GRID-seq reveals the global RNA-chromatin interactome

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Reproducibility of some plots from GRID-Seq paper

Authors Xiao Li, Bing Zhou, Luying Chen, Lantao Gou, Hai-Ri Li, Xiang-Dong Fu
Journal/Conference Name Nature Biotechnology
Paper Category
Paper 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.
Date of publication 2017
Code Programming Language Jupyter
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