Distal nucleotides affect the rate of stop codon read-through

Autores
Escobar, Luciana Ines; Alonso, Andrés Mariano; Ronderos, Jorge Rafael; Diambra, Luis Anibal
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position. However, it has been observed that ribosomes can misinterpret the stop codon and continue the translation in the 3 ′UTR region. This phenomenon is called stop codon read-through (SCR). It has been suggested that these events would occur on a programmed basis, but the underlying mechanisms are still not well understood. Methods: Here, we present a strategy for the comprehensive identification of SCR events in the Drosophila melanogaster transcriptome by evaluating the ribosomal density profiles. The associated ribosomal leak rate was estimated for every event identified. A statistical characterization of the frequency of nucleotide use in the proximal region to the stop codon in the sequences associated to SCR events was performed. Results: The results show that the nucleotide usage pattern in transcripts with the UGA codon is different from the pattern for those transcripts ending in the UAA codon, suggesting the existence of at least two mechanisms that could alter the translational termination process. Furthermore, a linear regression models for each of the three stop codons was developed, and we show that the models using the nucleotides at informative positions outperforms those models that consider the entire sequence context to the stop codon. Conclusions: We report that distal nucleotides can affect the SCR rate in a stop-codon dependent manner.
Fil: Escobar, Luciana Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
Fil: Alonso, Andrés Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Ronderos, Jorge Rafael. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; Argentina
Fil: Diambra, Luis Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
Materia
NUCLEOTIDE USAGE FREQUENCY
RIBOSOMAL DENSITY PROFILES
STOP CODONS
TRANSLATIONAL READTHROUGH
TRANSLATIONAL TERMINATION
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/215044
Acceder
id CONICETDig_2ba68c1432991e84ffe1a555109ad093
oai_identifier_str oai:ri.conicet.gov.ar:11336/215044
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Distal nucleotides affect the rate of stop codon read-throughEscobar, Luciana InesAlonso, Andrés MarianoRonderos, Jorge RafaelDiambra, Luis AnibalNUCLEOTIDE USAGE FREQUENCYRIBOSOMAL DENSITY PROFILESSTOP CODONSTRANSLATIONAL READTHROUGHTRANSLATIONAL TERMINATIONhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position. However, it has been observed that ribosomes can misinterpret the stop codon and continue the translation in the 3 ′UTR region. This phenomenon is called stop codon read-through (SCR). It has been suggested that these events would occur on a programmed basis, but the underlying mechanisms are still not well understood. Methods: Here, we present a strategy for the comprehensive identification of SCR events in the Drosophila melanogaster transcriptome by evaluating the ribosomal density profiles. The associated ribosomal leak rate was estimated for every event identified. A statistical characterization of the frequency of nucleotide use in the proximal region to the stop codon in the sequences associated to SCR events was performed. Results: The results show that the nucleotide usage pattern in transcripts with the UGA codon is different from the pattern for those transcripts ending in the UAA codon, suggesting the existence of at least two mechanisms that could alter the translational termination process. Furthermore, a linear regression models for each of the three stop codons was developed, and we show that the models using the nucleotides at informative positions outperforms those models that consider the entire sequence context to the stop codon. Conclusions: We report that distal nucleotides can affect the SCR rate in a stop-codon dependent manner.Fil: Escobar, Luciana Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaFil: Alonso, Andrés Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Ronderos, Jorge Rafael. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; ArgentinaFil: Diambra, Luis Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaHigher Education Press Limited Company2022-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/215044Escobar, Luciana Ines; Alonso, Andrés Mariano; Ronderos, Jorge Rafael; Diambra, Luis Anibal; Distal nucleotides affect the rate of stop codon read-through; Higher Education Press Limited Company; Quantitative Biology; 11; 1; 2-2022; 44-582095-4697CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://journal.hep.com.cn/qb/EN/10.15302/J-QB-022-0298info:eu-repo/semantics/altIdentifier/doi/10.15302/J-QB-022-0298info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:44:05Zoai:ri.conicet.gov.ar:11336/215044instacron: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 09:44:05.321CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Distal nucleotides affect the rate of stop codon read-through
title Distal nucleotides affect the rate of stop codon read-through
spellingShingle Distal nucleotides affect the rate of stop codon read-through
Escobar, Luciana Ines
NUCLEOTIDE USAGE FREQUENCY
RIBOSOMAL DENSITY PROFILES
STOP CODONS
TRANSLATIONAL READTHROUGH
TRANSLATIONAL TERMINATION
title_short Distal nucleotides affect the rate of stop codon read-through
title_full Distal nucleotides affect the rate of stop codon read-through
title_fullStr Distal nucleotides affect the rate of stop codon read-through
title_full_unstemmed Distal nucleotides affect the rate of stop codon read-through
title_sort Distal nucleotides affect the rate of stop codon read-through
dc.creator.none.fl_str_mv Escobar, Luciana Ines
Alonso, Andrés Mariano
Ronderos, Jorge Rafael
Diambra, Luis Anibal
author Escobar, Luciana Ines
author_facet Escobar, Luciana Ines
Alonso, Andrés Mariano
Ronderos, Jorge Rafael
Diambra, Luis Anibal
author_role author
author2 Alonso, Andrés Mariano
Ronderos, Jorge Rafael
Diambra, Luis Anibal
author2_role author
author
author
dc.subject.none.fl_str_mv NUCLEOTIDE USAGE FREQUENCY
RIBOSOMAL DENSITY PROFILES
STOP CODONS
TRANSLATIONAL READTHROUGH
TRANSLATIONAL TERMINATION
topic NUCLEOTIDE USAGE FREQUENCY
RIBOSOMAL DENSITY PROFILES
STOP CODONS
TRANSLATIONAL READTHROUGH
TRANSLATIONAL TERMINATION
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position. However, it has been observed that ribosomes can misinterpret the stop codon and continue the translation in the 3 ′UTR region. This phenomenon is called stop codon read-through (SCR). It has been suggested that these events would occur on a programmed basis, but the underlying mechanisms are still not well understood. Methods: Here, we present a strategy for the comprehensive identification of SCR events in the Drosophila melanogaster transcriptome by evaluating the ribosomal density profiles. The associated ribosomal leak rate was estimated for every event identified. A statistical characterization of the frequency of nucleotide use in the proximal region to the stop codon in the sequences associated to SCR events was performed. Results: The results show that the nucleotide usage pattern in transcripts with the UGA codon is different from the pattern for those transcripts ending in the UAA codon, suggesting the existence of at least two mechanisms that could alter the translational termination process. Furthermore, a linear regression models for each of the three stop codons was developed, and we show that the models using the nucleotides at informative positions outperforms those models that consider the entire sequence context to the stop codon. Conclusions: We report that distal nucleotides can affect the SCR rate in a stop-codon dependent manner.
Fil: Escobar, Luciana Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
Fil: Alonso, Andrés Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Ronderos, Jorge Rafael. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; Argentina
Fil: Diambra, Luis Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
description Background: A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position. However, it has been observed that ribosomes can misinterpret the stop codon and continue the translation in the 3 ′UTR region. This phenomenon is called stop codon read-through (SCR). It has been suggested that these events would occur on a programmed basis, but the underlying mechanisms are still not well understood. Methods: Here, we present a strategy for the comprehensive identification of SCR events in the Drosophila melanogaster transcriptome by evaluating the ribosomal density profiles. The associated ribosomal leak rate was estimated for every event identified. A statistical characterization of the frequency of nucleotide use in the proximal region to the stop codon in the sequences associated to SCR events was performed. Results: The results show that the nucleotide usage pattern in transcripts with the UGA codon is different from the pattern for those transcripts ending in the UAA codon, suggesting the existence of at least two mechanisms that could alter the translational termination process. Furthermore, a linear regression models for each of the three stop codons was developed, and we show that the models using the nucleotides at informative positions outperforms those models that consider the entire sequence context to the stop codon. Conclusions: We report that distal nucleotides can affect the SCR rate in a stop-codon dependent manner.
publishDate 2022
dc.date.none.fl_str_mv 2022-02
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/11336/215044
Escobar, Luciana Ines; Alonso, Andrés Mariano; Ronderos, Jorge Rafael; Diambra, Luis Anibal; Distal nucleotides affect the rate of stop codon read-through; Higher Education Press Limited Company; Quantitative Biology; 11; 1; 2-2022; 44-58
2095-4697
CONICET Digital
CONICET
url http://hdl.handle.net/11336/215044
identifier_str_mv Escobar, Luciana Ines; Alonso, Andrés Mariano; Ronderos, Jorge Rafael; Diambra, Luis Anibal; Distal nucleotides affect the rate of stop codon read-through; Higher Education Press Limited Company; Quantitative Biology; 11; 1; 2-2022; 44-58
2095-4697
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://journal.hep.com.cn/qb/EN/10.15302/J-QB-022-0298
info:eu-repo/semantics/altIdentifier/doi/10.15302/J-QB-022-0298
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Higher Education Press Limited Company
publisher.none.fl_str_mv Higher Education Press Limited Company
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
_version_ 1842268643691331584
score 13.13397

Publicaciones similares