GSE163115
The landscape of H3K4me3 associated interactions between chromatin and RNAs in rice [ChRD-PET]
High-order rice chromatin contains numerous interactions among DNA, RNA and protein to regulate critical biological processes in various aspects of rice life. We developed an effective method for mapping histone-mediated chromatin associated RNA-DNA interactions, followed by paired-end-tag sequencing (ChRD-PET) in rice. With H3K4me3-mediated ChRD-PET, H3  ChRD-PET and RNase H treated H3K4me3-mediated ChRD-PET data, we present a highly comprehensive map of RNA and chromatin interactions in rice MH63.  Through integrating ChIA-PET (published data) , ChRD-PET and ssDRIP-seq data analysis, we demonstrated the function of RNAs-chromatin interactions in different level. We also conducted ATAC-seq and integrative analysis uncovered the relationship of epigenetic modification and ChRD-PET interactions. Our findings  revealed the map and features of RNAs-chromatin interactions in rice. Overall design: Here, we developed a method for mapping  histone-mediated chromatin associated RNA-DNA interactions followed by paired-end-tag sequencing (ChRD-PET)  and  generate H3K4me3-mediated ChRD-PET data in rice. We also performed R-loop positions by ssDRIP-seq, whole-transcriptome by RNA-seq, and chromatin accessibility by ATAC-seq. Together, we revealed the map and features of RNAs-chromatin interactions in rice.