Open AccessInterplay of DNA and RNA N6-methyladenine with R-loops in regulating gene transcription in Arabidopsis
Author(s) -
Pengyue Zhang,
Jingjing Gao,
Xinxu Li,
Yilong Feng,
Minmin Shi,
Yining Shi,
Wenli Zhang
Publication year - 2021
Publication title -
physiology and molecular biology of plants/physiology and molecular biology of plants
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.754
H-Index - 35
eISSN - 0971-5894
pISSN - 0974-0430
DOI - 10.1007/s12298-021-01010-5
Subject(s) - transcription (linguistics) , gene , biology , histone , arabidopsis , genetics , dna , rna , transcription factor , eukaryotic transcription , microbiology and biotechnology , gene expression , promoter , mutant , philosophy , linguistics
R-loops and covalent modifications of N 6 -methyladenine on DNA (D-6 mA) or RNA (R-m 6 A) 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-m 6 A 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-m 6 A 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-m 6 A on R-loop intensity, however, D-6 mA may negatively regulate gene transcription when coexisted with R-m 6 A. Our analyses indicate that D-6 mA, R-m 6 A, 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-m 6 A in plants, thereby providing new insights into interactions between R-loops with D-6 mA, R-m 6 A, and histone marks for regulating gene transcription.