RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions.
journal contributionposted on 2020-11-10, 14:14 authored by Alessandro Bonetti, Federico Agostini, Ana Maria Suzuki, Kosuke Hashimoto, Giovanni Pascarella, Juliette Gimenez, Leonie Roos, Alex J Nash, Marco Ghilotti, Christopher JF Cameron, Matthew Valentine, Yulia A Medvedeva, Shuhei Noguchi, Eneritz Agirre, Kaori Kashi, Samudyata, Joachim Luginbühl, Riccardo Cazzoli, Saumya Agrawal, Nicholas M Luscombe, Mathieu Blanchette, Takeya Kasukawa, Michiel de Hoon, Erik Arner, Boris Lenhard, Charles Plessy, Gonçalo Castelo-Branco, Valerio Orlando, Piero Carninci
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, these methods have some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a 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, while increasing genomic coverage and unique mapping rate efficiency compared with 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 highlights the role of transcription in the establishment of chromatin structure.