R‐loop: The new genome regulatory element in plants

Abstract

An R‐loop is a three‐stranded chromatin structure that consists of a displaced single strand of DNA and an RNA:DNA hybrid duplex, which was thought to be a rare by‐product of transcription. However, recent genome‐wide data have shown that R‐loops are widespread and pervasive in a variety of genomes, and a growing body of experimental evidence indicates that R‐loops have both beneficial and harmful effects on an organism. To maximize benefit and avoid harm, organisms have evolved several means by which they tightly regulate R‐loop levels. Here, we summarize our current understanding of the biogenesis and effects of R‐loops, the mechanisms that regulate them, and methods of R‐loop profiling, reviewing recent research advances on R‐loops in plants. Furthermore, we provide perspectives on future research directions for R‐loop biology in plants, which might lead to a more comprehensive understanding of R‐loop functions in plant genome regulation and contribute to future agricultural improvements.

DDM1-mediated R-loop resolution and H2A.Z exclusion facilitates heterochromatin formation in Arabidopsis

“…Prevention and resolution of R-loops can occur through RNA processing factors, DNA topoisomerases, RNA:DNA helicases, ribonuclease H (RNase H) enzymes, as well as chromatin remodelers [reviewed in (21)]. We had developed an efficient R-loop profiling method ssDRIP-seq (single-strand DNA ligation-based library construction from RNA:DNA hybrid immunoprecipitation, followed by sequencing), which had been applied in multiple species to characterize R-loop formation and dynamic pattern genome-widely [ (22)(23)(24)(25)(26)(27)(28)(29)(30), reviewed in (31)]. Unexpectedly, we found that a large proportion of R-loops is correlated with H3K9me2 and H3K27me1 heterochromatic marks in Arabidopsis (22); however, the biological relevance of these observations was not clear.…”