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

Alessandro Bonetti (), Federico Agostini, Ana Maria Suzuki, Kosuke Hashimoto, Giovanni Pascarella, Juliette Gimenez, Leonie Roos, Alex J. Nash, Marco Ghilotti, Christopher J. F. 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 () and Piero Carninci ()
Additional contact information
Alessandro Bonetti: RIKEN Center for Integrative Medical Sciences
Federico Agostini: The Francis Crick Institute
Ana Maria Suzuki: RIKEN Center for Integrative Medical Sciences
Kosuke Hashimoto: RIKEN Center for Integrative Medical Sciences
Giovanni Pascarella: RIKEN Center for Integrative Medical Sciences
Juliette Gimenez: IRCCS Fondazione Santa Lucia
Leonie Roos: Institute of Clinical Sciences
Alex J. Nash: Institute of Clinical Sciences
Marco Ghilotti: RIKEN Center for Integrative Medical Sciences
Christopher J. F. Cameron: McGill University
Matthew Valentine: RIKEN Center for Integrative Medical Sciences
Yulia A. Medvedeva: Russian Academy of Science
Shuhei Noguchi: RIKEN Center for Integrative Medical Sciences
Eneritz Agirre: Karolinska Institutet
Kaori Kashi: RIKEN Center for Integrative Medical Sciences
Samudyata: Karolinska Institutet
Joachim Luginbühl: RIKEN Center for Integrative Medical Sciences
Riccardo Cazzoli: European Institute of Oncology IRCCS
Saumya Agrawal: RIKEN Center for Integrative Medical Sciences
Nicholas M. Luscombe: The Francis Crick Institute
Mathieu Blanchette: McGill University
Takeya Kasukawa: RIKEN Center for Integrative Medical Sciences
Michiel de Hoon: RIKEN Center for Integrative Medical Sciences
Erik Arner: RIKEN Center for Integrative Medical Sciences
Boris Lenhard: Institute of Clinical Sciences
Charles Plessy: RIKEN Center for Integrative Medical Sciences
Gonçalo Castelo-Branco: Karolinska Institutet
Valerio Orlando: IRCCS Fondazione Santa Lucia
Piero Carninci: RIKEN Center for Integrative Medical Sciences

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: Abstract 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.

Date: 2020
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DOI: 10.1038/s41467-020-14337-6

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