The landscape of H3K4me3 associate interactions between chromatin and RNAs in rice [ssDRIP-seq]

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 ChRD-PET, H3 ChRD-PET and RNase H treated H3K4me3 ChRD-PET, we present a highly comprehensive map of RNA and chromatin interactions around promoters 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 modifications and ChRD-PET interactions. Our findings firstly revealed the map and features of RNAs-chromatin interactions in rice. 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. Total RNA was isolated from seedlings at 8:00AM using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. 2µg of total RNA was depleted of ribosomal RNAs using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, RS-122-2401) for RNA-seq according to the manufacturer’s instructions. RNA sequencing was performed on an Illumina HiSeq X Ten system (paired-end 150 bp reads).