Interplay of DNA and RNA N6-methyladenine with R-loops in regulating gene transcription in Arabidopsis |
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Authors: | Pengyue Zhang Jingjing Gao Xinxu Li Yilong Feng Manli Shi Yining Shi Wenli Zhang |
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Affiliation: | 1.State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095 People’s Republic of China ;2.College of agronomy, Nanjing Agricultural University , Nanjing, 210095 People’s Republic of China |
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Abstract: | R-loops and covalent modifications of N6-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 InformationThe online version contains supplementary material available at 10.1007/s12298-021-01010-5. |
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Keywords: | R-loops, DNA-6 mA, RNA-m6A, Histone marks, Gene transcription, Plants |
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