Dataset Information

GRID-seq reveals the global RNA-chromatin interactome.

ABSTRACT: 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.

SUBMITTER: Li X

PROVIDER: S-EPMC5953555 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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GRID-seq reveals the global RNA-chromatin interactome.

Li Xiao X Zhou Bing B Chen Liang L Gou Lan-Tao LT Li Hairi H Fu Xiang-Dong XD

Nature biotechnology 20170918 10

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-s ...[more]

PMID: 28922346

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Dataset Information

GRID-seq reveals the global RNA-chromatin interactome.

Publications

GRID-seq reveals the global RNA-chromatin interactome.

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