The Dynamic Interactions of m6A Modification and R-Loops: Implications for Genome Stability

Abstract

R-loops, three-stranded RNA-DNA hybrid nucleic acid structures, are recognized for their roles in both physiological and pathological processes. Regulation of R-loops is critical for genome stability as disruption of R-loop homeostasis can lead to aberrant gene expression, replication stress, and DNA damage. Recent studies suggest that the RNA modification, N6-methyladenosine (m6A), can modify R-loops and the writers, erasers, and readers of m6A are involved in the dynamic regulation of R-loops. Here, we discuss the reported functions of various m6A regulatory proteins in relation to R-loops, highlighting their distinct roles in recognizing and modulating the formation, stability, and resolution of these structures. We further examine the functional implications of m6A and R-loop interaction in human diseases, with a particular emphasis on their roles in cancer.

Keywords: DNA damage; R-loops; genome stability; m6A RNA modification.

Figure 1

Reciprocal regulation between R-loop dynamics and m6A modification. R-loops can serve as platforms for RNA-binding proteins such as RBM15, which recruit the METTL3-METTL14 m6A methyltransferase complex to deposit m6A marks on nascent RNA within R-loops, using S-adenosylmethionine (SAM) as the methyl donor. The resulting m6A-modified R-loops are recognized by distinct m6A reader proteins such as YTHDC1, YTHDF2, and IGF2BPs. YTHDC1 accumulates at DSB sites, promoting R-loop accumulation and recruiting homologous recombination repair factors such as RAD51 and BRCA1. YTHDF2 facilitates degradation of m6A-marked RNA within R-loops, promoting their resolution. In contrast, IGF2BPs stabilize R-loops by binding m6A-modified RNA and preventing YTHDF2-mediated resolution. Together, these interactions illustrate the dynamic regulation between R-loops and m6A (created with Biorender.com, accessed on 10 June 2025).