Expanding the repertoire of human tandem repeat RNA-binding proteins

Autores
Ormazábal, Agustín; Carletti, Matías Sebastian; Saldaño, Tadeo Enrique; González Buitrón, Martín; Marchetti, Julia; Palopoli, Nicolás; Bateman, Alex
Año de publicación
2023
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Protein regions consisting of arrays of tandem repeats are known to bind other molecular partners, including nucleic acid molecules. Although the interactions between repeat proteins and DNA are already widely explored, studies characterising tandem repeat RNA-binding proteins are lacking. We performed a large-scale analysis of human proteins devoted to expanding the knowledge about tandem repeat proteins experimentally reported as RNA-binding molecules. This work is timely because of the release of a full set of accurate structural models for the human proteome amenable to repeat detection using structural methods. The main goal of our analysis was to build a comprehensive set of human RNA-binding proteins that contain repeats at the sequence or structure level. Our results showed that the combination of sequence and structural methods finds significantly more tandem repeat proteins than either method alone. We identified 219 tandem repeat proteins that bind RNA molecules and characterised the overlap between repeat regions and RNA-binding regions as a first step towards assessing their functional relationship. We observed differences in the characteristics of repeat regions predicted by sequence-based or structure-based methods in terms of their sequence composition, their functions and their protein domains.
Fil: Ormazábal, Agustín. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. European Molecular Biology Laboratory. European Bioinformatics Institute.; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Carletti, Matías Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
Fil: Saldaño, Tadeo Enrique. Universidad Nacional del Centro de la Pcia.de Bs.as.. Facultad de Agronomia. Dpto. Cs. Básicas Agronómicas y Biológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
Fil: González Buitrón, Martín. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
Fil: Marchetti, Julia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Palopoli, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
Fil: Bateman, Alex. European Molecular Biology Laboratory. European Bioinformatics Institute.; Reino Unido
Materia
Tandem repeats
RNA binding proteins
Intrinsically disordered proteins
AlphaFold
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/219992
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/219992
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Expanding the repertoire of human tandem repeat RNA-binding proteinsOrmazábal, AgustínCarletti, Matías SebastianSaldaño, Tadeo EnriqueGonzález Buitrón, MartínMarchetti, JuliaPalopoli, NicolásBateman, AlexTandem repeatsRNA binding proteinsIntrinsically disordered proteinsAlphaFoldhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Protein regions consisting of arrays of tandem repeats are known to bind other molecular partners, including nucleic acid molecules. Although the interactions between repeat proteins and DNA are already widely explored, studies characterising tandem repeat RNA-binding proteins are lacking. We performed a large-scale analysis of human proteins devoted to expanding the knowledge about tandem repeat proteins experimentally reported as RNA-binding molecules. This work is timely because of the release of a full set of accurate structural models for the human proteome amenable to repeat detection using structural methods. The main goal of our analysis was to build a comprehensive set of human RNA-binding proteins that contain repeats at the sequence or structure level. Our results showed that the combination of sequence and structural methods finds significantly more tandem repeat proteins than either method alone. We identified 219 tandem repeat proteins that bind RNA molecules and characterised the overlap between repeat regions and RNA-binding regions as a first step towards assessing their functional relationship. We observed differences in the characteristics of repeat regions predicted by sequence-based or structure-based methods in terms of their sequence composition, their functions and their protein domains.Fil: Ormazábal, Agustín. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. European Molecular Biology Laboratory. European Bioinformatics Institute.; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Carletti, Matías Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Saldaño, Tadeo Enrique. Universidad Nacional del Centro de la Pcia.de Bs.as.. Facultad de Agronomia. Dpto. Cs. Básicas Agronómicas y Biológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: González Buitrón, Martín. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Marchetti, Julia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Palopoli, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Bateman, Alex. European Molecular Biology Laboratory. European Bioinformatics Institute.; Reino UnidoPublic Library of Science2023-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/219992Ormazábal, Agustín; Carletti, Matías Sebastian; Saldaño, Tadeo Enrique; González Buitrón, Martín; Marchetti, Julia; et al.; Expanding the repertoire of human tandem repeat RNA-binding proteins; Public Library of Science; Plos One; 18; 9-2023; 1-251932-6203CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://dx.plos.org/10.1371/journal.pone.0290890info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0290890info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:46:49Zoai:ri.conicet.gov.ar:11336/219992instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:46:49.451CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Expanding the repertoire of human tandem repeat RNA-binding proteins
title Expanding the repertoire of human tandem repeat RNA-binding proteins
spellingShingle Expanding the repertoire of human tandem repeat RNA-binding proteins
Ormazábal, Agustín
Tandem repeats
RNA binding proteins
Intrinsically disordered proteins
AlphaFold
title_short Expanding the repertoire of human tandem repeat RNA-binding proteins
title_full Expanding the repertoire of human tandem repeat RNA-binding proteins
title_fullStr Expanding the repertoire of human tandem repeat RNA-binding proteins
title_full_unstemmed Expanding the repertoire of human tandem repeat RNA-binding proteins
title_sort Expanding the repertoire of human tandem repeat RNA-binding proteins
dc.creator.none.fl_str_mv Ormazábal, Agustín
Carletti, Matías Sebastian
Saldaño, Tadeo Enrique
González Buitrón, Martín
Marchetti, Julia
Palopoli, Nicolás
Bateman, Alex
author Ormazábal, Agustín
author_facet Ormazábal, Agustín
Carletti, Matías Sebastian
Saldaño, Tadeo Enrique
González Buitrón, Martín
Marchetti, Julia
Palopoli, Nicolás
Bateman, Alex
author_role author
author2 Carletti, Matías Sebastian
Saldaño, Tadeo Enrique
González Buitrón, Martín
Marchetti, Julia
Palopoli, Nicolás
Bateman, Alex
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Tandem repeats
RNA binding proteins
Intrinsically disordered proteins
AlphaFold
topic Tandem repeats
RNA binding proteins
Intrinsically disordered proteins
AlphaFold
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Protein regions consisting of arrays of tandem repeats are known to bind other molecular partners, including nucleic acid molecules. Although the interactions between repeat proteins and DNA are already widely explored, studies characterising tandem repeat RNA-binding proteins are lacking. We performed a large-scale analysis of human proteins devoted to expanding the knowledge about tandem repeat proteins experimentally reported as RNA-binding molecules. This work is timely because of the release of a full set of accurate structural models for the human proteome amenable to repeat detection using structural methods. The main goal of our analysis was to build a comprehensive set of human RNA-binding proteins that contain repeats at the sequence or structure level. Our results showed that the combination of sequence and structural methods finds significantly more tandem repeat proteins than either method alone. We identified 219 tandem repeat proteins that bind RNA molecules and characterised the overlap between repeat regions and RNA-binding regions as a first step towards assessing their functional relationship. We observed differences in the characteristics of repeat regions predicted by sequence-based or structure-based methods in terms of their sequence composition, their functions and their protein domains.
Fil: Ormazábal, Agustín. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. European Molecular Biology Laboratory. European Bioinformatics Institute.; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Carletti, Matías Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
Fil: Saldaño, Tadeo Enrique. Universidad Nacional del Centro de la Pcia.de Bs.as.. Facultad de Agronomia. Dpto. Cs. Básicas Agronómicas y Biológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
Fil: González Buitrón, Martín. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
Fil: Marchetti, Julia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Palopoli, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
Fil: Bateman, Alex. European Molecular Biology Laboratory. European Bioinformatics Institute.; Reino Unido
description Protein regions consisting of arrays of tandem repeats are known to bind other molecular partners, including nucleic acid molecules. Although the interactions between repeat proteins and DNA are already widely explored, studies characterising tandem repeat RNA-binding proteins are lacking. We performed a large-scale analysis of human proteins devoted to expanding the knowledge about tandem repeat proteins experimentally reported as RNA-binding molecules. This work is timely because of the release of a full set of accurate structural models for the human proteome amenable to repeat detection using structural methods. The main goal of our analysis was to build a comprehensive set of human RNA-binding proteins that contain repeats at the sequence or structure level. Our results showed that the combination of sequence and structural methods finds significantly more tandem repeat proteins than either method alone. We identified 219 tandem repeat proteins that bind RNA molecules and characterised the overlap between repeat regions and RNA-binding regions as a first step towards assessing their functional relationship. We observed differences in the characteristics of repeat regions predicted by sequence-based or structure-based methods in terms of their sequence composition, their functions and their protein domains.
publishDate 2023
dc.date.none.fl_str_mv 2023-09
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/219992
Ormazábal, Agustín; Carletti, Matías Sebastian; Saldaño, Tadeo Enrique; González Buitrón, Martín; Marchetti, Julia; et al.; Expanding the repertoire of human tandem repeat RNA-binding proteins; Public Library of Science; Plos One; 18; 9-2023; 1-25
1932-6203
CONICET Digital
CONICET
url http://hdl.handle.net/11336/219992
identifier_str_mv Ormazábal, Agustín; Carletti, Matías Sebastian; Saldaño, Tadeo Enrique; González Buitrón, Martín; Marchetti, Julia; et al.; Expanding the repertoire of human tandem repeat RNA-binding proteins; Public Library of Science; Plos One; 18; 9-2023; 1-25
1932-6203
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://dx.plos.org/10.1371/journal.pone.0290890
info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0290890
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.13397

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