Defining R-loop Classes and Their Contributions to Genome Instability

Overview

Journal DNA Repair (Amst)

Publisher Elsevier

Specialties Biochemistry
Molecular Biology

Date 2021 Jul 24

PMID 34303066

Citations 40

Authors

Daisy Castillo-Guzman

Frederic Chedin

Affiliations

Soon will be listed here.

Abstract

R-loops are non-B DNA structures that form during transcription when the nascent RNA anneals to the template DNA strand forming a RNA:DNA hybrid. Understanding the genomic distribution and function of R-loops is an important goal, since R-loops have been implicated in a number of adaptive and maladaptive processes under physiological and pathological conditions. Based on R-loop mapping datasets, we propose the existence of two main classes of R-loops, each associated with unique characteristics. Promoter-paused R-loops (Class I) are short R-loops that form at high frequency during promoter-proximal pausing by RNA polymerase II. Elongation-associated R-loops (Class II) are long structures that occur throughout gene bodies at modest frequencies. We further discuss the relationships between each R-loop class with instances of genome instability and suggest that increased class I R-loops, resulting from enhanced promoter-proximal pausing, represent the main culprits for R-loop mediated genome instability under pathological conditions.

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References

Hartono S, Korf I, Chedin F . GC skew is a conserved property of unmethylated CpG island promoters across vertebrates. Nucleic Acids Res. 2015; 43(20):9729-41. PMC: 4787789. DOI: 10.1093/nar/gkv811. View

Bayona-Feliu A, Barroso S, Munoz S, Aguilera A . The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription-replication conflicts. Nat Genet. 2021; 53(7):1050-1063. DOI: 10.1038/s41588-021-00867-2. View

Morimoto S, Tsuda M, Bunch H, Sasanuma H, Austin C, Takeda S . Type II DNA Topoisomerases Cause Spontaneous Double-Strand Breaks in Genomic DNA. Genes (Basel). 2019; 10(11). PMC: 6895833. DOI: 10.3390/genes10110868. View

Ginno P, Lott P, Christensen H, Korf I, Chedin F . R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell. 2012; 45(6):814-25. PMC: 3319272. DOI: 10.1016/j.molcel.2012.01.017. View

Xu B, Clayton D . A persistent RNA-DNA hybrid is formed during transcription at a phylogenetically conserved mitochondrial DNA sequence. Mol Cell Biol. 1995; 15(1):580-9. PMC: 232017. DOI: 10.1128/MCB.15.1.580. View

Stolz R, Sulthana S, Hartono S, Malig M, Benham C, Chedin F . Interplay between DNA sequence and negative superhelicity drives R-loop structures. Proc Natl Acad Sci U S A. 2019; 116(13):6260-6269. PMC: 6442632. DOI: 10.1073/pnas.1819476116. View

Malig M, Hartono S, Giafaglione J, Sanz L, Chedin F . Ultra-deep Coverage Single-molecule R-loop Footprinting Reveals Principles of R-loop Formation. J Mol Biol. 2020; 432(7):2271-2288. PMC: 7669280. DOI: 10.1016/j.jmb.2020.02.014. View

Verger A, Monte D, Villeret V . Take Your PIC. Trends Biochem Sci. 2021; 46(9):705-707. DOI: 10.1016/j.tibs.2021.05.008. View

Lam F, Kong Y, Huang Q, Vu Han T, Maffa A, Kasper E . BRD4 prevents the accumulation of R-loops and protects against transcription-replication collision events and DNA damage. Nat Commun. 2020; 11(1):4083. PMC: 7428008. DOI: 10.1038/s41467-020-17503-y. View

10.

Sheridan R, Fong N, DAlessandro A, Bentley D . Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5' Pause Release, Termination, and Transcription Elongation Rate. Mol Cell. 2018; 73(1):107-118.e4. PMC: 6320282. DOI: 10.1016/j.molcel.2018.10.031. View

11.

Wang J, Rojas P, Mao J, Sadurni M, Garnier O, Xiao S . Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M. Cell Rep. 2021; 34(7):108759. PMC: 7900609. DOI: 10.1016/j.celrep.2021.108759. View

12.

Xu W, Xu H, Li K, Fan Y, Liu Y, Yang X . The R-loop is a common chromatin feature of the Arabidopsis genome. Nat Plants. 2017; 3(9):704-714. DOI: 10.1038/s41477-017-0004-x. View

13.

DAlessandro G, Whelan D, Howard S, Vitelli V, Renaudin X, Adamowicz M . BRCA2 controls DNA:RNA hybrid level at DSBs by mediating RNase H2 recruitment. Nat Commun. 2018; 9(1):5376. PMC: 6299093. DOI: 10.1038/s41467-018-07799-2. View

14.

Barroso S, Herrera-Moyano E, Munoz S, Garcia-Rubio M, Gomez-Gonzalez B, Aguilera A . The DNA damage response acts as a safeguard against harmful DNA-RNA hybrids of different origins. EMBO Rep. 2019; 20(9):e47250. PMC: 6726908. DOI: 10.15252/embr.201847250. View

15.

Herold S, Kalb J, Buchel G, Ade C, Baluapuri A, Xu J . Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA polymerase. Nature. 2019; 567(7749):545-549. PMC: 7611299. DOI: 10.1038/s41586-019-1030-9. View

16.

Chen L, Chen J, Huang Y, Gu Y, Qiu J, Qian H . The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations. Mol Cell. 2018; 69(3):412-425.e6. PMC: 5957072. DOI: 10.1016/j.molcel.2017.12.029. View

17.

Belotserkovskii B, Shin J, Hanawalt P . Strong transcription blockage mediated by R-loop formation within a G-rich homopurine-homopyrimidine sequence localized in the vicinity of the promoter. Nucleic Acids Res. 2017; 45(11):6589-6599. PMC: 5499740. DOI: 10.1093/nar/gkx403. View

18.

St Germain C, Zhao H, Sinha V, Sanz L, Chedin F, Barlow J . Genomic patterns of transcription-replication interactions in mouse primary B cells. Nucleic Acids Res. 2022; 50(4):2051-2073. PMC: 8887484. DOI: 10.1093/nar/gkac035. View

19.

Sollier J, Cimprich K . Breaking bad: R-loops and genome integrity. Trends Cell Biol. 2015; 25(9):514-22. PMC: 4554970. DOI: 10.1016/j.tcb.2015.05.003. View

20.

Kogoma T . Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Microbiol Mol Biol Rev. 1997; 61(2):212-38. PMC: 232608. DOI: 10.1128/mmbr.61.2.212-238.1997. View