersen S, Jensen TH. Promoter-proximal polyadenylation sites reduce transcription activity. Genes Dev 2012, 26:2169-2179.
7. Ansari A, Hampsey M. A role for the CPF 3′-end processing machinery in RNAP II-dependent gene looping. Genes Dev 2005, 19:2969-2978.
8. Mapendano CK, Lykke-Andersen S, Kjems J, Bertrand E, Jensen TH. Crosstalk between mRNA 3′ end processing and transcription initiation. Mol Cell 2010, 40:410-422.
9. O'Sullivan JM, Tan-Wong SM, Morillon A, Lee B, Coles J, Mellor J, Proudfoot NJ. Gene loops juxtapose promoters and terminators in yeast. Nat Genet 2004, 36:1014-1018.
10. Tan-Wong SM, Wijayatilake HD, Proudfoot NJ. Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex. Genes Dev 2009, 23:2610-2624.
11. Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ: Gene loops enhance transcriptional directionality. Science 2012, 338: 671-675.
12. Yao J, Ardehali MB, Fecko CJ, Webb WW, Lis JT. Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation. Mol Cell 2007, 28:978-990.
13. Baumann M, Pontiller J, Ernst W. Structure and basal transcription complex of RNA polymerase II core promoters in the mammalian genome: an overview. Mol Biotechnol 2010, 45:241-247.
14. Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 2006, 38:626-635.
15. Malik S, Roeder RG. The metazoan mediator co-activator complex as an integrative hub for transcriptional regulation. Nat Rev Genet 2010, 11:761-772.
16. Cramer P. Structure and function of RNA polymerase II. Adv Protein Chem 2004, 67:1-42.
17. Fuda NJ, Ardehali MB, Lis JT. Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 2009, 461:186-192.
18. Sikorski TW, Buratowski S. The basal initiation machinery: beyond the general transcription factors. Curr Opin Cell Biol 2009, 21:344-351.
19. Yudkovsky N, Ranish JA, Hahn S. A transcription reinitiation intermediate that is stabilized by activator. Nature 2000, 408:225-229.
20. Licatalosi DD, Geiger G, Minet M, Schroeder S, Cilli K, McNeil JB, Bentley DL. Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II. Mol Cell 2002, 9:1101-1111.
21. Kim M, Ahn SH, Krogan NJ, Greenblatt JF, Buratowski S. Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes. EMBO J 2004, 23:354-364.
22. Zhang Z, Fu J, Gilmour DS. CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3′-end processing factor, Pcf11. Genes Dev 2005, 19:1572-1580.
23. Zhang Z, Gilmour DS. Pcf11 is a termination factor in Drosophila that dismantles the elongation complex by bridging the CTD of RNA polymerase II to the nascent transcript. Mol Cell 2006, 21:65-74.
24. West S, Gromak N, Proudfoot NJ. Human 5′ → 3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 2004, 432:522-525.
25. Kim M, Krogan NJ, Vasiljeva L, Rando OJ, Nedea E, Greenblatt JF, Buratowski S. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 2004, 432:517-522.
26. Gromak N, West S, Proudfoot NJ. Pause sites promote transcriptional termination of mammalian RNA polymerase II. Mol Cell Biol 2006, 26:3986-3996.
27. Skourti-Stathaki K, Proudfoot NJ, Gromak N. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Mol Cell 2011, 42:794-805.
28. Mischo HE, Gomez-Gonzalez B, Grzechnik P, Rondon AG, Wei W, Steinmetz L, Aguilera A, Proudfoot NJ. Yeast Sen1 helicase protects the genome from transcription-associated instability. Mol Cell 2011, 41:21-32.
29. Park NJ, Tsao DC, Martinson HG. The two steps of poly(A)-dependent termination, pausing and release, can be uncoupled by truncation of the RNA polymerase II carboxyl-terminal repeat domain. Mol Cell Biol 2004, 24:4092-4103.
30. Nag A, Narsinh K, Martinson HG. The poly(A)-dependent transcriptional pause is mediated by CPSF acting on the body of the polymerase. Nat Struct Mol Biol 2007, 14:662-669.
31. Kazerouninia A, Ngo B, Martinson HG. Poly(A) signal-dependent degradation of unprocessed nascent transcripts accompanies poly(A) signal-dependent transcriptional pausing in vitro. RNA 2010, 16:197-210.
32. Luo W, Johnson AW, Bentley DL. The role of Rat1 in coupling mRNA 3′-end processing to transcription termination: implications for a unified allosteric-torpedo model. Genes Dev 2006, 20:954-965.
33. Buratowski S. Progression through the RNA polymerase II CTD cycle. Mol Cell 2009, 36:541-546.
34. Egloff S, Dienstbier M, Murphy S. Updating the RNA polymerase CTD code: adding gene-specific layers. Trends Genet 2012, 28:333-341.
35. Heidemann M, Hintermair C, Voss K, Eick D. Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription. Biochim Biophys Acta 2013, 1829:55-62.
36. Hsin JP, Manley JL. The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev 2012, 26:2119-2137.
37. Zhang DW, Rodriguez-Molina JB, Tietjen JR, Nemec CM, Ansari AZ. Emerging views on the CTD Code. Genet Res Int 2012, 2012:347214.
38. Mayer A, Heidemann M, Lidschreiber M, Schreieck A, Sun M, Hintermair C, Kremmer E, Eick D, Cramer P. CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science 2012, 336:1723-1725.
39. Egloff S, O'Reilly D, Chapman RD, Taylor A, Tanzhaus K, Pitts L, Eick D, Murphy S. Serine-7 of the RNA polymerase II CTD is specifically required for snRNA gene expression. Science 2007, 318:1777-1779.
40. Egloff S, Szczepaniak SA, Dienstbier M, Taylor A, Knight S, Murphy S. The integrator complex recognizes a new double mark on the RNA polymerase II carboxyl-terminal domain. J Biol Chem 2010, 285:20564-20569.
41. Egloff S, Zaborowska J, Laitem C, Kiss T, Murphy S. Ser7 phosphorylation of the CTD recruits the RPAP2 Ser5 phosphatase to snRNA genes. Mol Cell 2012, 45:111-122.
42. Hintermair C, Heidemann M, Koch F, Descostes N, Gut M, Gut I, Fenouil R, Ferrier P, Flatley A, Kremmer E, et al.: Threonine-4 of mammalian RNA polymerase II CTD is targeted by polo-like kinase 3 and required for transcriptional elongation. EMBO J 2012, 31:2784-2797.
43. Hsin JP, Sheth A, Manley JL. RNAP II CTD phosphorylated on threonine-4 is required for histone mRNA 3′ end processing. Science 2011, 334:683-686.
44. Kim H, Erickson B, Luo W, Seward D, Graber JH, Pollock DD, Megee PC, Bentley DL. Gene-specific RNA polymerase II phosphorylation and the CTD code. Nat Struct Mol Biol 2010, 17:1279-1286.
45. Mayer A, Lidschreiber M, Siebert M, Leike K, Soding J, Cramer P. Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol 2010, 17:1272-1278.
46. Anamika K, Gyenis A, Poidevin L, Poch O, Tora L. RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts. PLoS One 2012, 7:e38769.
47. Zhang DW, Mosley AL, Ramisetty SR, Rodriguez-Molina JB, Washburn MP, Ansari AZ. Ssu72 phosphatase-dependent erasure of phospho-Ser7 marks on the RNA polymerase II C-terminal domain is essential for viability and transcription termination. J Biol Chem 2012, 287:8541-8551.
48. Bataille AR, Jeronimo C, Jacques PE, Laramee L, Fortin ME, Forest A, Bergeron M, Hanes SD, Robert F. A universal RNA polymerase II CTD cycle is orchestrated by complex interplays between kinase, phosphatase, and isomerase enzymes along genes. Mol Cell 2012, 45:158-170.
49. Glover-Cutter K, Kim S, Espinosa J, Bentley DL. RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat Struct Mol Biol 2008, 15:71-78.
50. Fuda NJ, Buckley MS, Wei W, Core LJ, Waters CT, Reinberg D, Lis JT. Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain is required for efficient transcription of heat shock genes. Mol Cell Biol 2012, 32:3428-3437.
51. Svejstrup JQ, Li Y, Fellows J, Gnatt A, Bjorklund S, Kornberg RD. Evidence for a mediator cycle at the initiation of transcription. Proc Natl Acad Sci U S A 1997, 94:6075-6078.
52. Bauren G, Belikov S, Wieslander L. Transcriptional termination in the Balbiani ring 1 gene is closely coupled to 3′-end formation and excision of the 3′-terminal intron. Genes Dev 1998, 12:2759-2769.
53. Boireau S, Maiuri P, Basyuk E, de la Mata M, Knezevich A, Pradet-Balade B, Backer V, Kornblihtt A, Marcello A, Bertrand E. The transcriptional cycle of HIV-1 in real-time and live cells. J Cell Biol 2007, 179:291-304.
54. West S, Proudfoot NJ, Dye MJ. Molecular dissection of mammalian RNA polymerase II transcriptional termination. Mol Cell 2008, 29:600-610.
55. Martins SB, Rino J, Carvalho T, Carvalho C, Yoshida M, Klose JM, de Almeida SF, Carmo-Fonseca M. Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3′ end of human genes. Nat Struct Mol Biol 2011, 18:1115-1123.
56. Rigo F, Martinson HG. Polyadenylation releases mRNA from RNA polymerase II in a process that is licensed by splicing. RNA 2009, 15:823-836.
57. Egloff S, O'Reilly D, Murphy S. Expression of human snRNA genes from beginning to end. Biochem Soc Trans 2008, 36:590-594.
58. Osley MA. The regulation of histone synthesis in the cell cycle. Annu Rev Biochem 1991, 60:827-861.
59. Marino-Ramirez L, Jordan IK, Landsman D. Multiple independent evolutionary solutions to core histone gene regulation. Genome Biol 2006, 7:R122.
60. Kuhlman TC, Cho H, Reinberg D, Hernandez N. The general transcription factors IIA, IIB, IIF, and IIE are required for RNA polymerase II transcription from the human U1 small nuclear RNA promoter. Mol Cell Biol 1999, 19:2130-2141.
61. Zaborowska J, Taylor A, Murphy S. A novel TBP-TAF complex on RNA polymerase II-transcribed snRNA genes. Transcription 2012, 3:92-104.
62. Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D. Patterns of variant polyadenylation signal usage in human genes. Genome Res 2000, 10:1001-1010.
63. Tian B, Hu J, Zhang H, Lutz CS. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 2005, 33:201-212.
64. Sheets MD, Ogg SC, Wickens MP. Point mutations in AAUAAA and the poly (A) addition site: effects on the accuracy and efficiency of cleavage and polyadenylation in vitro. Nucleic Acids Res 1990, 18:5799-5805.
65. Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 2010, 143:1018-1029.
66. Mandel CR, Bai Y, Tong L. Protein factors in pre-mRNA 3′-end processing. Cell Mol Life Sci 2008, 65:1099-1122.
67. Shi Y, Di Giammartino DC, Taylor D, Sarkeshik A, Rice WJ, Yates JR 3rd, Frank J, Manley JL. Molecular architecture of the human pre-mRNA 3′ processing complex. Mol Cell 2009, 33:365-376.
68. Takagaki Y, Ryner LC, Manley JL. Four factors are required for 3′-end cleavage of pre-mRNAs. Genes Dev 1989, 3:1711-1724.
69. Ryan K, Calvo O, Manley JL. Evidence that polyadenylation factor CPSF-73 is the mRNA 3′ processing endonuclease. RNA 2004, 10:565-573.
70. Takagaki Y, Manley JL. RNA recognition by the human polyadenylation factor CstF. Mol Cell Biol 1997, 17:3907-3914.
71. Martin G, Gruber AR, Keller W, Zavolan M. Genome-wide analysis of pre-mRNA 3′ end processing reveals a decisive role of human cleavage factor I in the regulation of 3′ UTR length. Cell Rep 2012, 1:753-763.
72. Kerwitz Y, Kuhn U, Lilie H, Knoth A, Scheuermann T, Friedrich H, Schwarz E, Wahle E. Stimulation of poly(A) polymerase through a direct interaction with the nuclear poly(A) binding protein allosterically regulated by RNA. EMBO J 2003, 22:3705-3714.
73. Kuhn U, Gundel M, Knoth A, Kerwitz Y, Rudel S, Wahle E. Poly(A) tail length is controlled by the nuclear poly(A)-binding protein regulating the interaction between poly(A) polymerase and the cleavage and polyadenylation specificity factor. J Biol Chem 2009, 284:22803-22814.
74. Wang Y, Fairley JA, Roberts SG. Phosphorylation of TFIIB links transcription initiation and termination. Curr Biol 2010, 20:548-553.
75. Dantonel JC, Murthy KG, Manley JL, Tora L. Transcription factor TFIID recruits factor CPSF for formation of 3′ end of mRNA. Nature 1997, 389:399-402.
76. Calvo O, Manley JL. Evolutionarily conserved interaction between CstF-64 and PC4 links transcription, polyadenylation, and termination. Mol Cell 2001, 7:1013-1023.
77. McCracken S, Fong N, Yankulov K, Ballantyne S, Pan G, Greenblatt J, Patterson SD, Wickens M, Bentley DL. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 1997, 385:357-361.
78. Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg RD. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 2001, 292:1876-1882.
79. Ghazy MA, Gordon JM, Lee SD, Singh BN, Bohm A, Hampsey M, Moore C. The interaction of Pcf11 and Clp1 is needed for mRNA 3′-end formation and is modulated by amino acids in the ATP-binding site. Nucleic Acids Res 2012, 40:1214-1225.
80. Sadowski M, Dichtl B, Hubner W, Keller W. Independent functions of yeast Pcf11p in pre-mRNA 3′ end processing and in transcription termination. EMBO J 2003, 22:2167-2177.
81. Meinhart A, Cramer P. Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors. Nature 2004, 430:223-226.
82. Marzluff WF, Gongidi P, Woods KR, Jin J, Maltais LJ. The human and mouse replication-dependent histone genes. Genomics 2002, 80:487-498.
83. Marzluff WF, Duronio RJ. Histone mRNA expression: multiple levels of cell cycle regulation and important developmental consequences. Curr Opin Cell Biol 2002, 14:692-699.
84. Rattray AM, Muller B. The control of histone gene expression. Biochem Soc Trans 2012, 40:880-885.
85. Chodchoy N, Pandey NB, Marzluff WF. An intact histone 3′-processing site is required for transcription termination in a mouse histone H2a gene. Mol Cell Biol 1991, 11:497-509.
86. Adamson TE, Price DH. Cotranscriptional processing of Drosophila histone mRNAs. Mol Cell Biol 2003, 23:4046-4055.
87. Scharl EC, Steitz JA. The site of 3′ end formation of histone messenger RNA is a fixed distance from the downstream element recognized by the U7 snRNP. EMBO J 1994, 13:2432-2440.
88. Furger A, Schaller A, Schumperli D. Functional importance of conserved nucleotides at the histone RNA 3′ processing site. RNA 1998, 4:246-256.
89. Dominski Z, Yang XC, Marzluff WF. The polyadenylation factor CPSF-73 is involved in histone-pre-mRNA processing. Cell 2005, 123:37-48.
90. Yang XC, Sullivan KD, Marzluff WF, Dominski Z. Studies of the 5′ exonuclease and endonuclease activities of CPSF-73 in histone pre-mRNA processing. Mol Cell Biol 2009, 29:31-42.
91. Kolev NG, Steitz JA. Symplekin and multiple other polyadenylation factors participate in 3′-end maturation of histone mRNAs. Genes Dev 2005, 19:2583-2592.
92. Wagner EJ, Burch BD, Godfrey AC, Salzler HR, Duronio RJ, Marzluff WF. A genome-wide RNA interference screen reveals that variant histones are necessary for replication-dependent histone pre-mRNA processing. Mol Cell 2007, 28:692-699.
93. Jaeger S, Martin F, Rudinger-Thirion J, Giege R, Eriani G. Binding of human SLBP on the 3′-UTR of histone precursor H4-12 mRNA induces structural rearrangements that enable U7 snRNA anchoring. Nucleic Acids Res 2006, 34:4987-4995.
94. Dominski Z, Erkmann JA, Yang X, Sanchez R, Marzluff WF. A novel zinc finger protein is associated with U7 snRNP and interacts with the stem-loop binding protein in the histone pre-mRNP to stimulate 3′-end processing. Genes Dev 2002, 16:58-71.
95. Azzouz TN, Gruber A, Schumperli D. U7 snRNP-specific Lsm11 protein: dual binding contacts with the 100 kDa zinc finger processing factor (ZFP100) and a ZFP100-independent function in histone RNA 3′ end processing. Nucleic Acids Res 2005, 33:2106-2117.
96. Wagner EJ, Ospina JK, Hu Y, Dundr M, Matera AG, Marzluff WF. Conserved zinc fingers mediate multiple functions of ZFP100, a U7snRNP associated protein. RNA 2006, 12:1206-1218.
97. Yang XC, Burch BD, Yan Y, Marzluff WF, Dominski Z. FLASH, a proapoptotic protein involved in activation of caspase-8, is essential for 3′ end processing of histone pre-mRNAs. Mol Cell 2009, 36:267-278.
98. Barcaroli D, Bongiorno-Borbone L, Terrinoni A, Hofmann TG, Rossi M, Knight RA, Matera AG, Melino G, De Laurenzi V. FLASH is required for histone transcription and S-phase progression. Proc Natl Acad Sci U S A 2006, 103:14808-14812.
99. Stiller JW, McConaughy BL, Hall BD. Evolutionary complementation for polymerase II CTD function. Yeast 2000, 16:57-64.
100. Schwer B, Shuman S. Deciphering the RNA polymerase II CTD code in fission yeast. Mol Cell 2011, 43:311-318.
101. Pirngruber J, Shchebet A, Schreiber L, Shema E, Minsky N, Chapman RD, Eick D, Aylon Y, Oren M, Johnsen SA. CDK9 directs H2B monoubiquitination and controls replication-dependent histone mRNA 3′-end processing. EMBO Rep 2009, 10:894-900.
102. Medlin J, Scurry A, Taylor A, Zhang F, Peterlin BM, Murphy S. P-TEFb is not an essential elongation factor for the intronless human U2 snRNA and histone H2b genes. EMBO J 2005, 24:4154-4165.
103. Jawdekar GW, Henry RW. Transcriptional regulation of human small nuclear RNA genes. Biochim Biophys Acta 2008, 1779:295-305.
104. Hernandez N, Weiner AM. Formation of the 3′ end of U1 snRNA requires compatible snRNA promoter elements. Cell 1986, 47:249-258.
105. Skuzeski JM, Lund E, Murphy JT, Steinberg TH, Burgess RR, Dahlberg JE. Synthesis of human U1 RNA. II. Identification of two regions of the promoter essential for transcription initiation at position +1. J Biol Chem 1984, 259:8345-8352.
106. Murphy JT, Skuzeski JT, Lund E, Steinberg TH, Burgess RR, Dahlberg JE. Functional elements of the human U1 RNA promoter. Identification of five separate regions required for efficient transcription and template competition. J Biol Chem 1987, 262:1795-1803.
107. Sadowski CL, Henry RW, Lobo SM, Hernandez N. Targeting TBP to a non-TATA box cis-regulatory element: a TBP-containing complex activates transcription from snRNA promoters through the PSE. Genes Dev 1993, 7:1535-1548.
108. Baillat D, Hakimi MA, Naar AM, Shilatifard A, Cooch N, Shiekhattar R. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 2005, 123:265-276.
109. Cuello P, Boyd DC, Dye MJ, Proudfoot NJ, Murphy S. Transcription of the human U2 snRNA genes continues beyond the 3′ box in vivo. EMBO J 1999, 18:2867-2877.
110. Kunkel GR, Pederson T. Transcription boundaries of U1 small nuclear RNA. Mol Cell Biol 1985, 5:2332-2340.
111. Medlin JE, Uguen P, Taylor A, Bentley DL, Murphy S. The C-terminal domain of pol II and a DRB-sensitive kinase are required for 3′ processing of U2 snRNA. EMBO J 2003, 22:925-934.
112. Jacobs EY, Ogiwara I, Weiner AM. Role of the C-terminal domain of RNA polymerase II in U2 snRNA transcription and 3′ processing. Mol Cell Biol 2004, 24:846-855.
113. Uguen P, Murphy S. The 3′ ends of human pre-snRNAs are produced by RNA polymerase II CTD-dependent RNA processing. EMBO J 2003, 22:4544-4554.
114. Ramamurthy L, Ingledue TC, Pilch DR, Kay BK, Marzluff WF. Increasing the distance between the snRNA promoter and the 3′ box decreases the efficiency of snRNA 3′-end formation. Nucleic Acids Res 1996, 24:4525-4534.
115. Hernandez N, Lucito R. Elements required for transcription initiation of the human U2 snRNA gene coincide with elements required for snRNA 3′ end formation. EMBO J 1988, 7:3125-3134.
116. de Vegvar HE, Lund E, Dahlberg JE. 3′ End formation of U1 snRNA precursors is coupled to transcription from snRNA promoters. Cell 1986, 47:259-266.
117. Steinmetz EJ, Conrad NK, Brow DA, Corden JL. RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts. Nature 2001, 413:327-331.
118. Arigo JT, Eyler DE, Carroll KL, Corden JL. Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. Mol Cell 2006, 23:841-851.
119. Thiebaut M, Kisseleva-Romanova E, Rougemaille M, Boulay J, Libri D. Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. Mol Cell 2006, 23:853-864.
120. Vasiljeva L, Buratowski S. Nrd1 interacts with the nuclear exosome for 3′ processing of RNA polymerase II transcripts. Mol Cell 2006, 21:239-248.
121. Steinmetz EJ, Brow DA. Repression of gene expression by an exogenous sequence element acting in concert with a heterogeneous nuclear ribonucleoprotein-like protein, Nrd1, and the putative helicase Sen1. Mol Cell Biol 1996, 16:6993-7003.
122. Kawauchi J, Mischo H, Braglia P, Rondon A, Proudfoot NJ. Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination. Genes Dev 2008, 22:1082-1092.
123. Steinmetz EJ, Warren CL, Kuehner JN, Panbehi B, Ansari AZ, Brow DA. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell 2006, 24:735-746.
124. Steinmetz EJ, Brow DA. Control of pre-mRNA accumulation by the essential yeast protein Nrd1 requires high-affinity transcript binding and a domain implicated in RNA polymerase II association. Proc Natl Acad Sci U S A 1998, 95:6699-6704.
125. Carroll KL, Pradhan DA, Granek JA, Clarke ND, Corden JL. Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. Mol Cell Biol 2004, 24:6241-6252.
126. Conrad NK, Wilson SM, Steinmetz EJ, Patturajan M, Brow DA, Swanson MS, Corden JL. A yeast heterogeneous nuclear ribonucleoprotein complex associated with RNA polymerase II. Genetics 2000, 154:557-571.
127. Carroll KL, Ghirlando R, Ames JM, Corden JL. Interaction of yeast RNA-binding proteins Nrd1 and Nab3 with RNA polymerase II terminator elements. RNA 2007, 13:361-373.
128. Gudipati RK, Villa T, Boulay J, Libri D. Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice. Nat Struct Mol Biol 2008, 15:786-794.
129. Kubicek K, Cerna H, Holub P, Pasulka J, Hrossova D, Loehr F, Hofr C, Vanacova S, Stefl R. Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1. Genes Dev 2012, 26:1891-1896.
130. Vasiljeva L, Kim M, Mutschler H, Buratowski S, Meinhart A. The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nat Struct Mol Biol 2008, 15:795-804.
131. He X, Khan AU, Cheng H, Pappas DL Jr, Hampsey M, Moore CL. Functional interactions between the transcription and mRNA 3′ end processing machineries mediated by Ssu72 and Sub1. Genes Dev 2003, 17:1030-1042.
132. Reyes-Reyes M, Hampsey M. Role for the Ssu72 C-terminal domain phosphatase in RNA polymerase II transcription elongation. Mol Cell Biol 2007, 27:926-936.
133. Singh BN, Hampsey M. A transcription-independent role for TFIIB in gene looping. Mol Cell 2007, 27:806-8016.
134. Tan-Wong SM, French JD, Proudfoot NJ, Brown MA. Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene. Proc Natl Acad Sci U S A 2008, 105:5160-5165.
135. Rondon AG, Mischo HE, Kawauchi J, Proudfoot NJ. Fail-safe transcriptional termination for protein-coding genes in S. cerevisiae. Mol Cell 2009, 36:88-98.
136. Niwa M, Rose SD, Berget SM. In vitro polyadenylation is stimulated by the presence of an upstream intron. Genes Dev 1990, 4:1552-1559.
137. Rigo F, Martinson HG. Functional coupling of last-intron splicing and 3′-end processing to transcription in vitro: the poly(A) signal couples to splicing before committing to cleavage. Mol Cell Biol 2008, 28:849-862.
138. Dye MJ, Proudfoot NJ. Terminal exon definition occurs cotranscriptionally and promotes termination of RNA polymerase II. Mol Cell 1999, 3:371-378.
139. Kyburz A, Friedlein A, Langen H, Keller W. Direct interactions between subunits of CPSF and the U2 snRNP contribute to the coupling of pre-mRNA 3′ end processing and splicing. Mol Cell 2006, 23:195-205.
140. Uguen P, Murphy S. 3′-Box-dependent processing of human pre-U1 snRNA requires a combination of RNA and protein co-factors. Nucleic Acids Res 2004, 32:2987-2994.
141. Lykke-Andersen S, Mapendano CK, Jensen TH. An ending is a new beginning: transcription termination supports re-initiation. Cell Cycle 2011, 10:863-865.
142. Shandilya J, Roberts SG. The transcription cycle in eukaryotes: from productive initiation to RNA polymerase II recycling. Biochim Biophys Acta 2012, 1819:391-400.
143. Darzacq X, Shav-Tal Y, de Turris V, Brody Y, Shenoy SM, Phair RD, Singer RH. In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol 2007, 14:796-806.
144. Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, Bahler J. Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell 2012, 151:671-683.