spongeScan: A web for detecting microRNA binding elements in lncRNA sequences

Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lnc...

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Detalhes bibliográficos
Autores: Furió-Tarí, Pedro, Tarazona, Sonia, Gabaldón Estevan, Juan Antonio, 1973-, Enright, Anton J., Conesa, Ana
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2016
País:España
Recursos:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/27981
Acesso em linha:http://hdl.handle.net/10230/27981
http://dx.doi.org/10.1093/nar/gkw443
Access Level:acceso abierto
Palavra-chave:RNA
Messenger
Surgical sponges
Micro RNA
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spelling spongeScan: A web for detecting microRNA binding elements in lncRNA sequencesFurió-Tarí, PedroTarazona, SoniaGabaldón Estevan, Juan Antonio, 1973-Enright, Anton J.Conesa, AnaRNAMessengerSurgical spongesMicro RNANon-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lncRNAs and that this creates competition for binding between the miRNA, a lncRNA and other regulatory targets. Indeed, various competitive endogenous RNAs (ceRNAs) have already been identified where a lncRNA acts by sequestering miRNAs. This implies the down-regulation in the interaction of the miRNAs with their mRNA targets, what has been called a sponge effect. Multiple approaches exist for the prediction of miRNA targets in mRNAs. However, few methods exist for the prediction of miRNA response elements (MREs) in lncRNAs acting as ceRNAs (sponges). Here, we present spongeScan (http://spongescan.rc.ufl.edu), a graphical web tool to compute and visualize putative MREs in lncRNAs, along with different measures to assess their likely behavior as ceRNAs.This work was supported by grant FP7 STATegra project [agreement number 36000]; MINECO, co-funded with European Regional Development Funds (ERDF) [BIO2012-40244]; European Molecular Biology Laboratory and the European Union and ERC Seventh Framework Programme (FP7/2007-2013) [ERC-2012-StG-310325].Oxford University Press201720172016info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/27981http://dx.doi.org/10.1093/nar/gkw443reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésNucleic Acids Research. 2016;44(W1):W176-W180info:eu-repo/grantAgreement/ES/3PN/BIO2012-40244info:eu-repo/grantAgreement/EC/FP7/36000info:eu-repo/grantAgreement/EC/FP7/310325© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/279812026-06-12T07:21:37Z
dc.title.none.fl_str_mv spongeScan: A web for detecting microRNA binding elements in lncRNA sequences
title spongeScan: A web for detecting microRNA binding elements in lncRNA sequences
spellingShingle spongeScan: A web for detecting microRNA binding elements in lncRNA sequences
Furió-Tarí, Pedro
RNA
Messenger
Surgical sponges
Micro RNA
title_short spongeScan: A web for detecting microRNA binding elements in lncRNA sequences
title_full spongeScan: A web for detecting microRNA binding elements in lncRNA sequences
title_fullStr spongeScan: A web for detecting microRNA binding elements in lncRNA sequences
title_full_unstemmed spongeScan: A web for detecting microRNA binding elements in lncRNA sequences
title_sort spongeScan: A web for detecting microRNA binding elements in lncRNA sequences
dc.creator.none.fl_str_mv Furió-Tarí, Pedro
Tarazona, Sonia
Gabaldón Estevan, Juan Antonio, 1973-
Enright, Anton J.
Conesa, Ana
author Furió-Tarí, Pedro
author_facet Furió-Tarí, Pedro
Tarazona, Sonia
Gabaldón Estevan, Juan Antonio, 1973-
Enright, Anton J.
Conesa, Ana
author_role author
author2 Tarazona, Sonia
Gabaldón Estevan, Juan Antonio, 1973-
Enright, Anton J.
Conesa, Ana
author2_role author
author
author
author
dc.subject.none.fl_str_mv RNA
Messenger
Surgical sponges
Micro RNA
topic RNA
Messenger
Surgical sponges
Micro RNA
description Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lncRNAs and that this creates competition for binding between the miRNA, a lncRNA and other regulatory targets. Indeed, various competitive endogenous RNAs (ceRNAs) have already been identified where a lncRNA acts by sequestering miRNAs. This implies the down-regulation in the interaction of the miRNAs with their mRNA targets, what has been called a sponge effect. Multiple approaches exist for the prediction of miRNA targets in mRNAs. However, few methods exist for the prediction of miRNA response elements (MREs) in lncRNAs acting as ceRNAs (sponges). Here, we present spongeScan (http://spongescan.rc.ufl.edu), a graphical web tool to compute and visualize putative MREs in lncRNAs, along with different measures to assess their likely behavior as ceRNAs.
publishDate 2016
dc.date.none.fl_str_mv 2016
2017
2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/27981
http://dx.doi.org/10.1093/nar/gkw443
url http://hdl.handle.net/10230/27981
http://dx.doi.org/10.1093/nar/gkw443
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Nucleic Acids Research. 2016;44(W1):W176-W180
info:eu-repo/grantAgreement/ES/3PN/BIO2012-40244
info:eu-repo/grantAgreement/EC/FP7/36000
info:eu-repo/grantAgreement/EC/FP7/310325
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by-nc/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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