Impairment of transcription elongation by R-loops in vitro

Biochemical and Biophysical Research Communications

Volumn 360, Issue 2, 2007, Pages 428-432

  Tous, Cristina ^a   Aguilera, Andrés ^a  

^a UNIVERSITY OF SEVILLE   (Spain)

Author keywords

DNA RNA hybrid; In vitro transcription; R loops; RNA; RNA polymerase II; S. cerevisiae; Transcription elongation

Indexed keywords

RNA POLYMERASE;

ARTICLE; DNA HELIX; DNA RNA HYBRIDIZATION; DNA STRAND; DNA STRAND BREAKAGE; DNA SUPERCOILING; MUTANT; NONHUMAN; PRIORITY JOURNAL; TRANSCRIPTION INITIATION; YEAST;

DNA DAMAGE; DNA, FUNGAL; RNA, FUNGAL; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ELONGATION FACTORS;

EID: 34447267682     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2007.06.098     Document Type: Article

References (26)

1. Erie D.A. The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription. Biochim. Biophys. Acta 1577 (2002) 224-239
2. Shilatifard A., Conaway R.C., and Conaway J.W. The RNA polymerase II elongation complex. Annu. Rev. Biochem. 72 (2003) 693-715
3. Kireeva M.L., Komissarova N., and Kashlev M. Overextended RNA: DNA hybrid as a negative regulator of RNA polymerase II processivity. J. Mol. Biol. 299 (2000) 325-335
4. Kettenberger H., Armache K.J., and Cramer P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 16 (2004) 955-965
5. Aguilera A. mRNA processing and genomic instability. Nat. Struct. Mol. Biol. 12 (2005) 737-738
6. Yu K., Chedin F., Hsieh C.L., Wilson T.E., and Lieber M.R. R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nat. Immunol. 4 (2003) 442-451
7. Huertas P., and Aguilera A. Cotranscriptionally formed DNA:RNA hybrids mediate transcription-elongation impairment and transcription-associated recombination. Mol. Cell 12 (2003) 711-721
8. Li X., and Manley J.L. New talents for an old acquaintance: the SR protein splicing factor ASF/SF2 functions in the maintenance of genome stability. Cell Cycle 4 (2005) 1706-1708
9. Krohn M., Pardon B., and Wagner R. Effects of template topology on RNA polymerase pausing during in vitro transcription of the Escherichia coli rrnB leader region. Mol. Microbiol. 6 (1992) 581-589
10. Hraiky C., Raymond M.A., and Drolet M. RNase H overproduction corrects a defect at the level of transcription elongation during rRNA synthesis in the absence of DNA topoisomerase I in Escherichia coli. J. Biol. Chem. 275 (2000) 11257-11263
11. Baaklini I., Hraiky C., Rallu F., Tse-Dinh Y.C., and Drolet M. RNase HI overproduction is required for efficient full-length RNA synthesis in the absence of topoisomerase I in Escherichia coli. Mol. Microbiol. 54 (2004) 198-211
12. Gopal V., Brieba L.G., Guajardo R., McAllister W.T., and Sousa R. Characterization of structural features important for T7 RNAP elongation complex stability reveals competing complex conformations and a role for the non-template strand in RNA displacement. J. Mol. Biol. 290 (1999) 411-431
13. Bentin T., Cherny D., Larsen H.J., and Nielsen P.E. Transcription arrest caused by long nascent RNA chains. Biochim. Biophys. Acta 1727 (2005) 97-105
14. Phoenix P., Raymond M.A., Masse E., and Drolet M. Roles of DNA topoisomerases in the regulation of R-loop formation in vitro. J. Biol. Chem. 272 (1997) 1473-1479
15. Chavez S., and Aguilera A. The yeast HPR1 gene has a functional role in transcriptional elongation that uncovers a novel source of genome instability. Genes Dev. 11 (1997) 3459-3470
16. Mason P.B., and Struhl K. Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol. Cell 17 (2005) 831-840
17. Rondon A.G., Jimeno S., Garcia-Rubio M., and Aguilera A. Molecular evidence that the eukaryotic THO/TREX complex is required for efficient transcription elongation. J. Biol. Chem. 278 (2003) 39037-39043
18. Jimeno S., Rondon A.G., Luna R., and Aguilera A. The yeast THO complex and mRNA export factors link RNA metabolism with transcription and genome instability. EMBO J. 21 (2002) 3526-3535
19. Vioque A., Arnez J., and Altman S. Protein-RNA interactions in the RNase P holoenzyme from Escherichia coli. J. Mol. Biol. 202 (1988) 835-848
20. Lee D.Y., and Clayton D.A. Properties of a primer RNA-DNA hybrid at the mouse mitochondrial DNA leading-strand origin of replication. J. Biol. Chem. 271 (1996) 24262-24269
21. Schultz M.C., Choe S.Y., and Reeder R.H. Specific initiation by RNA polymerase I in a whole-cell extract from yeast. Proc. Natl. Acad. Sci. USA 88 (1991) 1004-1008
22. Lopez de Heredia M., and Jansen R.P. RNA integrity as a quality indicator during the first steps of RNP purifications: a comparison of yeast lysis methods. BMC Biochem. 5 (2004) 14
23. Woontner M., Wade P.A., Bonner J., and Jaehning J.A. Transcriptional activation in an improved whole-cell extract from Saccharomyces cerevisiae. Mol. Cell Biol. 11 (1991) 4555-4560
24. Rondon A.G., Garcia-Rubio M., Gonzalez-Barrera S., and Aguilera A. Molecular evidence for a positive role of Spt4 in transcription elongation. EMBO J. 22 (2003) 612-620
25. Li X., and Manley J.L. Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 122 (2005) 365-378
26. Kaneko S., and Manley J.L. The mammalian RNA polymerase II C-terminal domain interacts with RNA to suppress transcription-coupled 3′ end formation. Mol. Cell 20 (2005) 91-103