The R-Loop Atlas of Arabidopsis Development and Responses to Environmental Stimuli

• Published in: The Plant cell Vol. 32; no. 4; pp. 888 - 903
• Main Authors: Xu, Wei, Li, Kuan, Li, Shuai, Hou, Quancan, Zhang, Yushun, Liu, Kunpeng, Sun, Qianwen
• Format: Journal Article
• Language: English
• Published: United States American Society of Plant Biologists 01.04.2020
• Subjects: Arabidopsis - genetics; Arabidopsis - physiology; Conserved Sequence; Environment; Fuzzy Logic; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genetic Loci; Genome, Plant; Large-Scale Biology; R-Loop Structures - genetics; RNA Polymerase III - metabolism; RNA, Plant - genetics; Transcription Initiation Site; Transcription, Genetic
• ISSN: 1040-4651; 1532-298X
• DOI: 10.1105/tpc.19.00802

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 ( ) 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 -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.