R‐loops act as regulatory switches modulating transcription of COLD‐responsive genes in rice

Abstract

Summary COLD is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in crops. R‐loops function in various cellular processes, including development and stress responses, in plants. However, how R‐loops function in COLD responses is largely unknown in COLD susceptible crops like rice (Oryza sativa L.). We conducted DRIP‐Seq along with other omics data (RNA‐Seq, DNase‐Seq and ChIP‐Seq) in rice with or without COLD treatment. COLD treatment caused R‐loop reprogramming across the genome. COLD‐biased R‐loops had higher GC content and novel motifs for the binding of distinct transcription factors (TFs). Moreover, R‐loops can directly/indirectly modulate the transcription of a subset of COLD‐responsive genes, which can be mediated by R‐loop overlapping TF‐centered or cis‐regulatory element‐related regulatory networks and lncRNAs, accounting for c. 60% of COLD‐induced expression of differential genes in rice, which is different from the findings in Arabidopsis. We validated two R‐loop loci with contrasting (negative/positive) roles in the regulation of two individual COLD‐responsive gene expression, as potential targets for enhanced COLD resistance. Our study provides detailed evidence showing functions of R‐loop reprogramming during COLD responses and provides some potential R‐loop loci for genetic and epigenetic manipulation toward breeding of rice varieties with enhanced COLD tolerance.