The R-loop Atlas of Arabidopsis Development and Responses to Environmental Stimuli
The R-loop Atlas of Arabidopsis Development and Responses to Environmental Stimuli
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拟南芥发育和对环境刺激的反应的 R 环图谱
作者：
Wei Xu;Kuan Li;Shuai Li;Quancan Hou;Yushun Zhang;Kunpeng Liu;Qianwen Sun
R环是一种常见的染色质特征，在多种细胞过程和疾病中具有重要功能。然而，很少有人知道的动态模式的R环在一个给定的有机体。在这里，使用我们最近开发的全基因组R-环分析方法，我们产生了一个全面的图集量化的R-环模式的拟南芥（拟南芥）在53个样品在发展过程中，并在对环境刺激的反应。在植物的营养生长阶段，R-环的模式是相当稳定的，并响应于不同的光谱和其他环境刺激。值得注意的是，R环在植物生命周期中表现出周转，在世代之间切换模式。重要的是，R环动力学与RNA丰度没有强烈的相关性，表明调节R环形成和RNA积累的机制是独立的。我们还观察到丰富的R-环的转录因子结合区域，这表明R-环可以作为潜在的顺式转录调节。本研究综述了拟南芥在发育和胁迫响应过程中的R环动态，突出了开花植物拟南芥中R环的独特动态，为阐明R环的功能奠定了基础。
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.