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 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.Fil: Crescente, Juan M. CONICET; ArgentinaFil: Zavallo, Diego. CONICET. INTA. Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA; ArgentinaFil: del Vas, Mariana. CONICET. INTA. Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA; ArgentinaFil: Asurmendi, Sebastián. CONICET. INTA. Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA; ArgentinaFil: Helguera, Marcelo. EEA INTA; ArgentinaFil: Fernandez, Elmer. Universidad Católica de Córdoba. Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE-CONICET); ArgentinaFil: Fernandez, Elmer. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales; ArgentinaFil: Vanzetti, Leonardo S. CONICET; ArgentinaFil: Vanzetti, Leonardo S. EEA INTA; Argentin