Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression
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 computati...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2014-10-01
|
| Series: | Genomics, Proteomics & Bioinformatics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672022914001077 |
| _version_ | 1797330699385044992 |
|---|---|
| author | Müşerref Duygu Saçar Caner Bağcı Jens Allmer |
| author_facet | Müşerref Duygu Saçar Caner Bağcı Jens Allmer |
| author_sort | Müşerref Duygu Saçar |
| collection | DOAJ |
| description | 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 regulation. 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. |
| first_indexed | 2024-03-08T07:23:27Z |
| format | Article |
| id | doaj.art-986158ef1e9d4789a914f0aa44a987c5 |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2024-03-08T07:23:27Z |
| publishDate | 2014-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-986158ef1e9d4789a914f0aa44a987c52024-02-02T22:36:50ZengElsevierGenomics, Proteomics & Bioinformatics1672-02292014-10-0112522823810.1016/j.gpb.2014.09.002Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene ExpressionMüşerref Duygu Saçar0Caner Bağcı1Jens Allmer2Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir 35430, TurkeyBiotechnology, Izmir Institute of Technology, Urla, Izmir 35430, TurkeyMolecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir 35430, TurkeyMicroRNAs (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 regulation. 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.http://www.sciencedirect.com/science/article/pii/S1672022914001077Toxoplasma gondiiMicroRNARegulationHost interactionParasite |
| spellingShingle | Müşerref Duygu Saçar Caner Bağcı Jens Allmer Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression Genomics, Proteomics & Bioinformatics Toxoplasma gondii MicroRNA Regulation Host interaction Parasite |
| title | Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression |
| title_full | Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression |
| title_fullStr | Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression |
| title_full_unstemmed | Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression |
| title_short | Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression |
| title_sort | computational prediction of micrornas from toxoplasma gondii potentially regulating the hosts gene expression |
| topic | Toxoplasma gondii MicroRNA Regulation Host interaction Parasite |
| url | http://www.sciencedirect.com/science/article/pii/S1672022914001077 |
| work_keys_str_mv | AT muserrefduygusacar computationalpredictionofmicrornasfromtoxoplasmagondiipotentiallyregulatingthehostsgeneexpression AT canerbagcı computationalpredictionofmicrornasfromtoxoplasmagondiipotentiallyregulatingthehostsgeneexpression AT jensallmer computationalpredictionofmicrornasfromtoxoplasmagondiipotentiallyregulatingthehostsgeneexpression |