RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions
Suzuki, Ana Maria
Nash, Alex J.
Cameron, Christopher JF
Medvedeva, Yulia A
Luscombe, Nicholas M
De Hoon, Michiel
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Permanent link to this recordhttp://hdl.handle.net/10754/660477
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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 remodelling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed. However, they still present 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 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.
CitationBonetti, A., Agostini, F., Suzuki, A. M., Hashimoto, K., Pascarella, G., Gimenez, J., … Carninci, P. (2019). RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. doi:10.1101/681924
SponsorsWe thank Mikael Rydén for providing logistical help. This work was founded by a Research Grant from MEXT to the RIKEN Center for Life Science Technologies (http://www.mext.go.jp/en/). This work was also supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC010110), the UK Medical Research Council (FC010110), and the Wellcome Trust (FC010110). NML is a Winton Group Leader in recognition of the Winton Charitable Foundation’s supporttowards the establishment of the Francis Crick Institute. NML is additionally funded by a Wellcome Trust Joint Investigator Award (103760/Z/14/Z) and the MRC eMedLab Medical Bioinformatics Infrastructure Award (MR/L016311/1). Work at the GCB lab was supported by European Union (Horizon 2020 European Research Council Consolidator Grant EPIScOPE) and Ming Wai Lau Centre for Reparative Medicine.
PublisherCold Spring Harbor Laboratory
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