| Competition between the RNA transcript and the nontemplate DNA strand during R-loop formation in vitro: a nick can serve as a strong R-loop initiation site. | |
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MedLine Citation:
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PMID: 19841062 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Upon transcription of some sequences by RNA polymerases in vitro or in vivo, the RNA transcript can thread back onto the template DNA strand, resulting in an R loop. Previously, we showed that initiation of R-loop formation at an R-loop initiation zone (RIZ) is favored by G clusters. Here, using a purified in vitro system with T7 RNA polymerase, we show that increased distance between the promoter and the R-loop-supporting G-rich region reduces R-loop formation. When the G-rich portion of the RNA transcript is downstream from the 5' end of the transcript, the ability of this portion of the transcript to anneal to the template DNA strand is reduced. When we nucleolytically resect the beginning of the transcript, R-loop formation increases because the G-rich portion of the RNA is now closer to the 5' end of the transcript. Short G-clustered regions can act as RIZs and reduce the distance-induced suppression of R-loop formation. Supercoiled DNA is known to favor transient separation of the two DNA strands, and we find that this favors R-loop formation even in non-G-rich regions. Most strikingly, a nick can serve as a strong RIZ, even in regions with no G richness. This has important implications for class switch recombination and somatic hypermutation and possibly for other biological processes in transcribed regions. |
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Authors:
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Deepankar Roy; Zheng Zhang; Zhengfei Lu; Chih-Lin Hsieh; Michael R Lieber |
Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural |
Journal Detail:
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Title: Molecular and cellular biology Volume: 30 ISSN: 1098-5549 ISO Abbreviation: Mol. Cell. Biol. Publication Date: 2010 Jan |
Date Detail:
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Created Date: 2009-12-16 Completed Date: 2010-01-14 Revised Date: 2010-09-28 |
Medline Journal Info:
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Nlm Unique ID: 8109087 Medline TA: Mol Cell Biol Country: United States |
Other Details:
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Languages: eng Pagination: 146-59 Citation Subset: IM |
Affiliation:
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Department of Pathology, USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089-9176, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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5' Flanking Region DNA / chemistry, genetics* DNA Breaks, Single-Stranded* DNA, Superhelical / chemistry, genetics DNA-Directed RNA Polymerases / chemistry RNA / chemistry, genetics* Templates, Genetic Transcription Initiation Site Transcription, Genetic* Viral Proteins / chemistry |
| Chemical | |
Reg. No./Substance:
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0/DNA, Superhelical; 0/Viral Proteins; 63231-63-0/RNA; 9007-49-2/DNA; EC 2.7.7.-/bacteriophage T7 RNA polymerase; EC 2.7.7.6/DNA-Directed RNA Polymerases |
| Comments/Corrections | |
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