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.

R环是常见的染色质特征，在多种细胞过程和疾病中具有必不可少的功能。然而，对于给定生物中R环的动态模式知之甚少。在这里，使用我们最近开发的全基因组R环分析方法，我们生成了一个完整的图集，量化了拟南芥（Arabidopsis thaliana）的R环模式）在开发过程中以及对环境刺激的反应中共53个样品。在营养阶段以及对不同光谱和其他环境刺激的响应中，R环模式在植物中相当稳定。值得注意的是，R环显示了植物生命周期中的周转率，并且模式在世代之间切换。重要的是，R环动力学与RNA的丰度没有强烈关联，表明调节R环形成和RNA积累的机制是独立的。我们还观察到转录因子结合区中R环的富集，这表明R环可能起潜在的顺式作用-转录调节剂。这项研究概述了拟南芥在发育和胁迫响应过程中的R-环动力学，突出了开花植物拟南芥中R-环的独特动力学，并为阐明R-环的功能奠定了基础。