The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex
- PMID: 10692458
- DOI: 10.1074/jbc.275.9.6530
The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex
Abstract
The sliding clamp model of transcription processivity, based on extensive studies of Escherichia coli RNA polymerase, suggests that formation of a stable elongation complex requires two distinct nucleic acid components: an 8-9-nt transcript-template hybrid, and a DNA duplex immediately downstream from the hybrid. Here, we address the minimal composition of the processive elongation complex in the eukaryotes by developing a method for promoter-independent assembly of functional elongation complex of S. cerevisiae RNA polymerase II from synthetic DNA and RNA oligonucleotides. We show that only one of the nucleic acid components, the 8-nt RNA:DNA hybrid, is necessary for the formation of a stable elongation complex with RNA polymerase II. The double-strand DNA upstream and downstream of the hybrid does not affect stability of the elongation complex. This finding reveals a significant difference in processivity determinants of RNA polymerase II and E. coli RNA polymerase. In addition, using the imperfect RNA:DNA hybrid disturbed by the mismatches in the RNA, we show that nontemplate DNA strand may reduce the elongation complex stability via the reduction of the RNA:DNA hybrid length. The structure of a "minimal stable" elongation complex suggests a key role of the RNA:DNA hybrid in RNA polymerase II processivity.
Similar articles
-
Overextended RNA:DNA hybrid as a negative regulator of RNA polymerase II processivity.J Mol Biol. 2000 Jun 2;299(2):325-35. doi: 10.1006/jmbi.2000.3755. J Mol Biol. 2000. PMID: 10860741
-
Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination.Mol Cell. 2002 Nov;10(5):1151-62. doi: 10.1016/s1097-2765(02)00738-4. Mol Cell. 2002. PMID: 12453422
-
[Mutations in beta'-subunit of the Escherichia coli RNA-polymerase influence interaction with downstream duplex DNA in the elongation complex].Genetika. 2002 Oct;38(10):1422-7. Genetika. 2002. PMID: 12449654 Russian.
-
The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase.Cell. 1997 Apr 4;89(1):33-41. doi: 10.1016/s0092-8674(00)80180-4. Cell. 1997. PMID: 9094712
-
Molecular basis of RNA-dependent RNA polymerase II activity.Nature. 2007 Nov 15;450(7168):445-9. doi: 10.1038/nature06290. Nature. 2007. PMID: 18004386
Cited by
-
Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence.Mol Cell Biol. 2001 Sep;21(17):5815-25. doi: 10.1128/MCB.21.17.5815-5825.2001. Mol Cell Biol. 2001. PMID: 11486021 Free PMC article.
-
CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3'-end processing factor, Pcf11.Genes Dev. 2005 Jul 1;19(13):1572-80. doi: 10.1101/gad.1296305. Genes Dev. 2005. PMID: 15998810 Free PMC article.
-
Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation.J Biol Chem. 2011 Sep 2;286(35):30898-30910. doi: 10.1074/jbc.M111.260844. Epub 2011 Jul 5. J Biol Chem. 2011. PMID: 21730074 Free PMC article.
-
Biochemical characterization of the helicase Sen1 provides new insights into the mechanisms of non-coding transcription termination.Nucleic Acids Res. 2017 Feb 17;45(3):1355-1370. doi: 10.1093/nar/gkw1230. Nucleic Acids Res. 2017. PMID: 28180347 Free PMC article.
-
Intrinsic translocation barrier as an initial step in pausing by RNA polymerase II.J Mol Biol. 2013 Feb 22;425(4):697-712. doi: 10.1016/j.jmb.2012.12.002. Epub 2012 Dec 10. J Mol Biol. 2013. PMID: 23238253 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Molecular Biology Databases
Research Materials
