R-loops are three-stranded structures that harbour an RNA-DNA hybrid and frequently form during transcription. R-loop misregulation is associated with DNA damage, transcription elongation defects, hyper-recombination and genome instability. In contrast to such 'unscheduled' R-loops, evidence is mounting that cells harness the presence of RNA-DNA hybrids in scheduled, 'regulatory' R-loops to promote DNA transactions, including transcription termination and other steps of gene regulation, telomere stability and DNA repair. R-loops formed by cellular RNAs can regulate histone post-translational modification and may be recognized by dedicated reader proteins. The two-faced nature of R-loops implies that their formation, location and timely removal must be tightly regulated. In this Perspective, we discuss the cellular processes that regulatory R-loops modulate, the regulation of R-loops and the potential differences that may exist between regulatory R-loops and unscheduled R-loops.

Regulatory R-loops as facilitators of gene expression and genome stability.

R-Loop Mediated trans Action of the APOLO Long Noncoding RNA.

ALBA proteins confer thermotolerance through stabilizing HSF messenger RNAs in cytoplasmic granules

http://www.cell.com/article/S1931312822003171/pdf

A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth.

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.

/pdf/the-r-loop-atlas-of-arabidopsis-development-and-responses-to-4fu4u8pbr5.pdf

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

Phenolic acid-induced phase separation and translation inhibition mediate plant interspecific competition.

Retraction of: The EMBO Journal DOI 10.15252/embj.201694284 | Published online 28.07.2016

The authors have requested retraction of the paper noting: ‘We found a mistake for the materials used …

/pdf/retraction-a-pair-of-transposon-derived-proteins-regulate-55o15jod2h.pdf

Retraction: ‘A pair of transposon‐derived proteins regulate active DNA demethylation in Arabidopsis’

The R-loop, composed of a DNA-RNA hybrid and the displaced single-stranded DNA, regulates diverse cellular processes. However, how cellular R-loops are recognized remains poorly understood. Here, we report the discovery of the evolutionally conserved ALBA proteins (AtALBA1 and AtALBA2) functioning as the genic R-loop readers in Arabidopsis. While AtALBA1 binds to the DNA-RNA hybrid, AtALBA2 associates with single-stranded DNA in the R-loops in vitro. In vivo, these two proteins interact and colocalize in the nucleus, where they preferentially bind to genic regions with active epigenetic marks in an R-loop–dependent manner. Depletion of AtALBA1 or AtALBA2 results in hypersensitivity of plants to DNA damaging agents. The formation of DNA breaks in alba mutants originates from unprotected R-loops. Our results reveal that the AtALBA1 and AtALBA2 protein complex is the genic R-loop reader crucial for genome stability in Arabidopsis.

https://advances.sciencemag.org/content/advances/5/5/eaav9040.full.pdf

ALBA protein complex reads genic R-loops to maintain genome stability in Arabidopsis.

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Papers

ALBA proteins confer thermotolerance through stabilizing HSF messenger RNAs in cytoplasmic granules

Phenolic acid-induced phase separation and translation inhibition mediate plant interspecific competition.

Retraction: ‘A pair of transposon‐derived proteins regulate active DNA demethylation in Arabidopsis’

ALBA protein complex reads genic R-loops to maintain genome stability in Arabidopsis.