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. 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.真核基因组可转录生成种类极其丰富的各类RNA。其中部分RNA——尤其是长链非编码RNA（long non-coding RNAs，lncRNAs）——可通过自身转录本结合于染色质，既能滞留于自身转录位点（顺式作用RNA，Cis-acting RNAs），也可被招募至其他基因组区域（反式作用RNA，Trans-acting RNAs），在调控基因转录、表观基因组修饰以及介导染色质状态方面发挥重要作用。本研究开发了TaDRIM-Seq（靶向DNA关联RNA与RNA-RNA相互作用测序，Targeted DNA-associated RNA and RNA-RNA Interactions Mapping by Sequencing）技术，用于捕获细胞核内特定蛋白区域的RNA-DNA相互作用与RNA-RNA空间相互作用。我们分别在水稻中针对组蛋白H3、H3K9ac及H3K27me3，在人类K562细胞中针对H3K4me3与CTCF开展了TaDRIM-Seq实验，以鉴定染色质关联RNA及RNA-RNA相互作用。本研究报道的TaDRIM-Seq技术采用PG-Tn5介导的靶向DNA元件捕获与邻近连接策略，可同时检测基因组不同区域的染色质关联RNA，以及细胞核内的RNA-RNA空间相互作用。