R-loops' m6A modification and its roles in cancers

Abstract

R-loops are three-stranded nucleic acid structures composed of an RNA-DNA hybrid and a displaced DNA strand. They are widespread and play crucial roles in regulating gene expression, DNA replication, and DNA and histone modifications. However, their regulatory mechanisms remain unclear. As R-loop detection technology advances, changes in R-loop levels have been observed in cancer models, often associated with transcription-replication conflicts and genomic instability. N6-methyladenosine (m6A) is an RNA epigenetic modification that regulates gene expression by affecting RNA localization, splicing, translation, and degradation. Upon reviewing the literature, we found that R-loops with m6A modifications are implicated in tumor development and progression. This article summarizes the molecular mechanisms and detection methods of R-loops and m6A modifications in gene regulation, and reviews recent research on m6A-modified R-loops in oncology. Our goal is to provide new insights into the origins of genomic instability in cancer and potential strategies for targeted therapy.

Keywords: Cancer; Gene expression; M6A modification; R-loop.

Fig. 1

IGF2BPs regulate R-loop metabolism in an m6A-dependent manner, leading to inhibition of cell migration and growth retardation in PCa. A Without IGF2BPs, YTHDF2 preferentially binds to R-loops containing m6A, leading to the elimination of R-loops. DNMT1 binds directly to the promoter of SEMA3F, forming CpG islands and inhibiting SEMA3F transcription. B IGF2BPs selectively bind to m6A-modified R-loops and cause R‑loop accumulation. IGF2BPs also upregulate SEMA3F expression via repelling DNMT1 and YTHDF2. SEMA3s, the expression products of SEMA3F, activate the Hippo pathway and inhibit tumorigenesis, angiogenesis, and tissue growth suppression

Fig. 2

m6A-modified R-loops and DNA damage are elevated in DDX41-mutated CD34 + cells of MDS patients. A In normal cells, DDX41 promotes the recruitment of YTHDC1 to the R-loops by facilitating the binding of the m6A complex to YTHDC1, thus participating in the DDR induced by R-loops and maintaining genome stability. B In DDX41-deficient cells, the binding affinity between YTHDC1 and METTL3/METTL14 is impaired, which results in the accumulation of R-loops and increased DNA damage, ultimately leading to genome instability and the onset of MDS

Fig. 3

METTL3-mediated TERRA m6A modification plays a role in telomere maintenance of ALT + NB. METTL3 catalyzes m6A modification of TERRA repeats containing UUAGGG and the m6A reader hnRNPA2B1 recognizes m6A. Subsequently, the m6A-modified TERRA invades telomeric DNA, leading to the formation of R-loops. This, in turn, promotes telomere maintenance in ALT + cells through HR

Fig. 4

The ARID1A-METTL3-m6A axis ensures effective RNase H1-mediated resolution of R-loops and genome stability. A Chromatin-enriched ARID1A recruits METTL3 and METTL14 to R-loops, catalyzing the m6A modification of RNA on the chromatin of the DNA DSB side in an ATM-dependent manner, and promotes HR repair in response to DNA damage. RNase H1 binds preferentially to m6A-modified R-loops and assists in their decomposition to maintain genome stability. B ARID1A deficiency results in HR defects, leading to disorders in R-loops clearance and chromatin homeostasis disruptions