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Review
. 2023 Oct 14;15(20):4986.
doi: 10.3390/cancers15204986.

R-Loops in Genome Instability and Cancer

Fang Li  1 , Alyan Zafar  1 , Liang Luo  1 , Ariana Maria Denning  1 , Jun Gu  2 , Ansley Bennett  1 , Fenghua Yuan  1 , Yanbin Zhang  1
Affiliations
Review

R-Loops in Genome Instability and Cancer

Fang Li et al. Cancers (Basel). .

Abstract

R-loops are unique, three-stranded nucleic acid structures that primarily form when an RNA molecule displaces one DNA strand and anneals to the complementary DNA strand in a double-stranded DNA molecule. R-loop formation can occur during natural processes, such as transcription, in which the nascent RNA molecule remains hybridized with the template DNA strand, while the non-template DNA strand is displaced. However, R-loops can also arise due to many non-natural processes, including DNA damage, dysregulation of RNA degradation pathways, and defects in RNA processing. Despite their prevalence throughout the whole genome, R-loops are predominantly found in actively transcribed gene regions, enabling R-loops to serve seemingly controversial roles. On one hand, the pathological accumulation of R-loops contributes to genome instability, a hallmark of cancer development that plays a role in tumorigenesis, cancer progression, and therapeutic resistance. On the other hand, R-loops play critical roles in regulating essential processes, such as gene expression, chromatin organization, class-switch recombination, mitochondrial DNA replication, and DNA repair. In this review, we summarize discoveries related to the formation, suppression, and removal of R-loops and their influence on genome instability, DNA repair, and oncogenic events. We have also discussed therapeutical opportunities by targeting pathological R-loops.

Keywords: DNA repair; R-loops; RNA–DNA hybrid; cancer; double-strand breaks; genome instability; transcription-coupled homologous recombination; transcription–replication conflicts.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Functions of R-loops. (A) R-loops act as a promoter. R-loops formation promotes the binding of tip60-p400 which activates chromatin for transcription. Moreover R-loop formation inhibits the binding of PRC2 which silences chromatin via DNA methyltransferase. TSS: transcription start site. TF: transcription factors. Red cross mark: stalled transcription. (B) Three mechanisms of R-loops as transcriptional termination; (C) R-loops promote antisense transcription to facilitate transcriptional termination; (D) R-loops in DSB repair: (a) DSBs promote R-loops formation. As the R-loop is formed, it recruits RAD52 and BRCA1. BRCA1 recruits BRCA2 and PALB2 which promotes the removal of the RNA from the RNA-DNA hybrids. XPG is then recruited to incise the R-loop which in turn promotes TA-HR. (b) DSBs promote the recruitment of SETX and RAD51 to promote HR at the RNA-DNA hybrid.
Figure 1
Figure 1
Functions of R-loops. (A) R-loops act as a promoter. R-loops formation promotes the binding of tip60-p400 which activates chromatin for transcription. Moreover R-loop formation inhibits the binding of PRC2 which silences chromatin via DNA methyltransferase. TSS: transcription start site. TF: transcription factors. Red cross mark: stalled transcription. (B) Three mechanisms of R-loops as transcriptional termination; (C) R-loops promote antisense transcription to facilitate transcriptional termination; (D) R-loops in DSB repair: (a) DSBs promote R-loops formation. As the R-loop is formed, it recruits RAD52 and BRCA1. BRCA1 recruits BRCA2 and PALB2 which promotes the removal of the RNA from the RNA-DNA hybrids. XPG is then recruited to incise the R-loop which in turn promotes TA-HR. (b) DSBs promote the recruitment of SETX and RAD51 to promote HR at the RNA-DNA hybrid.
Figure 2
Figure 2
R-loops in genome instability. (A) Mechanisms by which HO and CD collisions resolve/stall R-loops. (a) CD collisions resolve and prevent R-loop formation as RNA Pol II moves in the same direction as the DNA strand. (b) HO collision stalls R-loops as RNA Pol II moves in the opposite direction of the DNA strand thus promoting R-loop formation. (B) Mechanisms by which ATR and ATM signaling occurs. (a) Head-on collisions promote ATR signaling as RPA binds to ssDNA recruiting ATR. (b) Co-direction promotes ATM signaling via DSBs and nuclease activity. (c) ATM and ATR signaling is also promoted without the presence of replication forks. Stalled RNA Pol II recruits ATM whereas regular RNA Pol II recruits RPA and ATR. Gray arrows: direction of replication. Orange arrows: direction of transcription.
Figure 2
Figure 2
R-loops in genome instability. (A) Mechanisms by which HO and CD collisions resolve/stall R-loops. (a) CD collisions resolve and prevent R-loop formation as RNA Pol II moves in the same direction as the DNA strand. (b) HO collision stalls R-loops as RNA Pol II moves in the opposite direction of the DNA strand thus promoting R-loop formation. (B) Mechanisms by which ATR and ATM signaling occurs. (a) Head-on collisions promote ATR signaling as RPA binds to ssDNA recruiting ATR. (b) Co-direction promotes ATM signaling via DSBs and nuclease activity. (c) ATM and ATR signaling is also promoted without the presence of replication forks. Stalled RNA Pol II recruits ATM whereas regular RNA Pol II recruits RPA and ATR. Gray arrows: direction of replication. Orange arrows: direction of transcription.
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