smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites
Degradome sequencing is commonly used to generate high-throughput information on mRNA cleavage sites mediated by small RNAs (sRNA). In our datasets of potato (<i>Solanum tuberosum</i>, St) and <i>Phytophthora infestans</i> (Pi), initial predictions generated high numbers of c...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-04-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/8/4267 |
| _version_ | 1797537046373335040 |
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| author | Kristian Persson Hodén Xinyi Hu German Martinez Christina Dixelius |
| author_facet | Kristian Persson Hodén Xinyi Hu German Martinez Christina Dixelius |
| author_sort | Kristian Persson Hodén |
| collection | DOAJ |
| description | Degradome sequencing is commonly used to generate high-throughput information on mRNA cleavage sites mediated by small RNAs (sRNA). In our datasets of potato (<i>Solanum tuberosum</i>, St) and <i>Phytophthora infestans</i> (Pi), initial predictions generated high numbers of cleavage site predictions, which highlighted the need of improved analytic tools. Here, we present an R package based on a deep learning convolutional neural network (CNN) in a machine learning environment to optimize discrimination of false from true cleavage sites. When applying smartPARE to our datasets on potato during the infection process by the late blight pathogen, 7.3% of all cleavage windows represented true cleavages distributed on 214 sites in <i>P. infestans</i> and 444 sites in potato. The sRNA landscape of the two organisms is complex with uneven sRNA production and cleavage regions widespread in the two genomes. Multiple targets and several cases of complex regulatory cascades, particularly in potato, was revealed. We conclude that our new analytic approach is useful for anyone working on complex biological systems and with the interest of identifying cleavage sites particularly inferred by sRNA classes beyond miRNAs. |
| first_indexed | 2024-03-10T12:09:32Z |
| format | Article |
| id | doaj.art-4d103392d7b14e419106b7968ec7417c |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T12:09:32Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-4d103392d7b14e419106b7968ec7417c2023-11-21T16:19:00ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-04-01228426710.3390/ijms22084267smartPARE: An R Package for Efficient Identification of True mRNA Cleavage SitesKristian Persson Hodén0Xinyi Hu1German Martinez2Christina Dixelius3The Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, SwedenThe Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, SwedenThe Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, SwedenThe Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, SwedenDegradome sequencing is commonly used to generate high-throughput information on mRNA cleavage sites mediated by small RNAs (sRNA). In our datasets of potato (<i>Solanum tuberosum</i>, St) and <i>Phytophthora infestans</i> (Pi), initial predictions generated high numbers of cleavage site predictions, which highlighted the need of improved analytic tools. Here, we present an R package based on a deep learning convolutional neural network (CNN) in a machine learning environment to optimize discrimination of false from true cleavage sites. When applying smartPARE to our datasets on potato during the infection process by the late blight pathogen, 7.3% of all cleavage windows represented true cleavages distributed on 214 sites in <i>P. infestans</i> and 444 sites in potato. The sRNA landscape of the two organisms is complex with uneven sRNA production and cleavage regions widespread in the two genomes. Multiple targets and several cases of complex regulatory cascades, particularly in potato, was revealed. We conclude that our new analytic approach is useful for anyone working on complex biological systems and with the interest of identifying cleavage sites particularly inferred by sRNA classes beyond miRNAs.https://www.mdpi.com/1422-0067/22/8/4267cleavage sites<i>Phytophthora infestans</i>potatosmall RNA<i>Solanum tuberosum</i> |
| spellingShingle | Kristian Persson Hodén Xinyi Hu German Martinez Christina Dixelius smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites International Journal of Molecular Sciences cleavage sites <i>Phytophthora infestans</i> potato small RNA <i>Solanum tuberosum</i> |
| title | smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites |
| title_full | smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites |
| title_fullStr | smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites |
| title_full_unstemmed | smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites |
| title_short | smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites |
| title_sort | smartpare an r package for efficient identification of true mrna cleavage sites |
| topic | cleavage sites <i>Phytophthora infestans</i> potato small RNA <i>Solanum tuberosum</i> |
| url | https://www.mdpi.com/1422-0067/22/8/4267 |
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