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Article: Ularcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing

TitleUlarcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing
Authors
KeywordsNucleic acid structure
Computational Methods
Issue Date2019
PublisherOxford University Press (OUP): Policy C - Option B. The Journal's web site is located at http://nar.oxfordjournals.org/
Citation
Nucleic Acids Research, 2019, v. 47 n. 20, article no. e123 How to Cite?
AbstractCircular RNAs (circRNA) are a unique class of transcripts that can only be identified from sequence alignments spanning discordant junctions, commonly referred to as backsplice junctions (BSJ). Canonical splicing is also linked with circRNA biogenesis either from the parental transcript or internal to the circRNA, and is not fully utilized in circRNA software. Here we present Ularcirc, a software tool that integrates the visualization of both BSJ and forward splicing junctions and provides downstream analysis of selected circRNA candidates. Ularcirc utilizes the output of CIRI, circExplorer, or raw chimeric output of the STAR aligner and assembles BSJ count table to allow multi-sample analysis. We used Ularcirc to identify and characterize circRNA from public and in-house generated data sets and demonstrate how it can be used to (i) discover novel splicing patterns of parental transcripts, (ii) detect internal splicing patterns of circRNA, and (iii) reveal the complexity of BSJ formation. Furthermore, we identify circRNA that have potential open reading frames longer than their linear sequence. Finally, we detected and validated the presence of a novel class of circRNA generated from ApoA4 transcripts whose BSJ derive from multiple non-canonical splicing sites within coding exons.
Persistent Identifierhttp://hdl.handle.net/10722/275680
ISSN
2023 Impact Factor: 16.6
2023 SCImago Journal Rankings: 7.048
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorHumphreys, DT-
dc.contributor.authorFossat, N-
dc.contributor.authorDemuth, M-
dc.contributor.authorTam, PPL-
dc.contributor.authorHo, JWK-
dc.date.accessioned2019-09-10T02:47:27Z-
dc.date.available2019-09-10T02:47:27Z-
dc.date.issued2019-
dc.identifier.citationNucleic Acids Research, 2019, v. 47 n. 20, article no. e123-
dc.identifier.issn0305-1048-
dc.identifier.urihttp://hdl.handle.net/10722/275680-
dc.description.abstractCircular RNAs (circRNA) are a unique class of transcripts that can only be identified from sequence alignments spanning discordant junctions, commonly referred to as backsplice junctions (BSJ). Canonical splicing is also linked with circRNA biogenesis either from the parental transcript or internal to the circRNA, and is not fully utilized in circRNA software. Here we present Ularcirc, a software tool that integrates the visualization of both BSJ and forward splicing junctions and provides downstream analysis of selected circRNA candidates. Ularcirc utilizes the output of CIRI, circExplorer, or raw chimeric output of the STAR aligner and assembles BSJ count table to allow multi-sample analysis. We used Ularcirc to identify and characterize circRNA from public and in-house generated data sets and demonstrate how it can be used to (i) discover novel splicing patterns of parental transcripts, (ii) detect internal splicing patterns of circRNA, and (iii) reveal the complexity of BSJ formation. Furthermore, we identify circRNA that have potential open reading frames longer than their linear sequence. Finally, we detected and validated the presence of a novel class of circRNA generated from ApoA4 transcripts whose BSJ derive from multiple non-canonical splicing sites within coding exons.-
dc.languageeng-
dc.publisherOxford University Press (OUP): Policy C - Option B. The Journal's web site is located at http://nar.oxfordjournals.org/-
dc.relation.ispartofNucleic Acids Research-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectNucleic acid structure-
dc.subjectComputational Methods-
dc.titleUlarcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing-
dc.typeArticle-
dc.identifier.emailHo, JWK: jwkho@hku.hk-
dc.identifier.authorityHo, JWK=rp02436-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1093/nar/gkz718-
dc.identifier.scopuseid_2-s2.0-85074746544-
dc.identifier.hkuros303419-
dc.identifier.volume47-
dc.identifier.issue20-
dc.identifier.spagearticle no. e123-
dc.identifier.epagearticle no. e123-
dc.identifier.isiWOS:000501735500001-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl0305-1048-

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