Werner F, Grohmann D (2011) Evolution of multisubunit RNA polymerases in the three domains of life. Nat Rev Microbiol 9:85–98.
Ponting CP (2002) Novel domains and orthologues of eukaryotic transcription elongation factors. Nucleic Acids Res 30:3643–3652.
Hartzog GA, Fu J (2013) The Spt4-Spt5 complex: a multi-faceted regulator of transcription elongation. Biochim Biophys Acta 1829:105–115.
Hirtreiter A, Damsma GE, Cheung A, Klose D, Grohmann D, Vojnic E, Martin ACR, Cramer P, Werner F (2010) Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif. Nucleic Acids Res 38:4040–4051.
Guo M, Xu F, Yamada J, Egelhofer T, Gao Y, Hartzog GA, Teng M, Niu L (2008) Core structure of the yeast Spt4-Spt5 complex: a conserved module for regulation of transcription elongation. Structure 16:1649–1658.
Wenzel S, Martins B, Rosch P, Wohrl B (2009) Crystal structure of the human transcription elongation factor DSIF hSpt4 subunit in complex with the hSpt5 dimerization interface. Biochem J 425:373–380.
Bernecky C, Herzog F, Baumeister W, Plitzko JM, Cramer P (2016) Structure of transcribing mammalian RNA polymerase II. Nature 529:551–554.
Martinez-Rucobo FW, Sainsbury S, Cheung ACM, Cramer P (2011) Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. Embo J 30:1302–1310.
Sevostyanova A, Belogurov GA, Mooney RA, Landick R, Artsimovitch I (2011) The beta subunit gate loop is required for RNA polymerase modification by RfaH and NusG. Mol Cell 43:253–262.
Klein BJ, Bose D, Baker KJ, Yusoff ZM, Zhang X, Murakami KS (2011) RNA polymerase and transcription elongation factor Spt4/5 complex structure. Proc Natl Acad Sci USA 108:546.
Guo G, Gao Y, Zhu Z, Zhao D, Liu Z, Zhou H, Niu L, Teng M (2015) Structural and biochemical insights into the DNA-binding mode of MjSpt4p:Spt5 complex at the exit tunnel of RNAPII. J Struct Biol 192:418–425.
Yakhnin AV, Murakami KS, Babitzke P (2016) NusG is a sequence-specific RNA polymerase pause factor that binds to the non-template DNA within the paused transcription bubble. J Biol Chem 291:5299–5308.
Crickard JB, Fu J, Reese JC (2016) Biochemical analysis of yeast suppressor of Ty 4/5 (Spt4/5) reveals the importance of nucleic acid interactions in the prevention of RNA polymerase II arrest. J Biol Chem 291:9853–9870.
Diamant G, Amir-Zilberstein L, Yamaguchi Y, Handa H, Dikstein R (2012) DSIF restricts NF-kappaB signaling by coordinating elongation with mRNA processing of negative feedback genes. Cell Rep 2:722–731.
Chen H, Contreras X, Yamaguchi Y, Handa H, Peterlin BM, Guo S (2009) Repression of RNA polymerase II elongation in vivo is critically dependent on the C-terminus of Spt5. PLoS One 4:e6918.
Schneider S, Pei Y, Shuman S, Schwer B (2010) Separable functions of the fission yeast Spt5 carboxyl-terminal domain (CTD) in capping enzyme binding and transcription elongation overlap with those of the RNA polymerase II CTD. Mol Cell Biol 30:2353–2364.
Lindstrom DL, Hartzog GA (2001) Genetic interactions of Spt4-Spt5 and TFIIS with the RNA polymerase II CTD and CTD modifying enzymes in Saccharomyces cerevisiae. Genetics 159:487–497.
Liu Y, Warfield L, Zhang C, Luo J, Allen J, Lang WH, Ranish J, Shokat KM, Hahn S (2009) Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol Cell Biol 29:4852–4863.
Zhou K, Kuo WH, Fillingham J, Greenblatt JF (2009) Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5. Proc Natl Acad Sci USA 106:6956–6961.
Wier AD, Mayekar MK, Heroux A, Arndt KM, Vandemark AP (2013) Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin. Proc Natl Acad Sci USA 110:17290–17295.
Qiu H, Hu C, Gaur NA, Hinnebusch AG (2012) Pol II CTD kinases Bur1 and Kin28 promote Spt5 CTR-independent recruitment of Paf1 complex. Embo J 31:3494–3505.
Wen Y, Shatkin AJ (1999) Transcription elongation factor hSPT5 stimulates mRNA capping. Genes Dev 13:1774–1779.
Pei Y, Shuman S (2002) Interactions between fission yeast mRNA capping enzymes and elongation factor Spt5. J Biol Chem 277:19639–19648.
Lindstrom DL, Squazzo SL, Muster N, Burckin TA, Wachter KC, Emigh CA, McCleery JA, Yates JR III, Hartzog GA (2003) Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol Cell Biol 23:1368–1378.
Shen Z, St-Denis A, Chartrand P (2010) Cotranscriptional recruitment of She2p by RNA pol II elongation factor Spt4-Spt5/DSIF promotes mRNA localization to the yeast bud. Genes Dev 24:1914–1926.
Burckin T, Nagel R, Mandel-Gutfreund Y, Shiue L, Clark TA, Chong JL, Chang TH, Squazzo S, Hartzog G, Ares M Jr (2005) Exploring functional relationships between components of the gene expression machinery. Nat Struct Mol Biol 12:175–182.
Mayer A, Schreieck A, Lidschreiber M, Leike K, Martin DE, Cramer P (2012) The Spt5 C-terminal region recruits yeast 3 ' RNA cleavage factor I. Mol Cell Biol 32:1321–1331.
Xiao Y, Yang YH, Burckin TA, Shiue L, Hartzog GA, Segal MR (2005) Analysis of a splice array experiment elucidates roles of chromatin elongation factor Spt4-5 in splicing. PLoS Comput Biol 1:e39.
Bucheli ME, Buratowski S (2005) Npl3 is an antagonist of mRNA 3' end formation by RNA polymerase II. Embo J 24:2150–2160.
Kaplan CD, Holland MJ, Winston F (2005) Interaction between transcription elongation factors and mRNA 3'-end formation at the Saccharomyces cerevisiae GAL10-GAL7 locus. J Biol Chem 280:913–922.
Cui Y, Denis CL (2003) In vivo evidence that defects in the transcriptional elongation factors RPB2, TFIIS, and SPT5 enhance upstream poly(A) site utilization. Mol Cell Biol 23:7887–7901.
Diamant G, Eisenbaum T, Leshkowitz D, Dikstein R (2016) Analysis of subcellular RNA fractions revealed a transcription-independent effect of TNFalpha on splicing mediated by Spt5. Mol Cell Biol 36:1342–1353.
Steiner T, Kaiser JT, Marinkovic S, Huber R, Wahl MC (2002) Crystal Strucures of transcription factor NusG in light of its nucleic acid and protein-binding activities. Embo J 21:4641–4653.
Viktorovskaya OV, Appling FD, Schneider DA (2011) Yeast transcription elongation factor Spt5 associates with RNA polymerase I and RNA polymerase II directly. J Biol Chem 286:18825–18833.
Andrulis ED, Guzman E, Daring P, Werner J, Lis J (2000) High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: roles in promoter proximal pausing and transcription elongation. Genes Dev 14:2635–2649.
Hanna MM (1993) Photocrosslinking analysis of protein-RNA interactions in E. coli transcription complexes. Cell Mol Biol Res 39:393–399.
Cheng B, Price DH (2008) Analysis of factor interactions with RNA polymerase II elongation complexes using a new electrophoretic mobility shift assay. Nucleic Acid Res 36:e135.
Missra A, Gilmour DS (2010) Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex. Proc Natl Acad Sci USA 107:11301–11306.
Weir JR, Bonneau F, Hentschel J, Conti E (2010) Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance. Proc Natl Acad Sci USA 107:12139–12144.
Zhang W, Dunkle JA, Cate JH (2009) Structures of the ribosome in intermediate states of ratcheting. Science 325:1014–1017.
Selmer M, Dunham CM, Murphy FVT, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313:1935–1942.
Meyer PA, Li S, Zhang M, Yamada K, Takagi Y, Hartzog GA, Fu J (2015) Structures and functions of the multiple KOW domains of transcription elongation factor Spt5. Mol Cell Biol 35:3354–3369.
Ivanov D, Kwak YT, Guo J, Gaynor RB (2000) Domains in the SPT5 protein that modulate its transcriptional regulatory properties. Mol Cell Biol 20:2970–2983.
Yamaguchi Y, Wada T, Watanabe D, Takagi T, Hasegawa J, Handa H (1999) Structure and function of the human transcription elongation factor DSIF. J Biol Chem 274:8085–8092.
Bendak K, Loughlin FE, Cheung V, O'Connell MR, Crossley M, Mackay JP (2012) A rapid method for assessing the RNA-binding potential of a protein. Nucleic Acids Res 40:e105.
Kwan AH, Czolij R, Mackay JP, Crossley M (2003) Pentaprobe: a comprehensive sequence for the one-step detection of DNA-binding activities. Nucleic Acids Res 31:e124.
Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510.
Djordjevic M (2007) SELEX experiments: new prospects, applications and data analysis in inferring regulatory pathways. Biomol Eng 24:179–189.
Yang X, Li H, Huang Y, Liu S (2013) The dataset for protein-RNA binding affinity. Protein Sci 22:1808–1811.
Mayer A, Lidschreiber M, Siebert M, Leike K, Soding J, Cramer P (2010) Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol 17:1272–1278.
Liu CR, Chang CR, Chern Y, Wang TH, Hsieh WC, Shen WC, Chang CY, Chu IC, Deng N, Cohen SN, Cheng T-H (2012) Spt4 is selectively required for transcription of extended trinucleotide repeats. Cell 148:690–701.
Li W, Giles C, Li S (2014) Insights into how Spt5 functions in transcription elongation and repressing transcription coupled DNA repair. Nucleic Acids Res 42:7069–7083.
Deo RC, Bonanno JB, Sonenberg N, Burley SK (1999) Recognition of polyadenylate RNA by the poly(A)-binding protein. Cell 98:835–845.
Oberstrass FC, Auweter SD, Erat M, Hargous Y, Henning A, Wenter P, Reymond L, Amir-Ahmady B, Pitsch S, Black DL, Allain FH T (2005) Structure of PTB bound to RNA: specific binding and implications for splicing regulation. Science 309:2054–2057.
Belogurov GA, Mooney RA, Svetlov V, Landick R, Artsimovitch I (2009) Functional specialization of transcription elongation factors. Embo J 28:112–122.
Belogurov GA, Sevostyanova A, Svetlov V, Artsimovitch I (2010) Functional regions of the N-terminal domain of the antiterminator RfaH. Mol Microbiol 76:286–301.
Artsimovitch I, Landick R (2002) The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand. Cell 109:193–203.
Yakhnin AV, Yakhnin H, Babitzke P (2008) Function of the Bacillus subtilis transcription elongation factor NusG in hairpin-dependent RNA polymerase pausing in the trp leader. Proc Natl Acad Sci USA 105:16131–16136.
Yakhnin AV, Babitzke P (2014) NusG/Spt5: are there common functions of this ubiquitous transcription elongation factor? Curr Opin Microbiol 18:68–71.
Ujvari A, Luse DS (2006) RNA emerging from the active site of RNA polymerase II interacts with the Rpb7 subunit. Nat Struct Mol Biol 13:49–54.
Andrecka J, Lewis R, Bruckner F, Lehmann E, Cramer P, Michaelis J (2008) Single-molecule tracking of mRNA exiting from RNA polymerase II. Proc Natl Acad Sci USA 105:135–140.
Huertas P, Aguilera A (2003) Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol Cell 12:711–721.
Rondon AG, Garcia-Rubio M, Gonzalez-Barrera S, Aguilera A (2003) Molecular evidence for a positive role of Spt4 in transcription elongation. Embo J 22:612–620.
Wahba L, Costantino L, Tan FJ, Zimmer A, Koshland D (2016) S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation. Genes Dev 30:1327–1338.
Blythe A, Gunasekara S, Walshe J, Mackay JP, Hartzog GA, Vrielink A (2014) Ubiquitin fusion constructs allow the expression and purification of multi-KOW domain complexes of the Saccharomyces cerevisiae transcription elongation factor Spt4/5. Protein Expr Purif 100:54–60.
Zakov S, Goldberg Y, Elhadad M, Ziv-Ukelson M (2011) Rich parameterization improves RNA structure prediction. J Comput Biol 18:1525–1542.
Shroedinger, LLC. The PyMOL Molecular Graphics System, Version 1.5.0.4.
Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA, Kaplan CD, Calero G (2015) Crystal structure of a transcribing RNA polymerase II complex reveals a complete transcription bubble. Mol Cell 59:258–269.
