Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2

Specific recognition of N6-methyladenosine (m6A) in mRNA by RNA-binding proteins containing a YT521-B homology (YTH) domain is important in eukaryotic gene regulation. The Arabidopsis YTH domain protein ECT2 is thought to bind to mRNA at URU(m6A)Y sites, yet RR(m6A)CH is the canonical m6A consensus...

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Autores: Arribas-Hernández, Laura, Rennie, Sarah, Köster, Tino, Porcelli, Carlotta, Lewinski, Martin, Staiger, Dorothee, Andersson, Robin, Brodersen, Peter
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2021
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/378878
Acceso en línea:http://hdl.handle.net/10261/378878
https://api.elsevier.com/content/abstract/scopus_id/85116861691
Access Level:acceso abierto
Palabra clave:A. thaliana
ECT2
GGAU
RRACH
URUAY
Genetics
Genomics
hyperTRIBE
iCLIP
m6A
Motif
Plant biology
Target
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spelling Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2Arribas-Hernández, LauraRennie, SarahKöster, TinoPorcelli, CarlottaLewinski, MartinStaiger, DorotheeAndersson, RobinBrodersen, PeterA. thalianaECT2GGAURRACHURUAYGeneticsGenomicshyperTRIBEiCLIPm6AMotifPlant biologyTargetSpecific recognition of N6-methyladenosine (m6A) in mRNA by RNA-binding proteins containing a YT521-B homology (YTH) domain is important in eukaryotic gene regulation. The Arabidopsis YTH domain protein ECT2 is thought to bind to mRNA at URU(m6A)Y sites, yet RR(m6A)CH is the canonical m6A consensus site in all eukaryotes and ECT2 functions require m6A-binding activity. Here, we apply iCLIP (individual nucleotide resolution crosslinking and immunoprecipitation) and HyperTRIBE (targets of RNA-binding proteins identified by editing) to define high-quality target sets of ECT2 and analyze the patterns of enriched sequence motifs around ECT2 crosslink sites. Our analyses show that ECT2 does in fact bind to RR(m6A)CH. Pyrimidine-rich motifs are enriched around, but not at m6A sites, reflecting a preference for N6-adenosine methylation of RRACH/GGAU islands in pyrimidine-rich regions. Such motifs, particularly oligo-U and UNUNU upstream of m6A sites, are also implicated in ECT2 binding via its intrinsically disordered region (IDR). Finally, URUAY-type motifs are enriched at ECT2 crosslink sites, but their distinct properties suggest function as sites of competition between binding of ECT2 and as yet unidentified RNA-binding proteins. Our study provides coherence between genetic and molecular studies of m6A-YTH function in plants and reveals new insight into the mode of RNA recognition by YTH domain-containing proteins.The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publicationPeer reviewedeLife Sciences PublicationsEuropean CommissionIndependent Research Fund DenmarkEMBOGerman Research FoundationConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202520252021info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Postprintinfo:eu-repo/semantics/acceptedVersionhttp://hdl.handle.net/10261/378878https://api.elsevier.com/content/abstract/scopus_id/85116861691reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#ERC-2016-COG 7264179040-00409BSTF 7614STA653/14-1eLifehttps://doi.org/10.7554/eLife.72375Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3788782026-05-22T06:33:51Z
dc.title.none.fl_str_mv Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2
title Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2
spellingShingle Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2
Arribas-Hernández, Laura
A. thaliana
ECT2
GGAU
RRACH
URUAY
Genetics
Genomics
hyperTRIBE
iCLIP
m6A
Motif
Plant biology
Target
title_short Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2
title_full Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2
title_fullStr Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2
title_full_unstemmed Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2
title_sort Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2
dc.creator.none.fl_str_mv Arribas-Hernández, Laura
Rennie, Sarah
Köster, Tino
Porcelli, Carlotta
Lewinski, Martin
Staiger, Dorothee
Andersson, Robin
Brodersen, Peter
author Arribas-Hernández, Laura
author_facet Arribas-Hernández, Laura
Rennie, Sarah
Köster, Tino
Porcelli, Carlotta
Lewinski, Martin
Staiger, Dorothee
Andersson, Robin
Brodersen, Peter
author_role author
author2 Rennie, Sarah
Köster, Tino
Porcelli, Carlotta
Lewinski, Martin
Staiger, Dorothee
Andersson, Robin
Brodersen, Peter
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Commission
Independent Research Fund Denmark
EMBO
German Research Foundation
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv A. thaliana
ECT2
GGAU
RRACH
URUAY
Genetics
Genomics
hyperTRIBE
iCLIP
m6A
Motif
Plant biology
Target
topic A. thaliana
ECT2
GGAU
RRACH
URUAY
Genetics
Genomics
hyperTRIBE
iCLIP
m6A
Motif
Plant biology
Target
description Specific recognition of N6-methyladenosine (m6A) in mRNA by RNA-binding proteins containing a YT521-B homology (YTH) domain is important in eukaryotic gene regulation. The Arabidopsis YTH domain protein ECT2 is thought to bind to mRNA at URU(m6A)Y sites, yet RR(m6A)CH is the canonical m6A consensus site in all eukaryotes and ECT2 functions require m6A-binding activity. Here, we apply iCLIP (individual nucleotide resolution crosslinking and immunoprecipitation) and HyperTRIBE (targets of RNA-binding proteins identified by editing) to define high-quality target sets of ECT2 and analyze the patterns of enriched sequence motifs around ECT2 crosslink sites. Our analyses show that ECT2 does in fact bind to RR(m6A)CH. Pyrimidine-rich motifs are enriched around, but not at m6A sites, reflecting a preference for N6-adenosine methylation of RRACH/GGAU islands in pyrimidine-rich regions. Such motifs, particularly oligo-U and UNUNU upstream of m6A sites, are also implicated in ECT2 binding via its intrinsically disordered region (IDR). Finally, URUAY-type motifs are enriched at ECT2 crosslink sites, but their distinct properties suggest function as sites of competition between binding of ECT2 and as yet unidentified RNA-binding proteins. Our study provides coherence between genetic and molecular studies of m6A-YTH function in plants and reveals new insight into the mode of RNA recognition by YTH domain-containing proteins.
publishDate 2021
dc.date.none.fl_str_mv 2021
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Postprint
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/378878
https://api.elsevier.com/content/abstract/scopus_id/85116861691
url http://hdl.handle.net/10261/378878
https://api.elsevier.com/content/abstract/scopus_id/85116861691
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
ERC-2016-COG 726417
9040-00409B
STF 7614
STA653/14-1
eLife
https://doi.org/10.7554/eLife.72375
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv eLife Sciences Publications
publisher.none.fl_str_mv eLife Sciences Publications
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.812429

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