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Sources, resolution and physiological relevance of R-loops and RNA–DNA hybrids

An Author Correction to this article was published on 05 May 2022

This article has been updated

Abstract

RNA–DNA hybrids are generated during transcription, DNA replication and DNA repair and are crucial intermediates in these processes. When RNA–DNA hybrids are stably formed in double-stranded DNA, they displace one of the DNA strands and give rise to a three-stranded structure called an R-loop. R-loops are widespread in the genome and are enriched at active genes. R-loops have important roles in regulating gene expression and chromatin structure, but they also pose a threat to genomic stability, especially during DNA replication. To keep the genome stable, cells have evolved a slew of mechanisms to prevent aberrant R-loop accumulation. Although R-loops can cause DNA damage, they are also induced by DNA damage and act as key intermediates in DNA repair such as in transcription-coupled repair and RNA-templated DNA break repair. When the regulation of R-loops goes awry, pathological R-loops accumulate, which contributes to diseases such as neurodegeneration and cancer. In this Review, we discuss the current understanding of the sources of R-loops and RNA–DNA hybrids, mechanisms that suppress and resolve these structures, the impact of these structures on DNA repair and genome stability, and opportunities to therapeutically target pathological R-loops.

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Fig. 1: Sources of R-loops and other RNA–DNA hybrids (part I).
Fig. 2: Sources of R-loops and other RNA–DNA hybrids (part II).
Fig. 3: Effects of R-loops and RNA–DNA hybrids on genome stability.
Fig. 4: Mechanisms of R-loop suppression and resolution.
Fig. 5: Roles of R-loops and RNA–DNA hybrids in DNA repair.
Fig. 6: R-loops in pathology.
Fig. 7: Targeting R-loop-associated vulnerabilities in cancer therapy.

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Acknowledgements

We apologize to those authors whose work could not be cited due to space constrains. E.P. is supported by Cancer Research UK (C25526/A28275) and Medical Research Council (MR/S021310/1). L.L. is supported by the NIH (GM118833). L.Z. is the James & Patricia Poitras Endow Chair for Cancer Research and support by the NIH (CA263934).

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Glossary

Transcription–replication conflicts

Refers to collisions between transcription and DNA replication complexes and their consequences in both transcription and DNA replication.

Class switch recombination

The process of switching the antibody type produced by mature B cells, during which the immunoglobulin gene is subject to transcription-dependent DNA damage followed by repair-mediated rearrangements.

C-rich strand of telomere DNA

Telomere DNA consists of TTAGGG repeats on the G-rich strand and CCCTAA repeats on the C-rich strand.

Replication stress

A plethora of DNA replication impediments that compromise the efficiency or fidelity of DNA synthesis and increase genomic instability.

Control region of mtDNA

A non-coding region of the mitochondrial genome that controls RNA and DNA synthesis.

Replication fork reversal

Backward movement of the replication fork during which the nascent newly synthesized strands dissociate from the template strands and anneal together to form a four-way junction.

G-quadruplexes

(G4s). DNA secondary structures formed by guanine (G)-rich sequences through G–G base pairing.

Backtracking

Backward movement of transcribing RNA polymerase, which enables proofreading and regulation of transcript elongation.

Integrator complex

A multisubunit protein complex with RNA endonuclease activity that controls the expression and processing of RNA polymerase II (Pol II) transcripts.

RNA exosome

A multisubunit protein complex with 3′-5′exoribonuclease activity that degrades non-coding Pol II transcripts.

Break-induced replication

(BIR). A process in which one-ended DNA breaks generated at replication forks are extended using homologous DNA as template.

DNA end resection

A process in which exonucleases cleave one of the DNA strands at DNA double-stranded breaks to generate overhangs.

Donor DNA

The DNA sequence used as template for DNA repair during homologous recombination.

Translesion synthesis

A process in which a group of specialized DNA polymerases at or behind replication forks bypass DNA lesions to ensue replication.

RNA editing

Post-transcriptional enzymatic process that changes RNA nucleotides, for example, by deaminating adenosine to inosine.

Cerebellar ataxias

Progressive neurological disorders caused by damage to the cerebellum, characterized by inability to control balance, gait and muscle coordination.

cGAS–STING pathway

Cellular signalling pathway that senses DNA in the cytoplasm as a sign of viral or bacterial infection and activates innate immunity responses.

Nonsense-mediated mRNA decay

(NMD). A cellular surveillance mechanism that detects and degrades mRNAs harbouring premature termination codons.

Tumour-treating electric fields

A non-invasive treatment, in which alternating electric fields are applied to tumour sites to inhibit cancer cell proliferation.

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Petermann, E., Lan, L. & Zou, L. Sources, resolution and physiological relevance of R-loops and RNA–DNA hybrids. Nat Rev Mol Cell Biol 23, 521–540 (2022). https://doi.org/10.1038/s41580-022-00474-x

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