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
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/11871
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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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