Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions

RNA-RNA spatial interactions play crucial roles in various cellular processes, including gene transcriptional and post-transcriptional regulations. However, research on this area of RNA regulation remains limited in plants.

Here, we adapt the global RNA-RNA interaction mapping method for plants and develop plant RNA in situ conformation sequencing, pRIC-seq, to generate comprehensive RNA-RNA spatial interaction maps for diploid and tetraploid cotton. We also perform global nuclear run-on followed by cap-selection assay, GRO-cap, and integrate multi-omics data to construct enhancer landscapes in these cotton species. Focusing on enhancer-promoter (E-P) RNA interactions, we find that tetraploid cotton, following polyploidy, innovates numerous novel E-P RNA interactions, thereby increasing its genomic regulatory complexity. Comparative analyses between wild-type and mutant fuzzless/lintless in tetraploid cotton reveal that RNA-RNA interactions, including E-P RNA interactions, play pivotal roles in fiber development. Our study also identifies short tandem repeats and transposable elements as potential mediators of E-P RNA interactions through base pairing within the cotton genome. Finally, integrating with genome-wide association studies (GWAS) and eQTLs from previous studies, we observe that our RNA-RNA interactions are significantly enriched near those functional mutation sites. Importantly, by using RAP-qPCR, we confirm that GWAS related enhancers interact with the promoters of protein-coding genes, explaining their regulatory mechanisms in fiber trait control.

Our results provide the first genome-wide RNA-RNA interaction map in higher plants and offer valuable insights into the enhancer-regulated pathway and targets for future breeding studies.