Journal
PLANT CELL
Volume 32, Issue 4, Pages 888-903Publisher
OXFORD UNIV PRESS INC
DOI: 10.1105/tpc.19.00802
Keywords
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Funding
- National Natural Science Foundation of China [91740105, 31822028, 91940306, 31900302, 31971333]
- Ministry of Science and Technology of China [2016YFA0500800]
- Tsinghua-Peking Joint Center for Life Sciences
- 1000 Young Talent Program of China
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R-loops are a common chromatin feature with essential functions in multiple cellular processes and diseases. However, little is known about the dynamic patterns of R-loops in a given organism. Here, using our recently developed genome-wide R-loop profiling method, we generated a comprehensive atlas quantifying the R-loop patterns of Arabidopsis (Arabidopsis thaliana) in 53 samples during development and during responses to environmental stimuli. The R-loop patterns were fairly stable in plants at the vegetative stage and in response to different light spectra and other environmental stimuli. Notably, the R-loops showed turnover during the plant life cycle, with patterns switching between generations. Importantly, R-loop dynamics was not strongly associated with RNA abundance, indicating that the mechanisms regulating R-loop formation and RNA accumulation are independent. We also observed enrichment of R-loops in transcription factor binding regions, suggesting that R-loops could function as potential cis-transcriptional regulators. This study provides an overview of R-loop dynamics in Arabidopsis during development and stress responses, highlights the unique dynamics of R-loops in the flowering plant Arabidopsis, and lays the groundwork for elucidating the functions of R-loops. This study provides the landscape of R-loops in Arabidopsis during development and stress responses and lays the groundwork for future investigation of the diverse functions of R-loops.
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