Computer analysis shows differences between mitochondrial miRNAs and other miRNAs
A subclass of miRNAs with as yet unknown specific functions is mitomiRs – mitochondrial miRNAs that are mainly derived from nuclear DNA and are imported into mitochondria; moreover, changes in the expression levels of mitomiRs are associated with some diseases. To identify the most pronounced charac...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2025-01-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/4405 |
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| _version_ | 1832575024787095552 |
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| author | P. S. Vorozheykin I. I. Titov |
| author_facet | P. S. Vorozheykin I. I. Titov |
| author_sort | P. S. Vorozheykin |
| collection | DOAJ |
| description | A subclass of miRNAs with as yet unknown specific functions is mitomiRs – mitochondrial miRNAs that are mainly derived from nuclear DNA and are imported into mitochondria; moreover, changes in the expression levels of mitomiRs are associated with some diseases. To identify the most pronounced characteristics of mitochondrial miRNAs that distinguish them from other miRNAs, we classified mitomiR sequences using the Random Forest algorithm. The analysis revealed, for the first time, a significant difference between mitomiRs and other microRNAs by the following criteria (in descending order of importance in the classification): mitomiRs are evolutionarily older (have a lower phylostratigraphic age index, PAI); have more targets and disease associations, including mitochondrial ones (twosided Fisher’s exact test, average p-values 1.82×10–89/1.13×10–96 for all mRNA/diseases and 6.01×10–22/1.09×10–9 for mitochondria, respectively); and are in the class of “circulating” miRNAs (average pvalue 1.20×10–56). The identified differences between mitomiRs and other miRNAs may help uncover the mode of miRNA delivery into mitochondria, indicate the evolutionary conservation and importance of mitomiRs in the regulation of mitochondrial function and metabolism, and generally show that mitomiRs are not randomly encountered miRNAs. Information on 1,312 experimentally validated mitomiR sequences for three organisms (Homo sapiens, Mus musculus and Rattus norvegicus) is collected in the mitomiRdb database (https://mitomiRdb.org). |
| format | Article |
| id | doaj-art-7c62a8ffaa92411997e326032987e9d3 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-7c62a8ffaa92411997e326032987e9d32025-02-01T09:58:14ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592025-01-0128883484210.18699/vjgb-24-911518Computer analysis shows differences between mitochondrial miRNAs and other miRNAsP. S. Vorozheykin0I. I. Titov1Novosibirsk State UniversityNovosibirsk State University; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RASA subclass of miRNAs with as yet unknown specific functions is mitomiRs – mitochondrial miRNAs that are mainly derived from nuclear DNA and are imported into mitochondria; moreover, changes in the expression levels of mitomiRs are associated with some diseases. To identify the most pronounced characteristics of mitochondrial miRNAs that distinguish them from other miRNAs, we classified mitomiR sequences using the Random Forest algorithm. The analysis revealed, for the first time, a significant difference between mitomiRs and other microRNAs by the following criteria (in descending order of importance in the classification): mitomiRs are evolutionarily older (have a lower phylostratigraphic age index, PAI); have more targets and disease associations, including mitochondrial ones (twosided Fisher’s exact test, average p-values 1.82×10–89/1.13×10–96 for all mRNA/diseases and 6.01×10–22/1.09×10–9 for mitochondria, respectively); and are in the class of “circulating” miRNAs (average pvalue 1.20×10–56). The identified differences between mitomiRs and other miRNAs may help uncover the mode of miRNA delivery into mitochondria, indicate the evolutionary conservation and importance of mitomiRs in the regulation of mitochondrial function and metabolism, and generally show that mitomiRs are not randomly encountered miRNAs. Information on 1,312 experimentally validated mitomiR sequences for three organisms (Homo sapiens, Mus musculus and Rattus norvegicus) is collected in the mitomiRdb database (https://mitomiRdb.org).https://vavilov.elpub.ru/jour/article/view/4405mitomirmitochondriamirnaevolutiondatabase |
| spellingShingle | P. S. Vorozheykin I. I. Titov Computer analysis shows differences between mitochondrial miRNAs and other miRNAs Вавиловский журнал генетики и селекции mitomir mitochondria mirna evolution database |
| title | Computer analysis shows differences between mitochondrial miRNAs and other miRNAs |
| title_full | Computer analysis shows differences between mitochondrial miRNAs and other miRNAs |
| title_fullStr | Computer analysis shows differences between mitochondrial miRNAs and other miRNAs |
| title_full_unstemmed | Computer analysis shows differences between mitochondrial miRNAs and other miRNAs |
| title_short | Computer analysis shows differences between mitochondrial miRNAs and other miRNAs |
| title_sort | computer analysis shows differences between mitochondrial mirnas and other mirnas |
| topic | mitomir mitochondria mirna evolution database |
| url | https://vavilov.elpub.ru/jour/article/view/4405 |
| work_keys_str_mv | AT psvorozheykin computeranalysisshowsdifferencesbetweenmitochondrialmirnasandothermirnas AT iititov computeranalysisshowsdifferencesbetweenmitochondrialmirnasandothermirnas |