Global profiling of RNA–chromatin interactions reveals co-regulatory gene expression networks in Arabidopsis

It is increasingly evident that various RNAs can bind chromatin to regulate gene expression and genome organization. Here we adapted a sequencing-based technique to profile RNA–chromatin interactions at a genome-wide scale in Arabidopsis seedlings. We identified more than 10,000 RNA–chromatin interactions mediated by protein-coding RNAs and non-coding RNAs. Cis and intra-chromosomal interactions are mainly mediated by protein-coding RNAs, whereas inter-chromosomal interactions are primarily mediated by non-coding RNAs. Many RNA–chromatin interactions tend to positively correlate with DNA–DNA interactions, suggesting their mutual influence and reinforcement. We further show that some RNA–chromatin interactions undergo alterations in response to biotic and abiotic stresses and that altered RNA–chromatin interactions form co-regulatory networks. Our study provides a global view on RNA–chromatin interactions in Arabidopsis and a rich resource for future investigations of regulatory roles of RNAs in gene expression and genome organization. Genome-wide profiles of RNA–chromatin interactions in Arabidopsis reveal the types of RNAs that mediate cis, intra-chromosomal and inter-chromosomal interactions and suggest the formation of co-regulatory gene expression networks in response to stresses.