Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat

Autores
Crescente, Juan Manuel; Zavallo, Diego; Del Vas, Mariana; Asurmendi, Sebastian; Helguera, Marcelo; Fernandez, Elmer; Vanzetti, Leonardo Sebastian
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Plant miRNAs are a class of small non-coding RNAs that can repress gene expression at the post-transcriptional level by targeting RNA degradation or promoting translational repression. There is increasing evidence that some miRNAs can derive from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs). Results: We used public small RNA and degradome libraries from Triticum aestivum to screen for microRNAs production and predict their cleavage target sites. In parallel, we also created a comprehensive wheat MITE database by identifying novel elements and compiling known ones. When comparing both data sets, we found high homology between MITEs and 14% of all the miRNAs production sites detected. Furthermore, we show that MITE-derived miRNAs have preference for targeting degradation sites with MITE insertions in the 3’ UTR regions of the transcripts. Conclusions: Our results revealed that MITE-derived miRNAs can underlay the origin of some miRNAs and potentially shape a regulatory gene network. Since MITEs are found in millions of insertions in the wheat genome and are closely linked to genic regions, this kind of regulatory network could have a significant impact on the post-transcriptional control of gene expression.
Instituto de Biotecnología
Fil: Crescente, Juan Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Zavallo, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Del Vas, Mariana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Del Vas, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Asurmendi, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones Agropecuarias; Argentina
Fil: Fernandez, Elmer. Universidad Católica de Córdoba. Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas; Argentina
Fil: Fernandez, Elmer. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Vanzetti, Leonardo Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez; Argentina
Fil: Vanzetti, Leonardo Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fuente
BMC Genomics 23 (1) : 154 (Febrero 2022)
Materia
MicroRNA
Gene Expression
Gene Regulatory Networks
Wheat
Soft Wheat
MicroARN
Triticum aestivum
Expresión Génica
Redes de Regulación Génica
Trigo
Trigo Harinero
Trigo Pan
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/11871
Acceder
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oai_identifier_str oai:localhost:20.500.12123/11871
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling Genome-wide identification of MITE-derived microRNAs and their targets in bread wheatCrescente, Juan ManuelZavallo, DiegoDel Vas, MarianaAsurmendi, SebastianHelguera, MarceloFernandez, ElmerVanzetti, Leonardo SebastianMicroRNAGene ExpressionGene Regulatory NetworksWheatSoft WheatMicroARNTriticum aestivumExpresión GénicaRedes de Regulación GénicaTrigoTrigo HarineroTrigo PanBackground: Plant miRNAs are a class of small non-coding RNAs that can repress gene expression at the post-transcriptional level by targeting RNA degradation or promoting translational repression. There is increasing evidence that some miRNAs can derive from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs). Results: We used public small RNA and degradome libraries from Triticum aestivum to screen for microRNAs production and predict their cleavage target sites. In parallel, we also created a comprehensive wheat MITE database by identifying novel elements and compiling known ones. When comparing both data sets, we found high homology between MITEs and 14% of all the miRNAs production sites detected. Furthermore, we show that MITE-derived miRNAs have preference for targeting degradation sites with MITE insertions in the 3’ UTR regions of the transcripts. Conclusions: Our results revealed that MITE-derived miRNAs can underlay the origin of some miRNAs and potentially shape a regulatory gene network. Since MITEs are found in millions of insertions in the wheat genome and are closely linked to genic regions, this kind of regulatory network could have a significant impact on the post-transcriptional control of gene expression.Instituto de BiotecnologíaFil: Crescente, Juan Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Zavallo, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Del Vas, Mariana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Del Vas, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Asurmendi, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones Agropecuarias; ArgentinaFil: Fernandez, Elmer. Universidad Católica de Córdoba. Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas; ArgentinaFil: Fernandez, Elmer. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Vanzetti, Leonardo Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez; ArgentinaFil: Vanzetti, Leonardo Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaBioMed Central2022-05-13T10:46:54Z2022-05-13T10:46:54Z2022-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/11871https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08364-41471-2164https://doi.org/10.1186/s12864-022-08364-4BMC Genomics 23 (1) : 154 (Febrero 2022)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/PNBIO-1131022/AR./Genómica funcional y biología de sistemas.info:eu-repograntAgreement/INTA/2019-PD-E6-I116-001/2019-PD-E6-I116-001/AR./Identificación y análisis funcional de genes o redes génicas de interés biotecnológico con fin agropecuario, forestal, agroalimentario y/o agroindustrial.info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-10-23T11:17:58Zoai:localhost:20.500.12123/11871instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-23 11:17:58.399INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
title Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
spellingShingle Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
Crescente, Juan Manuel
MicroRNA
Gene Expression
Gene Regulatory Networks
Wheat
Soft Wheat
MicroARN
Triticum aestivum
Expresión Génica
Redes de Regulación Génica
Trigo
Trigo Harinero
Trigo Pan
title_short Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
title_full Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
title_fullStr Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
title_full_unstemmed Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
title_sort Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
dc.creator.none.fl_str_mv Crescente, Juan Manuel
Zavallo, Diego
Del Vas, Mariana
Asurmendi, Sebastian
Helguera, Marcelo
Fernandez, Elmer
Vanzetti, Leonardo Sebastian
author Crescente, Juan Manuel
author_facet Crescente, Juan Manuel
Zavallo, Diego
Del Vas, Mariana
Asurmendi, Sebastian
Helguera, Marcelo
Fernandez, Elmer
Vanzetti, Leonardo Sebastian
author_role author
author2 Zavallo, Diego
Del Vas, Mariana
Asurmendi, Sebastian
Helguera, Marcelo
Fernandez, Elmer
Vanzetti, Leonardo Sebastian
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv MicroRNA
Gene Expression
Gene Regulatory Networks
Wheat
Soft Wheat
MicroARN
Triticum aestivum
Expresión Génica
Redes de Regulación Génica
Trigo
Trigo Harinero
Trigo Pan
topic MicroRNA
Gene Expression
Gene Regulatory Networks
Wheat
Soft Wheat
MicroARN
Triticum aestivum
Expresión Génica
Redes de Regulación Génica
Trigo
Trigo Harinero
Trigo Pan
dc.description.none.fl_txt_mv Background: Plant miRNAs are a class of small non-coding RNAs that can repress gene expression at the post-transcriptional level by targeting RNA degradation or promoting translational repression. There is increasing evidence that some miRNAs can derive from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs). Results: We used public small RNA and degradome libraries from Triticum aestivum to screen for microRNAs production and predict their cleavage target sites. In parallel, we also created a comprehensive wheat MITE database by identifying novel elements and compiling known ones. When comparing both data sets, we found high homology between MITEs and 14% of all the miRNAs production sites detected. Furthermore, we show that MITE-derived miRNAs have preference for targeting degradation sites with MITE insertions in the 3’ UTR regions of the transcripts. Conclusions: Our results revealed that MITE-derived miRNAs can underlay the origin of some miRNAs and potentially shape a regulatory gene network. Since MITEs are found in millions of insertions in the wheat genome and are closely linked to genic regions, this kind of regulatory network could have a significant impact on the post-transcriptional control of gene expression.
Instituto de Biotecnología
Fil: Crescente, Juan Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Zavallo, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Del Vas, Mariana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Del Vas, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Asurmendi, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigaciones Agropecuarias; Argentina
Fil: Fernandez, Elmer. Universidad Católica de Córdoba. Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas; Argentina
Fil: Fernandez, Elmer. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Vanzetti, Leonardo Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez; Argentina
Fil: Vanzetti, Leonardo Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Background: Plant miRNAs are a class of small non-coding RNAs that can repress gene expression at the post-transcriptional level by targeting RNA degradation or promoting translational repression. There is increasing evidence that some miRNAs can derive from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs). Results: We used public small RNA and degradome libraries from Triticum aestivum to screen for microRNAs production and predict their cleavage target sites. In parallel, we also created a comprehensive wheat MITE database by identifying novel elements and compiling known ones. When comparing both data sets, we found high homology between MITEs and 14% of all the miRNAs production sites detected. Furthermore, we show that MITE-derived miRNAs have preference for targeting degradation sites with MITE insertions in the 3’ UTR regions of the transcripts. Conclusions: Our results revealed that MITE-derived miRNAs can underlay the origin of some miRNAs and potentially shape a regulatory gene network. Since MITEs are found in millions of insertions in the wheat genome and are closely linked to genic regions, this kind of regulatory network could have a significant impact on the post-transcriptional control of gene expression.
publishDate 2022
dc.date.none.fl_str_mv 2022-05-13T10:46:54Z
2022-05-13T10:46:54Z
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/20.500.12123/11871
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08364-4
1471-2164
https://doi.org/10.1186/s12864-022-08364-4
url http://hdl.handle.net/20.500.12123/11871
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08364-4
https://doi.org/10.1186/s12864-022-08364-4
identifier_str_mv 1471-2164
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/PNBIO-1131022/AR./Genómica funcional y biología de sistemas.
info:eu-repograntAgreement/INTA/2019-PD-E6-I116-001/2019-PD-E6-I116-001/AR./Identificación y análisis funcional de genes o redes génicas de interés biotecnológico con fin agropecuario, forestal, agroalimentario y/o agroindustrial.
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv BMC Genomics 23 (1) : 154 (Febrero 2022)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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