Genome‐wide identification of microRNAs and their targets in the zoonotic parasite Echinococcus canadensis

NATALIA MACCHIAROLI; MARCELA CUCHER; LUCAS MALDONADO; LAURA KAMENETZKY; MARA ROSENZVIT

Conferencia; VI Argentinian Conference on Bioinformatics and Computational Biology; 2015

Genome‐wide identification of microRNAs and their targets in the zoonotic parasiteEchinococcus canadensisNatalia Macchiaroli1, Marcela Cucher1, Lucas Maldonado1, Laura Kamenetzky1, Mara Rosenzvit11Instituto de Investigaciones en Microbiología y Parasitología Médica, IMPaM (UBA‐CONICET),Facultad de Medicina, Paraguay 2155, Piso 13, CP 1121 Buenos Aires, ArgentinaBackgroundMicroRNAs (miRNAs), a class of small non‐coding RNAs, are key regulators of gene expression atpost‐transcriptional level and play essential roles in biological processes such as development andmetabolism. MiRNAs silence target mRNAs by binding to complementary sequences in the3´untranslated regions (UTRs) of their target mRNAs. Here, we perform a comprehensive analysisof miRNAs and their targets in the cestode parasite Echinococcus canadensis, one of the causativeagents of the neglected zoonotic disease cystic echinococcosis.Materials and methodsSmall cDNA libraries from two developmental stages, protoscoleces and cyst walls of E. canadensiswere sequenced using Illumina technology. For miRNA prediction, miRDeep2 core algorithm wasused. Differential expression analysis of miRNAs between developmental stages was estimatedwith DESeq and validated using poly‐A RT‐qPCR. Potential mRNA targets of differentially expressedmiRNAs were identified using miRanda algorithm and then filtered using different criteria such asconservation of miRNA binding sites in orthologous mRNAs of other cestode parasites in order toobtain a high confidence set of predictions. Functional information of the potential mRNA targetswas obtained from GeneDB, wormParasite DataBase and KEEG databases.ResultsIn this study we used a high‐throughput approach to expand the miRNA repertoire of E.canadensis. Differential expression analysis showed highly regulated miRNAs between life cyclestages, suggesting a role in maintaining the features of each developmental stage or in theregulation of developmental timing. Here we confirmed the remarkable loss of conserved miRNAfamilies in E. canadensis, reflecting their low morphological complexity and high adaptation toparasitism.ConclusionsWe performed the first in‐depth study profiling of small RNAs in the zoonotic parasite E.canadensis. We found that miRNAs are the preponderant small RNA silencing molecules,suggesting that these small RNAs could be an essential mechanism of gene regulation in thisspecies. Functional analysis of the differentially expressed miRNAs and their potential targets willcontribute to elucidate their role in the parasite biology. MicroRNAs associated with parasitedevelopment, metabolism, host‐parasite interaction and survival represent potential targets forthe development of new therapeutic interventions.