GRID-seq reveals the global RNA-chromatin interactome.
Xiao LiBing ZhouLiang ChenLan-Tao GouHairi LiXiang-Dong FuPublished in: Nature biotechnology (2017)
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.
Keyphrases
- transcription factor
- genome wide
- gene expression
- single cell
- dna damage
- dna methylation
- rna seq
- endothelial cells
- induced apoptosis
- nucleic acid
- physical activity
- binding protein
- single molecule
- functional connectivity
- high density
- mental health
- resting state
- induced pluripotent stem cells
- endoplasmic reticulum stress
- circulating tumor