Identification and Characterization of microRNAS from <i>Entamoeba histolytica</i> HM1-IMSS

<div><p>Background</p><p><i>Entamoeba histolytica</i> is the causative agent of amebiasis, a disease that is a major source of morbidity and mortality in the developing world. MicroRNAs (miRNAs) are a large group of non-coding RNAs that play important roles in regulating gene expression and protein translation in animals. Genome-wide identification of miRNAs is a critical step to facilitating our understanding of genome organization, genome biology, evolution, and post-transcriptional regulation.</p><p>Methodology/Principal Findings</p><p>We sequenced a small RNA library prepared from a culture of trophozoites of <i>Entamoeba histolytica</i> Strain HM1-IMSS using a deep DNA sequencing approach. Deep sequencing yielded 16 million high-quality short sequence reads containing a total of 5 million non-redundant sequence reads. Based on a bioinformatics pipeline, we found that only 0.5% of these non-redundant small RNA reads were a perfect match with the drafted <i>E. histolytica</i> genome. We did not find miRNA homologs in plant or animal miRNAs. We discovered 199 new potential <i>Entamoeba histolytica</i> miRNAs. The expression and sequence of these Ehi-miRNAs were further validated through microarray by µParaflo Microfluidic Biochip Technology. Ten potential miRNAs were additionally confirmed by real time RT-PCR analysis. Prediction of target genes matched 32 known genes and 34 hypothetical genes.</p><p>Conclusions/Significance</p><p>These results show that there is a number of regulatory miRNAs in <i>Entamoeba histolytica</i>. The collection of miRNAs in this parasite could be used as a new platform to study genomic structure, gene regulation and networks, development, and host-parasite interactions.</p>