Genome-wide identification of RNA-chromatin interactions in Arabidopsis

It is increasingly evident that various RNA molecules 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 ten thousand RNA-chromatin interactions mediated by protein-coding RNAs, long non-coding RNAs (ncRNAs) and small ncRNAs in Arabidopsis. These RNAs preferentially target genic regions, especially exonic regions. Protein-coding RNAs primarily engage in local and cis-chromosomal interactions, whereas long ncRNAs (lncRNAs) and small ncRNAs preferentially engage in trans-chromosomal interactions. RNA-chromatin interactions tend to positively correlate with DNA-DNA interactions, suggesting a role of DNA-DNA interactions in confining RNA-chromatin interactions and/or a role of RNA-chromatin interactions in shaping genome organization at a global level. We further show that some RNA-chromatin interactions undergo alterations in response to biotic and abiotic stresses. Our study provides a global view of RNA-chromatin interactions in Arabidopsis and a rich resource for future investigation of the regulatory roles of RNAs in gene expression and genome organization. Overall design: To identify chromatin-associated RNAs and their target sites in Arabidopsis, we conducted GRID-seq using Arabidopsis wild-type Col-0 seedlings. To evaluate the contribution of RNA transcription level to the abundance of RNAs detected in GRID-seq, we conducted global nuclear run-on sequencing (Gro-seq) to detect the levels of nascent RNAs and compared RNA reads in GRID-seq and Gro-seq. To determine the overlap between RNA-chromatin interactions and DNA-DNA interactions, we conducted BL-Hi-C and compared interactions identified by GRID-seq and BL-Hi-C. To determine whether RNA-chromatin interactions are dynamic and respond to environmental cues, we conducted GRID-seq using heat-treated and DC3000-treated seedlings.