Interplay of DNA and RNA N ⁶ -methyladenine with R-loops in regulating gene transcription in Arabidopsis

R-loops and covalent modifications of N ⁶ -methyladenine on DNA (D-6 mA) or RNA (R-m⁶A) have been documented to function in various cellular processes in eukaryotes. However, the relationships between R-loops and both covalent modifications are still elusive in plants. Here, we integrated existing ssDRIP-seq with D-6 mA and R-m⁶A data from Arabidopsis thaliana. We found that the presence of either of both modifications facilitates R-loop formation and transcription of overlapping genes. Interestingly, our study suggests that the presence of R-m⁶A is key to affect R-loop intensity and positively regulate gene transcription. Moreover, the presence of D-6 mA plays an additive role to facilitate the effect of R-m⁶A on R-loop intensity, however, D-6 mA may negatively regulate gene transcription when coexisted with R-m⁶A. Our analyses indicate that D-6 mA, R-m⁶A, or histone marks may act individually and cooperatively with R-loops in regulating gene transcription. Our study is the first to link R-loops with D-6 mA and R-m⁶A in plants, thereby providing new insights into interactions between R-loops with D-6 mA, R-m⁶A, and histone marks for regulating gene transcription.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-021-01010-5.