RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions (RADICL-seq)

Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs,, methods to massively map the genomic interacting sites of multiple transcripts have been developed. However they present still some limitations. Here, we introduce RNA and DNA interacting complexes ligated and sequenced (RADICL-seq), a novel technology that maps genome-wide RNA-chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation based methodology that reduces the bias for nascent transcription, increases genomic coverage and unique mapping rate efficiency compared to existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and emphasizes the role of transcription in the establishment of chromatin structure. Identification of genome-wide RNA-chromatin interactions in 2 cell types