Abstract
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.
Highlights
R-loops are chromosomal structures composed of a DNA:RNA hybrid double helix and a single-stranded DNA molecule
To explore the dynamic patterns and interactions of R-loops during development and environmental responses in Arabidopsis, we collected data from four sets of plants grown under various conditions, including different developmental stages, temperatures, light levels, and biotic and abiotic stimuli (Figure 1A; Supplemental Data Set)
Snapshots of R-loops showed that the signals from R-loops formed in the Watson strand of DNA and R-loops formed in the Crick strand of DNA were present in different regions of the DNA, with very little overlap, demonstrating a high degree of strand specificity (Figure 1C)
Summary
R-loops are chromosomal structures composed of a DNA:RNA hybrid double helix and a single-stranded DNA (ssDNA) molecule. An increasing number of studies have revealed that R-loops are unique, prevalent, multifunctional genomic structures that are present in organisms from prokaryotes to eukaryotes (Ginno et al, 2012, 2013; Sun et al, 2013; Skourti-Stathaki et al, 2014; Chen et al, 2015, 2018; SantosPereira and Aguilera, 2015; Al-Hadid and Yang, 2016; Sanz et al, 2016; Wahba et al, 2016). Most studies of plant R-loop function have focused on specific R-loop loci (Santos-Pereira and Aguilera, 2015)
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