1. KuehnerJN, PearsonEL, MooreC (2011) Unravelling the means to an end: RNA polymerase II transcription termination. Nat Rev Mol Cell Biol 12: 283–294.
2. MischoHE, ProudfootNJ (2013) Disengaging polymerase: terminating RNA polymerase II transcription in budding yeast. Biochim Biophys Acta 1829: 174–185.
3. CloutierSC, WangS, MaWK, PetellCJ, TranEJ (2013) Long noncoding RNAs promote transcriptional poising of inducible genes. PLoS Biol 11: e1001715.
4. CastelnuovoM, RahmanS, GuffantiE, InfantinoV, StutzF, et al. (2013) Bimodal expression of PHO84 is modulated by early termination of antisense transcription. Nat Struct Mol Biol 20: 851–858.
5. ShearwinKE, CallenBP, EganJB (2005) Transcriptional interference–a crash course. Trends Genet 21: 339–345.
6. ArigoJT, CarrollKL, AmesJM, CordenJL (2006) Regulation of yeast NRD1 expression by premature transcription termination. Mol Cell 21: 641–651.
7. KuehnerJN, BrowDA (2008) Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation. Mol Cell 31: 201–211.
8. CreamerTJ, DarbyMM, JamonnakN, SchaughencyP, HaoH, et al. (2011) Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1. PLoS Genet 7: e1002329.
9. ThiebautM, ColinJ, NeilH, JacquierA, SeraphinB, et al. (2008) Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae. Mol Cell 31: 671–682.
10. Tan-WongSM, ZauggJB, CamblongJ, XuZ, ZhangDW, et al. (2012) Gene loops enhance transcriptional directionality. Science 338: 671–675.
11. GrzechnikP, Tan-WongSM, ProudfootNJ (2014) Terminate and make a loop: regulation of transcriptional directionality. Trends Biochem Sci 39: 319–27.
12. JacquierA (2009) The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet 10: 833–844.
13. JensenTH, JacquierA, LibriD (2013) Dealing with pervasive transcription. Mol Cell 52: 473–484.
14. BerrettaJ, MorillonA (2009) Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep 10: 973–982.
15. ArigoJT, EylerDE, CarrollKL, CordenJL (2006) Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. Mol Cell 23: 841–851.
16. DavisCA, AresMJr (2006) Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 103: 3262–3267.
17. GudipatiRK, XuZ, LebretonA, SeraphinB, SteinmetzLM, et al. (2012) Extensive degradation of RNA precursors by the exosome in wild-type cells. Mol Cell 48: 409–421.
18. NeilH, MalabatC, d'Aubenton-CarafaY, XuZ, SteinmetzLM, et al. (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457: 1038–1042.
19. ThiebautM, Kisseleva-RomanovaE, RougemailleM, BoulayJ, LibriD (2006) Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. Mol Cell 23: 853–864.
20. WyersF, RougemailleM, BadisG, RousselleJC, DufourME, et al. (2005) Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121: 725–737.
21. XuZ, WeiW, GagneurJ, PerocchiF, Clauder-MunsterS, et al. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457: 1033–1037.
22. BuratowskiS (2005) Connections between mRNA 3′ end processing and transcription termination. Curr Opin Cell Biol 17: 257–261.
23. HsinJP, ManleyJL (2012) The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev 26: 2119–2137.
24. KimM, VasiljevaL, RandoOJ, ZhelkovskyA, MooreC, et al. (2006) Distinct pathways for snoRNA and mRNA termination. Mol Cell 24: 723–734.
25. UrsicD, ChinchillaK, FinkelJS, CulbertsonMR (2004) Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processing. Nucleic Acids Res 32: 2441–2452.
26. SteinmetzEJ, BrowDA (1996) 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 16: 6993–7003.
27. SteinmetzEJ, BrowDA (1998) 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 95: 6699–6704.
28. SteinmetzEJ, ConradNK, BrowDA, CordenJL (2001) RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts. Nature 413: 327–331.
29. ConradNK, WilsonSM, SteinmetzEJ, PatturajanM, BrowDA, et al. (2000) A yeast heterogeneous nuclear ribonucleoprotein complex associated with RNA polymerase II. Genetics 154: 557–571.
30. SteinmetzEJ, NgSB, ClouteJP, BrowDA (2006) cis- and trans-Acting determinants of transcription termination by yeast RNA polymerase II. Mol Cell Biol 26: 2688–2696.
31. CarrollKL, GhirlandoR, AmesJM, CordenJL (2007) Interaction of yeast RNA-binding proteins Nrd1 and Nab3 with RNA polymerase II terminator elements. RNA 13: 361–373.
32. CarrollKL, PradhanDA, GranekJA, ClarkeND, CordenJL (2004) Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. Mol Cell Biol 24: 6241–6252.
33. PorruaO, HoborF, BoulayJ, KubicekK, D'Aubenton-CarafaY, et al. (2012) In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination. EMBO J 31: 3935–3948.
34. WlotzkaW, KudlaG, GrannemanS, TollerveyD (2011) The nuclear RNA polymerase II surveillance system targets polymerase III transcripts. EMBO J 30: 1790–1803.
35. VasiljevaL, BuratowskiS (2006) Nrd1 interacts with the nuclear exosome for 3′ processing of RNA polymerase II transcripts. Mol Cell 21: 239–248.
36. KimM, KroganNJ, VasiljevaL, RandoOJ, NedeaE, et al. (2004) The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432: 517–522.
37. WestS, GromakN, ProudfootNJ (2004) Human 5′→3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 432: 522–525.
38. BrannanK, BentleyDL (2012) Control of Transcriptional Elongation by RNA Polymerase II: A Retrospective. Genet Res Int 2012: 170173.
39. LoganJ, Falck-PedersenE, DarnellJEJr, ShenkT (1987) A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene. Proc Natl Acad Sci U S A 84: 8306–8310.
40. ZhangZ, GilmourDS (2006) 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 21: 65–74.
41. ZhangZ, KlattA, HendersonAJ, GilmourDS (2007) Transcription termination factor Pcf11 limits the processivity of Pol II on an HIV provirus to repress gene expression. Genes Dev 21: 1609–1614.
42. ChinchillaK, Rodriguez-MolinaJB, UrsicD, FinkelJS, AnsariAZ, et al. (2012) Interactions of Sen1, Nrd1, and Nab3 with multiple phosphorylated forms of the Rpb1 C-terminal domain in Saccharomyces cerevisiae. Eukaryot Cell 11: 417–429.
43. KimHD, ChoeJ, SeoYS (1999) The sen1(+) gene of Schizosaccharomyces pombe, a homologue of budding yeast SEN1, encodes an RNA and DNA helicase. Biochemistry 38: 14697–14710.
44. BrowDA (2011) Sen-sing RNA terminators. Mol Cell 42: 717–718.
45. SteinmetzEJ, WarrenCL, KuehnerJN, PanbehiB, AnsariAZ, et al. (2006) Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell 24: 735–746.
46. PorruaO, LibriD (2013) A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast. Nat Struct Mol Biol 20: 884–891.
47. HafnerM, LandthalerM, BurgerL, KhorshidM, HausserJ, et al. (2010) PAR-CliP–a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp
48. HafnerM, LandthalerM, BurgerL, KhorshidM, HausserJ, et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129–141.
49. JamonnakN, CreamerTJ, DarbyMM, SchaughencyP, WheelanSJ, et al. (2011) Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing. RNA 17: 2011–2025.
50. HarukiH, NishikawaJ, LaemmliUK (2008) The anchor-away technique: rapid, conditional establishment of yeast mutant phenotypes. Mol Cell 31: 925–932.
51. FanX, MoqtaderiZ, JinY, ZhangY, LiuXS, et al. (2010) Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3′-end formation. Proc Natl Acad Sci U S A 107: 17945–17950.
52. BurgerK, MuhlB, KellnerM, RohrmoserM, Gruber-EberA, et al. (2013) 4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response. RNA Biol 10.
53. ChurchmanLS, WeissmanJS (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469: 368–373.
54. PelechanoV, ChavezS, Perez-OrtinJE (2010) A complete set of nascent transcription rates for yeast genes. PLoS One 5: e15442.
55. ZhelkovskyA, TacahashiY, NasserT, HeX, SterzerU, et al. (2006) The role of the Brr5/Ysh1 C-terminal domain and its homolog Syc1 in mRNA 3′-end processing in Saccharomyces cerevisiae. RNA 12: 435–445.
56. BrendoliseC, RouillardJM, DufourME, LacrouteF (2002) Expression analysis of RNA14, a gene involved in mRNA 3′ end maturation in yeast: characterization of the rna14-5 mutant strain. Mol Genet Genomics 267: 515–525.
57. MandartE (1998) Effects of mutations in the Saccharomyces cerevisiae RNA14 gene on the abundance and polyadenylation of its transcripts. Mol Gen Genet 258: 16–25.
58. CloutierSC, MaWK, NguyenLT, TranEJ (2012) The DEAD-box RNA helicase Dbp2 connects RNA quality control with repression of aberrant transcription. J Biol Chem 287: 26155–26166.
59. MaWK, CloutierSC, TranEJ (2013) The DEAD-box protein Dbp2 functions with the RNA-binding protein Yra1 to promote mRNP assembly. J Mol Biol 425: 3824–3838.
60. BartaI, IggoR (1995) Autoregulation of expression of the yeast Dbp2p ‘DEAD-box’ protein is mediated by sequences in the conserved DBP2 intron. EMBO J 14: 3800–3808.
61. OzsolakF, KapranovP, FoissacS, KimSW, FishilevichE, et al. (2010) Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 143: 1018–1029.
62. WilkeningS, PelechanoV, JarvelinAI, TekkedilMM, AndersS, et al. (2013) An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Res 41: e65.
63. MoqtaderiZ, GeisbergJV, JinY, FanX, StruhlK (2013) Species-specific factors mediate extensive heterogeneity of mRNA 3′ ends in yeasts. Proc Natl Acad Sci U S A 110: 11073–11078.
64. VasiljevaL, KimM, MutschlerH, BuratowskiS, MeinhartA (2008) The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nat Struct Mol Biol 15: 795–804.
65. SchulzD, SchwalbB, KieselA, BaejenC, TorklerP, et al. (2013) Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis. Cell
66. RahlPB, LinCY, SeilaAC, FlynnRA, McCuineS, et al. (2010) c-Myc regulates transcriptional pause release. Cell 141: 432–445.
67. GromakN, WestS, ProudfootNJ (2006) Pause sites promote transcriptional termination of mammalian RNA polymerase II. Mol Cell Biol 26: 3986–3996.
68. HymanLE, MooreCL (1993) Termination and pausing of RNA polymerase II downstream of yeast polyadenylation sites. Mol Cell Biol 13: 5159–5167.
69. KazerouniniaA, NgoB, MartinsonHG (2010) Poly(A) signal-dependent degradation of unprocessed nascent transcripts accompanies poly(A) signal-dependent transcriptional pausing in vitro. RNA 16: 197–210.
70. LarsonDR, ZenklusenD, WuB, ChaoJA, SingerRH (2011) Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 332: 475–478.
71. BaileyTL, BodenM, BuskeFA, FrithM, GrantCE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202–208.
72. BacikovaV, PasulkaJ, KubicekK, SteflR (2014) Structure and semi-sequence-specific RNA binding of Nrd1. Nucleic Acids Res 42: 8024–38.
73. BirseCE, Minvielle-SebastiaL, LeeBA, KellerW, ProudfootNJ (1998) Coupling termination of transcription to messenger RNA maturation in yeast. Science 280: 298–301.
74. LuoW, BentleyD (2004) A ribonucleolytic rat torpedoes RNA polymerase II. Cell 119: 911–914.
75. CalvoO, ManleyJL (2001) Evolutionarily conserved interaction between CstF-64 and PC4 links transcription, polyadenylation, and termination. Mol Cell 7: 1013–1023.
76. NagA, NarsinhK, KazerouniniaA, MartinsonHG (2006) The conserved AAUAAA hexamer of the poly(A) signal can act alone to trigger a stable decrease in RNA polymerase II transcription velocity. RNA 12: 1534–1544.
77. ConnellyS, ManleyJL (1988) A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. Genes Dev 2: 440–452.
78. LuoW, JohnsonAW, BentleyDL (2006) The role of Rat1 in coupling mRNA 3′-end processing to transcription termination: implications for a unified allosteric-torpedo model. Genes Dev 20: 954–965.
79. NagA, NarsinhK, MartinsonHG (2007) The poly(A)-dependent transcriptional pause is mediated by CPSF acting on the body of the polymerase. Nat Struct Mol Biol 14: 662–669.
80. PearsonEL, MooreCL (2013) Dismantling promoter-driven RNA polymerase II transcription complexes in vitro by the termination factor Rat1. J Biol Chem 288: 19750–19759.
81. KimM, AhnSH, KroganNJ, GreenblattJF, BuratowskiS (2004) Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes. EMBO J 23: 354–364.
82. SchreieckA, EasterAD, EtzoldS, WiederholdK, LidschreiberM, et al. (2014) RNA polymerase II termination involves C-terminal-domain tyrosine dephosphorylation by CPF subunit Glc7. Nat Struct Mol Biol 21: 175–179.
83. Al HusiniN, KudlaP, AnsariA (2013) A role for CF1A 3′ end processing complex in promoter-associated transcription. PLoS Genet 9: e1003722.
84. HuangY, WengX, RussuIM (2010) Structural energetics of the adenine tract from an intrinsic transcription terminator. J Mol Biol 397: 677–688.
85. MartinFH, TinocoIJr (1980) DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription. Nucleic Acids Res 8: 2295–2299.
86. KireevaML, KomissarovaN, WaughDS, KashlevM (2000) The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J Biol Chem 275: 6530–6536.
87. TagwerkerC, ZhangH, WangX, LarsenLS, LathropRH, et al. (2006) HB tag modules for PCR-based gene tagging and tandem affinity purification in Saccharomyces cerevisiae. Yeast 23: 623–632.
88. MarquardtS, HazelbakerDZ, BuratowskiS (2011) Distinct RNA degradation pathways and 3′ extensions of yeast non-coding RNA species. Transcription 2: 145–154.
89. RinesDR, ThomannD, DornJF, GoodwinP, SorgerPK (2011) Live cell imaging of yeast. Cold Spring Harb Protoc 2011
90. GentlemanRC, CareyVJ, BatesDM, BolstadB, DettlingM, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
91. LangmeadB (2010) Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics Chapter 11: Unit 11 17.
92. CrooksGE, HonG, ChandoniaJM, BrennerSE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188–1190.