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RNA modifications detection by comparative Nanopore direct RNA sequencing.

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cam.issuedOnline2021-12-10
datacite.isderivedfrom.doi10.1101/843136
dc.contributor.authorLeger, Adrien
dc.contributor.authorAmaral, Paulo P
dc.contributor.authorPandolfini, Luca
dc.contributor.authorCapitanchik, Charlotte
dc.contributor.authorCapraro, Federica
dc.contributor.authorMiano, Valentina
dc.contributor.authorMigliori, Valentina
dc.contributor.authorToolan-Kerr, Patrick
dc.contributor.authorSideri, Theodora
dc.contributor.authorEnright, Anton J
dc.contributor.authorTzelepis, Konstantinos
dc.contributor.authorvan Werven, Folkert J
dc.contributor.authorLuscombe, Nicholas M
dc.contributor.authorBarbieri, Isaia
dc.contributor.authorUle, Jernej
dc.contributor.authorFitzgerald, Tomas
dc.contributor.authorBirney, Ewan
dc.contributor.authorLeonardi, Tommaso
dc.contributor.authorKouzarides, Tony
dc.contributor.orcidLeger, Adrien [0000-0001-8772-6776]
dc.contributor.orcidPandolfini, Luca [0000-0003-1444-8167]
dc.contributor.orcidCapraro, Federica [0000-0001-8974-4951]
dc.contributor.orcidMiano, Valentina [0000-0002-0260-5885]
dc.contributor.orcidTzelepis, Konstantinos [0000-0002-4865-7648]
dc.contributor.orcidvan Werven, Folkert J [0000-0002-6685-2084]
dc.contributor.orcidLuscombe, Nicholas M [0000-0001-5293-4778]
dc.contributor.orcidBarbieri, Isaia [0000-0003-3035-8970]
dc.contributor.orcidUle, Jernej [0000-0002-2452-4277]
dc.contributor.orcidFitzgerald, Tomas [0000-0002-2370-8496]
dc.contributor.orcidBirney, Ewan [0000-0001-8314-8497]
dc.contributor.orcidLeonardi, Tommaso [0000-0002-4449-1863]
dc.contributor.orcidKouzarides, Tony [0000-0002-8918-4162]
dc.date.accessioned2022-01-04T13:28:32Z
dc.date.available2022-01-04T13:28:32Z
dc.date.issued2021-12-10
dc.date.submitted2021-08-31
dc.date.updated2022-01-04T13:28:30Z
dc.description.abstractRNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties. In recent years, a growing number of PTMs have been successfully mapped to the transcriptome using experimental approaches relying on high-throughput sequencing. Oxford Nanopore direct-RNA sequencing has been shown to be sensitive to RNA modifications. We developed and validated Nanocompore, a robust analytical framework that identifies modifications from these data. Our strategy compares an RNA sample of interest against a non-modified control sample, not requiring a training set and allowing the use of replicates. We show that Nanocompore can detect different RNA modifications with position accuracy in vitro, and we apply it to profile m6A in vivo in yeast and human RNAs, as well as in targeted non-coding RNAs. We confirm our results with orthogonal methods and provide novel insights on the co-occurrence of multiple modified residues on individual RNA molecules.
dc.description.sponsorshipThe Kouzarides laboratory is supported by Cancer Research UK (grant reference RG72100) and core support from the Wellcome Trust (core grant reference WT203144) and Cancer Research UK (grant reference C6946/A24843). PPA was supported by a Borysiewicz Biomedical Sciences postdoctoral fellowship (University of Cambridge) and AL by a COFUND Marie Skłodowska-Curie Actions postdoctoral fellowship (EMBL). FW and TS are supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001203), the UK Medical Research Council (FC001203), and the Wellcome Trust (FC001203). IB and V Miano are supported by Cancer Research UK (grant reference RG86786) and by the Joseph Mitchell Fund.
dc.identifier.doi10.17863/CAM.79319
dc.identifier.eissn2041-1723
dc.identifier.issn2041-1723
dc.identifier.others41467-021-27393-3
dc.identifier.other27393
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/331869
dc.languageen
dc.language.isoeng
dc.publisherSpringer Science and Business Media LLC
dc.publisher.urlhttp://dx.doi.org/10.1038/s41467-021-27393-3
dc.subjectBase Sequence
dc.subjectComputational Biology
dc.subjectGene Expression Profiling
dc.subjectGenetic Techniques
dc.subjectHigh-Throughput Nucleotide Sequencing
dc.subjectHumans
dc.subjectNanopore Sequencing
dc.subjectNanopores
dc.subjectRNA
dc.subjectRNA Processing, Post-Transcriptional
dc.subjectSequence Analysis, RNA
dc.subjectSoftware
dc.subjectTranscriptome
dc.titleRNA modifications detection by comparative Nanopore direct RNA sequencing.
dc.typeArticle
dcterms.dateAccepted2021-11-09
prism.issueIdentifier1
prism.publicationNameNat Commun
prism.volume12
pubs.funder-project-idWellcome Trust (092096/Z/10/Z)
pubs.funder-project-idCancer Research UK (A27321)
pubs.funder-project-idCancer Research UK (17001)
pubs.funder-project-idCancer Research UK (C7/A18061)
pubs.funder-project-idCancer Research UK (C6946/A24843)
pubs.funder-project-idWellcome Trust (203144/Z/16/Z)
pubs.funder-project-idBiotechnology and Biological Sciences Research Council (BB/K017438/1)
pubs.funder-project-idWellcome Trust (203144/A/16/Z)
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
rioxxterms.versionVoR
rioxxterms.versionofrecord10.1038/s41467-021-27393-3

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