Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
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 transp...
| Autores principales: | , , , , , , |
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| Formato: | info:ar-repo/semantics/artículo |
| Lenguaje: | Inglés |
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BioMed Central
2022
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| Materias: | |
| Acceso en línea: | 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 |
| _version_ | 1855036652415614976 |
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| author | Crescente, Juan Manuel Zavallo, Diego Del Vas, Mariana Asurmendi, Sebastian Helguera, Marcelo Fernandez, Elmer Vanzetti, Leonardo Sebastian |
| author_browse | Asurmendi, Sebastian Crescente, Juan Manuel Del Vas, Mariana Fernandez, Elmer Helguera, Marcelo Vanzetti, Leonardo Sebastian Zavallo, Diego |
| author_facet | Crescente, Juan Manuel Zavallo, Diego Del Vas, Mariana Asurmendi, Sebastian Helguera, Marcelo Fernandez, Elmer Vanzetti, Leonardo Sebastian |
| author_sort | Crescente, Juan Manuel |
| collection | INTA Digital |
| 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. |
| format | info:ar-repo/semantics/artículo |
| id | INTA11871 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | BioMed Central |
| publisherStr | BioMed Central |
| record_format | dspace |
| spelling | INTA118712022-08-23T09:29:02Z Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat Crescente, Juan Manuel Zavallo, Diego Del Vas, Mariana Asurmendi, Sebastian Helguera, Marcelo Fernandez, Elmer Vanzetti, Leonardo Sebastian MicroRNA Gene Expression Gene Regulatory Networks Wheat Soft Wheat MicroARN Triticum aestivum Expresión Génica Redes de Regulación Génica Trigo Trigo Harinero Trigo Pan 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 2022-05-13T10:46:54Z 2022-05-13T10:46:54Z 2022-02 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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. 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) application/pdf BioMed Central BMC Genomics 23 (1) : 154 (Febrero 2022) |
| spellingShingle | MicroRNA Gene Expression Gene Regulatory Networks Wheat Soft Wheat MicroARN Triticum aestivum Expresión Génica Redes de Regulación Génica Trigo Trigo Harinero Trigo Pan Crescente, Juan Manuel Zavallo, Diego Del Vas, Mariana Asurmendi, Sebastian Helguera, Marcelo Fernandez, Elmer Vanzetti, Leonardo Sebastian 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 |
| 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_short | 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 |
| topic | MicroRNA Gene Expression Gene Regulatory Networks Wheat Soft Wheat MicroARN Triticum aestivum Expresión Génica Redes de Regulación Génica Trigo Trigo Harinero Trigo Pan |
| 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 |
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