Toward an understanding of the detection and function of R-loops in plants.

Although lagging behind studies in humans and other mammals, R-loop studies in plants have recently entered an exciting stage in which the roles of R-loops in gene expression, genome stability, epigenomic signatures, and plant development and stress responses are being elucidated. Here, we reviewed the strengths and weaknesses of existing methodologies, which were largely developed for R-loop studies in mammals, and then we discussed the potential challenges of applying these methodologies to R-loop studies in plants. We then focused on recent advances in the functional characterization of R-loops in Arabidopsis thaliana and rice. Recent studies in plants indicate that there are coordinated relationships between R-loops and gene expression, and between R-loops and epigenomic signatures that depend, in part, on the types of R-loops involved. Finally, the emerging roles of R-loops in plants and directions for future research were discussed.