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

Abstract
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 [ver mas...]
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. [Cerrar]
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Author
Crescente, Juan Manuel;   Zavallo, Diego;   Del Vas, Mariana;   Asurmendi, Sebastian;   Helguera, Marcelo;   Fernandez, Elmer;   Vanzetti, Leonardo Sebastian;  
Fuente
BMC Genomics 23 (1) : 154 (Febrero 2022)
Date
2022-02
Editorial
BioMed Central
ISSN
1471-2164
URI
http://hdl.handle.net/20.500.12123/11871
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08364-4
DOI
https://doi.org/10.1186/s12864-022-08364-4
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Proyectos (ver más)

INTA/PNBIO-1131022/AR./Genómica funcional y biología de sistemas.

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.

Palabras Claves
MicroRNA; MicroARN; Triticum aestivum; Gene Expression; Expresión Génica; Gene Regulatory Networks; Redes de Regulación Génica; Trigo; Wheat; Trigo Harinero; Soft Wheat; Trigo Pan;
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