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Computational Prediction of Micro RNAs from Toxoplasma gondii Potentially Regulating the hosts' Gene Expression

Genomics, Proteomics & Bioinformatics 2014年第5期12卷 228-238页

作者： Müs?erref Duygu Saar Caner Bagc? Jens Allmer Molecular Biology and Genetics Izmir Institute of Technology Urla Izmir 35430 Turkey Biotechnology Izmir Institute of Technology Urla Izmir 35430 Turkey Bionia Incorporated IZTEKGEB A8 Urla Izmir 35430 Turkey

MicroRNAs （miRNAs） were discovered two decades ago, yet there is still a great need for further studies elucidating their genesis and targeting in different phyla. Since experimental discovery and validation of miRNAs is difficult, computational predictions are indispensable and today most computational approaches employ machine learning. Toxoplasma gondii, a parasite residing within the cells of its hosts like human, uses miRNAs for its post-transcriptional gene reg- ulation. It may also regulate its hosts＇ gene expression, which has been shown in brain cancer. Since previous studies have shown that overexpressed miRNAs within the host are causal for disease onset, we hypothesized that T. gondii could export miRNAs into its host cell. We computationally predicted all hairpins from the genome of T. gondii and used mouse and human models to filter possible candidates. These were then further compared to known miRNAs in human and rodents and their expression was examined for T. gondii grown in mouse and human hosts, respectively. We found that among the millions of potential hairpins in T. gondii, only a few thousand pass filtering using a human or mouse model and that even fewer of those are expressed. Since they are expressed and differentially expressed in rodents and human, we suggest that there is a chance that T. gondii may export miRNAs into its hosts for direct regulation.

关键词： Toxoplasma gondii MicroRNA Regulation host interaction Parasite

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