Architecture of the RNA polymerase II elongation complex: new insights into Spt4/5 and Elf1

References

• Nogales E, Louder RK, He Y. Structural insights into the eukaryotic transcription initiation machinery. Annu Rev Biophys. 2017 May;46:59–83. doi:10.1146/annurev-biophys-070816-033751. PMID:28532216.
   PubMed Web of Science ®Google Scholar
• Ehara H, Yokoyama T, Shigematsu H, et al. Structure of the complete elongation complex of RNA polymerase II with basal factors. Science. 2017 Sep;357(6354):921–924. doi:10.1126/science.aan8552. PMID:28775211.
   PubMed Web of Science ®Google Scholar
• Wada T, Takagi T, Yamaguchi Y, et al. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 1998 Feb;12(3):343–356. PMID:9450929.
   PubMed Web of Science ®Google Scholar
• Hirtreiter A, Damsma GE, Cheung AC, et al. Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif. Nucleic Acids Res. 2010 Jul;38(12):4040–4051. doi:10.1093/nar/gkq135. PMID:20197319.
   PubMed Web of Science ®Google Scholar
• Li J, Gilmour DS. Promoter proximal pausing and the control of gene expression. Curr Opin Genet Dev. 2011 Apr;21(2):231–235. doi:10.1016/j.gde.2011.01.010. PMID:21324670.
   PubMed Web of Science ®Google Scholar
• Smollett K, Blombach F, Reichelt R, et al. A global analysis of transcription reveals two modes of Spt4/5 recruitment to archaeal RNA polymerase. Nat Microbiol. 2017 Mar;2:17021. doi:10.1038/nmicrobiol.2017.21. PMID:28248297.
   PubMed Web of Science ®Google Scholar
• Wier AD, Mayekar MK, Héroux A, et al. Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin. Proc Natl Acad Sci USA. 2013 Oct;110(43):17290–17295. doi:10.1073/pnas.1314754110. PMID:24101474.
   PubMed Web of Science ®Google Scholar
• Mayer A, Schreieck A, Lidschreiber M, et al. The spt5 C-terminal region recruits yeast 3' RNA cleavage factor I. Mol Cell Biol. 2012 Apr;32(7):1321–31. doi:10.1128/MCB.06310-11. PMID:22290438.
   PubMed Web of Science ®Google Scholar
• Ding B, LeJeune D, Li S. The C-terminal repeat domain of Spt5 plays an important role in suppression of Rad26-independent transcription coupled repair. J Biol Chem. 2010 Feb;285(8):5317–526. doi:10.1074/jbc.M109.082818. PMID:20042611.
   PubMed Web of Science ®Google Scholar
• Prather D, Krogan NJ, Emili A, et al. Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae. Mol Cell Biol. 2005 Nov;25(22):10122–10135. doi:10.1128/MCB.25.22.10122-10135.2005. PMID:16260625.
   PubMed Web of Science ®Google Scholar
• Daniels JP, Kelly S, Wickstead B, et al. Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in Archaea. Biol Direct. 2009 Jul;4:24. PMID:19640276.
   PubMed Web of Science ®Google Scholar
• Mayer A, Lidschreiber M, Siebert M, et al. Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol. 2010 Oct;17(10):1272–1278. doi:10.1038/nsmb.1903. PMID:20818391.
   PubMed Web of Science ®Google Scholar
• Hogan BP, Hartsch T, Erie DA. Transcript cleavage by Thermus thermophilus RNA polymerase. Effects of GreA and anti-GreA factors. J Biol Chem. 2002 Jan;277(2):967–975. doi:10.1074/jbc.M108737200. PMID:11606592.
   PubMed Web of Science ®Google Scholar
• Kettenberger H, Armache KJ, Cramer P. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell. 2003 Aug;114(3):347–357. PMID:12914699.
   PubMed Web of Science ®Google Scholar
• Wang D, Bushnell DA, Huang X, et al. Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science. 2009 May;324(5931):1203–1206. doi:10.1126/science.1168729. PMID:19478184.
   PubMed Web of Science ®Google Scholar
• Plaschka C, Larivière L, Wenzeck L, et al. Architecture of the RNA polymerase II-Mediator core initiation complex. Nature. 2015 Feb;518(7539):376–380. doi:10.1038/nature14229. PMID:25652824.
   PubMed Web of Science ®Google Scholar
• Plaschka C, Hantsche M, Dienemann C, et al. Transcription initiation complex structures elucidate DNA opening. Nature. 2016 May;533(7603):353–358. doi:10.1038/nature17990. PMID:27193681.
   PubMed Web of Science ®Google Scholar
• Klein BJ, Bose D, Baker KJ, et al. RNA polymerase and transcription elongation factor Spt4/5 complex structure. Proc Natl Acad Sci USA. 2011 Jan;108(2):546–550. doi:10.1073/pnas.1013828108. PMID:21187417.
   PubMed Web of Science ®Google Scholar
• Liu B, Steitz TA. Structural insights into NusG regulating transcription elongation. Nucleic Acids Res. 2017 Jan;45(2):968–974. doi:10.1093/nar/gkw1159. PMID:27899640.
   PubMed Web of Science ®Google Scholar
• Martinez-Rucobo FW, Sainsbury S, Cheung AC, et al. Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. EMBO J. 2011 Apr;30(7):1302–1310. doi:10.1038/emboj.2011.64. PMID:21386817.
   PubMed Web of Science ®Google Scholar
• Said N, Krupp F, Anedchenko E, et al. Structural basis for λN-dependent processive transcription antitermination. Nat Microbiol. 2017 Apr;2:17062. doi:10.1038/nmicrobiol.2017.62. PMID:28452979.
   PubMed Web of Science ®Google Scholar
• Xu J, Lahiri I, Wang W, et al. Structural basis for the initiation of eukaryotic transcription-coupled DNA repair. Nature. 2017 Nov;551(7682):653–657. doi:10.1038/nature24658. PMID:29168508;
   PubMed Web of Science ®Google Scholar
• Sekine S, Murayama Y, Svetlov V, et al. The ratcheted and ratchetable structural states of RNA polymerase underlie multiple transcriptional functions. Mol Cell. 2015 Feb;57(3):408–421. doi:10.1016/j.molcel.2014.12.014. PMID:25601758.
   PubMed Web of Science ®Google Scholar
• Bernecky C, Plitzko JM, Cramer P. Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nat Struct Mol Biol. 2017 Oct;24(10):809–815. doi:10.1038/nsmb.3465. PMID:28892040.
   PubMed Web of Science ®Google Scholar
• Bernecky C, Herzog F, Baumeister W, et al. Structure of transcribing mammalian RNA polymerase II. Nature. 2016 Jan;529(7587):551–554. doi:10.1038/nature16482. PMID:26789250.
   PubMed Web of Science ®Google Scholar
• Hirata A, Klein BJ, Murakami KS. The X-ray crystal structure of RNA polymerase from Archaea. Nature. 2008 Feb;451(7180):851–854. doi:10.1038/nature06530. PMID:18235446.
   PubMed Web of Science ®Google Scholar
• Viktorovskaya OV, Appling FD, Schneider DA. Yeast transcription elongation factor Spt5 associates with RNA polymerase I and RNA polymerase II directly. J Biol Chem. 2011 May;286(21):18825–18833. doi:10.1074/jbc.M110.202119. PMID:21467036.
   PubMed Web of Science ®Google Scholar
• Anderson SJ, Sikes ML, Zhang Y, et al. The transcription elongation factor Spt5 influences transcription by RNA polymerase I positively and negatively. J Biol Chem. 2011 May;286(21):18816–18824. doi:10.1074/jbc.M110.202101. PMID:21467039.
   PubMed Web of Science ®Google Scholar
• Tafur L, Sadian Y, Hoffmann NA, et al. Molecular Structures of Transcribing RNA Polymerase I. Mol Cell. 2016 Dec;64(6):1135–1143. doi:10.1016/j.molcel.2016.11.013. PMID:27867008.
   PubMed Web of Science ®Google Scholar
• Engel C, Sainsbury S, Cheung AC, et al. RNA polymerase I structure and transcription regulation. Nature. 2013 Oct;502(7473):650–655. doi: 10.1038/nature12712. PMID:24153182.
   PubMed Web of Science ®Google Scholar