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Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications.
Acera Mateos, P; J Sethi, A; Ravindran, A; Srivastava, A; Woodward, K; Mahmud, S; Kanchi, M; Guarnacci, M; Xu, J; W S Yuen, Z; Zhou, Y; Sneddon, A; Hamilton, W; Gao, J; M Starrs, L; Hayashi, R; Wickramasinghe, V; Zarnack, K; Preiss, T; Burgio, G; Dehorter, N; E Shirokikh, N; Eyras, E.
Affiliation
  • Acera Mateos P; EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia.
  • J Sethi A; The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Ravindran A; The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Srivastava A; EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia.
  • Woodward K; The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Mahmud S; The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Kanchi M; EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia.
  • Guarnacci M; The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Xu J; The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • W S Yuen Z; EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia.
  • Zhou Y; The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Sneddon A; The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Hamilton W; The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Gao J; The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • M Starrs L; The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Hayashi R; The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Wickramasinghe V; EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia.
  • Zarnack K; EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia.
  • Preiss T; The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Burgio G; The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
  • Dehorter N; Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
  • E Shirokikh N; EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia.
  • Eyras E; The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
Nat Commun ; 15(1): 3899, 2024 May 09.
Article de En | MEDLINE | ID: mdl-38724548
ABSTRACT
The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI's capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.
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Texte intégral: 1 Collection: 01-internacional Base de données: MEDLINE Sujet principal: Adénosine / Analyse de séquence d'ARN / 5-Méthyl-cytosine / Transcriptome Limites: Humans Langue: En Journal: Nat Commun Sujet du journal: BIOLOGIA / CIENCIA Année: 2024 Type de document: Article Pays d'affiliation: Australie
Texte intégral
Ajouter à My VHL
Imprimer
XML
PubMed Links
Recherche sur Google

Texte intégral: 1 Collection: 01-internacional Base de données: MEDLINE Sujet principal: Adénosine / Analyse de séquence d'ARN / 5-Méthyl-cytosine / Transcriptome Limites: Humans Langue: En Journal: Nat Commun Sujet du journal: BIOLOGIA / CIENCIA Année: 2024 Type de document: Article Pays d'affiliation: Australie