Downstream Boundary of Chromosomal R-loops at Murine Switch Regions: Implications for the Mechanism of Class Switch Recombination

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2006 Mar 21

PMID 16547142

Citations 39

Authors

Feng-Ting Huang

Kefei Yu

Chih-Lin Hsieh

Michael R Lieber

Affiliations

Soon will be listed here.

Abstract

R-loops form at Sgamma3 and Sgamma2b Ig class switch regions in the chromosomes of stimulated murine primary B cells and are suspected to be a general feature of mammalian class switch regions. The in vivo upstream boundary of the R-loops is known to begin within the switch repeats. To determine how precisely the R-loop structure conforms to the repetitive zone of the murine Sgamma3 and Sgamma2b switch regions, a chemical probing method was used to obtain structural information on the downstream boundary. We find that only 61-67% of the R-loops terminate within the Sgamma3 and the Sgamma2b repetitive zones, and the remainder terminate downstream, usually within the first 600 bp immediately downstream of the core switch repeats. Interestingly, the nontemplate strand G density falls to the random level gradually through this same region. Hence, the R-loops terminate as the G-richness of the nascent RNA strand falls. This finding is consistent with thermodynamic predictions for RNA:DNA duplex strength relative to that of DNA:DNA duplexes. This result contrasts with the location of known recombination breakpoints, which correlate not with G-richness and R-loop location but rather with AGCT density. The implications of these findings are discussed in the context of models for the targeting of class switch recombination.

Citing Articles

Mapping R-Loops and RNA:DNA Hybrids with S9.6-Based Immunoprecipitation Methods.

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Emerging roles for R-loop structures in the management of topological stress.

Chedin F, Benham C J Biol Chem. 2020; 295(14):4684-4695.

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Ultra-deep Coverage Single-molecule R-loop Footprinting Reveals Principles of R-loop Formation.

Malig M, Hartono S, Giafaglione J, Sanz L, Chedin F J Mol Biol. 2020; 432(7):2271-2288.

PMID: 32105733 PMC: 7669280. DOI: 10.1016/j.jmb.2020.02.014.

Current insights into the mechanism of mammalian immunoglobulin class switch recombination.

Yu K, Lieber M Crit Rev Biochem Mol Biol. 2019; 54(4):333-351.

PMID: 31509023 PMC: 6856442. DOI: 10.1080/10409238.2019.1659227.

Interplay between DNA sequence and negative superhelicity drives R-loop structures.

Stolz R, Sulthana S, Hartono S, Malig M, Benham C, Chedin F Proc Natl Acad Sci U S A. 2019; 116(13):6260-6269.

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