Higher eukaryotic genomes are bound by a large number of coding and non-coding RNAs, but approaches to comprehensively map the identity and binding sites of these RNAs are lacking. Here we report a method to capture in situ global RNA interactions with DNA by deep sequencing (GRID-seq), which enables the comprehensive identification of the entire repertoire of chromatin-interacting RNAs and their respective binding sites. In human, mouse, and Drosophila cells, we detected a large set of tissue-specific coding and non-coding RNAs that are bound to active promoters and enhancers, especially super-enhancers. Assuming that most mRNA-chromatin interactions indicate the physical proximity of a promoter and an enhancer, we constructed a three-dimensional global connectivity map of promoters and enhancers, revealing transcription-activity-linked genomic interactions in the nucleus.

中文翻译：

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GRID-seq揭示了全球RNA染色质相互作用组。

较高水平的真核生物基因组受大量编码和非编码RNA的束缚，但缺乏全面绘制这些RNA的身份和结合位点的方法。在这里，我们报告了一种通过深度测序（GRID-seq）捕获与DNA原位全局RNA相互作用的方法，该方法能够全面鉴定与染色质相互作用的RNA的整个库及其各自的结合位点。在人，小鼠和果蝇细胞中，我们检测到大量与活性启动子和增强子（特别是超级增强子）结合的组织特异性编码和非编码RNA。假设大多数mRNA-染色质相互作用表明启动子和增强子的物理接近性，我们构建了启动子和增强子的三维全局连接图，