A Genome-wide Study On RNA-chromatin Interactions In Arabidopsis Thaliana

The vast majority of RNA molecules are located in the nucleus.Accumulating evidence indicates that various RNA molecules can bind to specific chromatin loci to recruit downstream regulatory factors and regulate gene expression through changing histone modifications or DNA methylation status or reconstructing chromatin structures.Determining the specific binding sites of RNAs on chromatin is crucial for dissecting the functions of nuclear RNAs.Global RNA interactions with DNA by deep sequencing(GRID-seq)is one of the technologies recently developed for genome-wide identification of RNA-chromatin interactions.In this study,we employed GRID-seq to profile RNA-chromatin interactions at genome-wide scale in Arabidopsis seedlings.We identified 40,737RNA-chromatin interaction mediated by protein-coding RNAs,long non-coding RNAs(nc RNAs)and small nc RNAs in Arabidopsis.Whereas protein-coding transcripts primarily engage in local chromosomal interactions,long nc RNAs and small nc RNAs preferentially engage in long-range interactions including cis-chromosomal and trans-chromosomal interactions.The majority of RNAs interact with limited numbers of genomic loci,but a small number of RNAs interact with numerous genomic loci.In the present study,we further show that RNA-chromatin interactions among genes in a common signaling pathway are rich and undergo more extensive alterations in response to biotic and abiotic stresses and a hormonal stimulus.In conclusion,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.We propose that protein-coding RNAs may have other regulatory functions in nucleus in addition to their function of encoding proteins and that stress-inducible RNA-chromatin interactions and the networks of such interactions may play a role in regulating plant responses to stresses.