Simultaneous Profiling of Chromatin-Associated RNA at Targeted DNA Loci and RNA-RNA Interactions through TaDRIM-Seq
The enormous variety of different RNAs are transcribed from eukaryotic genome. Some RNAs, particular long non-coding RNAs (lncRNAs),  enrich on chromatin via transcribed RNAs to retain at their transcription site (Cis-acting RNAs) and recruited to different genomic regions (Trans-acting RNAs), which play significant roles in regulating gene transcription, epigenomic modifications and mediating chromatin states. Here, we developed TaDRIM-Seq (Targeted DNA-associated RNA and RNA-RNA Interactions Mapping by Sequencing) method to capture RNA-DNA  on specific protein region and RNA-RNA spatial interactions in nuclei. We performed TaDRIM-Seq of antibodies H3, H3K9ac and H3K27me3 in rice and H3K4me3 and CTCF in human K562 cells, to identify chromatin-interacting RNAs and RNA-RNA interactions. Overall design: We report TaDRIM-Seq technique PG-Tn5-mediated targeted DNA element and proximity ligation to simultaneously detect chromatin-associated RNAs in diverse regions of the genome and RNA-RNA spatial interactions in nuclei.