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

Author:

Bonetti AlessandroORCID,Agostini FedericoORCID,Suzuki Ana Maria,Hashimoto Kosuke,Pascarella Giovanni,Gimenez JulietteORCID,Roos Leonie,Nash Alex J.,Ghilotti Marco,Cameron Christopher J.  F.,Valentine MatthewORCID,Medvedeva Yulia A.,Noguchi Shuhei,Agirre EneritzORCID,Kashi Kaori,Samudyata ,Luginbühl Joachim,Cazzoli Riccardo,Agrawal Saumya,Luscombe Nicholas M.ORCID,Blanchette Mathieu,Kasukawa TakeyaORCID,Hoon Michiel de,Arner Erik,Lenhard BorisORCID,Plessy CharlesORCID,Castelo-Branco GonçaloORCID,Orlando Valerio,Carninci PieroORCID

Abstract

AbstractMammalian 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.

Publisher

Springer Science and Business Media LLC

Subject

General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry

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