Abstract
Background Entamoeba histolytica 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.Methodology/Principal FindingsWe sequenced a small RNA library prepared from a culture of trophozoites of Entamoeba histolytica 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 E. histolytica genome. We did not find miRNA homologs in plant or animal miRNAs. We discovered 199 new potential Entamoeba histolytica 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.Conclusions/SignificanceThese results show that there is a number of regulatory miRNAs in Entamoeba histolytica. 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.
Highlights
Entamoeba histolytica causes amebic dysentery and liver abscesses
We performed several ‘‘mappings’’ on unique seqs against pre-miRNA and mature miRNA sequences listed in the latest release of miRBase [12], or genome based on the public releases of appropriate species
The mapped unique seqs were grouped as ‘‘unique seqs mapped to selected pre-miRNA in miRbase’’, while the remaining ones were grouped as ‘‘unique seqs un-mapped to selected pre-miRNA in miRbase’’
Summary
Entamoeba histolytica causes amebic dysentery and liver abscesses. The parasite and host factors that control the outcome of this infection (asymptomatic infection versus amebic dysentery and/or liver abscesses) are not well understood, there is emerging evidence that host, parasite and environmental factors influence the outcome of infection [1,2,3]. The latent period between infection and disease in humans suggests that the parasite adapts to the host via altered gene expression [4]. This is best illustrated by the ability of E. histolytica to select for increased virulence of an axenic strain of E. histolytica by multiple rounds of passage through animals [5]. Genome-wide identification of miRNAs is a critical step to facilitating our understanding of genome organization, genome biology, evolution, and post-transcriptional regulation
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