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dc.contributor.authorBonetti, Alessandro
dc.contributor.authorAgostini, Federico
dc.contributor.authorSuzuki, Ana Maria
dc.contributor.authorHashimoto, Kosuke
dc.contributor.authorPascarella, Giovanni
dc.contributor.authorGimenez, Juliette
dc.contributor.authorRoos, Leonie
dc.contributor.authorNash, Alex J.
dc.contributor.authorGhilotti, Marco
dc.contributor.authorCameron, Christopher JF
dc.contributor.authorValentine, Matthew
dc.contributor.authorMedvedeva, Yulia A
dc.contributor.authorNoguchi, Shuhei
dc.contributor.authorAgirre, Eneritz
dc.contributor.authorKashi, Kaori
dc.contributor.authorSamudyata,
dc.contributor.authorLuginbuehl, Joachim
dc.contributor.authorCazzoli, Riccardo
dc.contributor.authorAgrawal, Saumya
dc.contributor.authorLuscombe, Nicholas M
dc.contributor.authorBlanchette, Mathieu
dc.contributor.authorKasukawa, Takeya
dc.contributor.authorDe Hoon, Michiel
dc.contributor.authorArner, Erik
dc.contributor.authorLenhard, Boris
dc.contributor.authorPlessy, Charles
dc.contributor.authorCastelo-Branco, Gonçalo
dc.contributor.authorOrlando, Valerio
dc.contributor.authorCarninci, Piero
dc.date.accessioned2019-12-09T12:25:07Z
dc.date.available2019-12-09T12:25:07Z
dc.date.issued2019-06-28
dc.identifier.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
dc.identifier.doi10.1101/681924
dc.identifier.urihttp://hdl.handle.net/10754/660477
dc.description.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.
dc.description.sponsorshipWe 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.
dc.publisherCold Spring Harbor Laboratory
dc.relation.urlhttp://biorxiv.org/lookup/doi/10.1101/681924
dc.relation.urlhttps://www.biorxiv.org/content/biorxiv/early/2019/06/27/681924.full.pdf
dc.rightsArchived with thanks to Cold Spring Harbor Laboratory. The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.titleRADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions
dc.typePreprint
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.eprint.versionPre-print
kaust.personOrlando, Valerio
refterms.dateFOA2019-12-09T12:26:14Z


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Archived with thanks to Cold Spring Harbor Laboratory. The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Except where otherwise noted, this item's license is described as Archived with thanks to Cold Spring Harbor Laboratory. The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.