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...

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Autores principales: Crescente, Juan M., Zavallo, Diego, del Vas, Mariana, Asurmendi, Sebastián, Helguera, Marcelo, Fernández, Elmer Andrés, Vanzetti, Leonardo S.
Formato: Artículo
Lenguaje:Español
Publicado: BioMed Central Ltd 2022
Materias:
Q Ciencia (General)
QK Botánica
Acceso en línea:http://pa.bibdigital.ucc.edu.ar/3302/1/A_Crescente_del%20Vas_Asurmendi.pdf
Aporte de:
Producción Académica Universidad Católica de Córdoba (UCCor) de Universidad Católica de Córdoba
id I38-R144-3302
record_format dspace
spelling I38-R144-33022025-04-08T20:28:45Z http://pa.bibdigital.ucc.edu.ar/3302/ Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat Crescente, Juan M. Zavallo, Diego del Vas, Mariana Asurmendi, Sebastián Helguera, Marcelo Fernández, Elmer Andrés Vanzetti, Leonardo S. Q Ciencia (General) QK Botánica 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. BioMed Central Ltd 2022-12 info:eu-repo/semantics/article info:eu-repo/semantics/closedAccess application/pdf spa http://pa.bibdigital.ucc.edu.ar/3302/1/A_Crescente_del%20Vas_Asurmendi.pdf Crescente, Juan M., Zavallo, Diego ORCID: https://orcid.org/0000-0002-9021-2175 <https://orcid.org/0000-0002-9021-2175>, del Vas, Mariana ORCID: https://orcid.org/0000-0002-8365-8582 <https://orcid.org/0000-0002-8365-8582>, Asurmendi, Sebastián ORCID: https://orcid.org/0000-0001-9516-5948 <https://orcid.org/0000-0001-9516-5948>, Helguera, Marcelo ORCID: https://orcid.org/0000-0003-4401-8731 <https://orcid.org/0000-0003-4401-8731>, Fernández, Elmer Andrés ORCID: https://orcid.org/0000-0002-4711-8634 <https://orcid.org/0000-0002-4711-8634> and Vanzetti, Leonardo S. ORCID: https://orcid.org/0000-0002-7688-5648 <https://orcid.org/0000-0002-7688-5648> (2022) Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat. BMC Genomics, 23 (1). ISSN 1471-2164 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08364-4 info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-022-08364-4
institution Universidad Católica de Córdoba
institution_str I-38
repository_str R-144
collection Producción Académica Universidad Católica de Córdoba (UCCor)
language Español
orig_language_str_mv spa
topic Q Ciencia (General)
QK Botánica
spellingShingle Q Ciencia (General)
QK Botánica
Crescente, Juan M.
Zavallo, Diego
del Vas, Mariana
Asurmendi, Sebastián
Helguera, Marcelo
Fernández, Elmer Andrés
Vanzetti, Leonardo S.
Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
topic_facet Q Ciencia (General)
QK Botánica
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 Artículo
author Crescente, Juan M.
Zavallo, Diego
del Vas, Mariana
Asurmendi, Sebastián
Helguera, Marcelo
Fernández, Elmer Andrés
Vanzetti, Leonardo S.
author_facet Crescente, Juan M.
Zavallo, Diego
del Vas, Mariana
Asurmendi, Sebastián
Helguera, Marcelo
Fernández, Elmer Andrés
Vanzetti, Leonardo S.
author_sort Crescente, Juan M.
title 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_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
publisher BioMed Central Ltd
publishDate 2022
url http://pa.bibdigital.ucc.edu.ar/3302/1/A_Crescente_del%20Vas_Asurmendi.pdf
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