Evolutionary Changes in the Interaction of miRNA With mRNA of Candidate Genes for Parkinson’s Disease
Parkinson’s disease (PD) exhibits the second-highest rate of mortality among neurodegenerative diseases. PD is difficult to diagnose and treat due to its polygenic nature. In recent years, numerous studies have established a correlation between this disease and miRNA expression; however, it remains...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.647288/full |
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| author | Saltanat Kamenova Assel Aralbayeva Aida Kondybayeva Aigul Akimniyazova Aigul Akimniyazova Anna Pyrkova Anatoliy Ivashchenko |
| author_facet | Saltanat Kamenova Assel Aralbayeva Aida Kondybayeva Aigul Akimniyazova Aigul Akimniyazova Anna Pyrkova Anatoliy Ivashchenko |
| author_sort | Saltanat Kamenova |
| collection | DOAJ |
| description | Parkinson’s disease (PD) exhibits the second-highest rate of mortality among neurodegenerative diseases. PD is difficult to diagnose and treat due to its polygenic nature. In recent years, numerous studies have established a correlation between this disease and miRNA expression; however, it remains necessary to determine the quantitative characteristics of the interactions between miRNAs and their target genes. In this study, using novel bioinformatics approaches, the quantitative characteristics of the interactions between miRNAs and the mRNAs of candidate PD genes were established. Of the 6,756 miRNAs studied, more than one hundred efficiently bound to mRNA of 61 candidate PD genes. The miRNA binding sites (BS) were located in the 5′-untranslated region (5′UTR), coding sequence (CDS) and 3′-untranslated region (3′UTR) of the mRNAs. In the mRNAs of many genes, the locations of miRNA BS with overlapping nucleotide sequences (clusters) were identified. Such clusters substantially reduced the proportion of nucleotide sequences of miRNA BS in the 5′UTRs, CDSs, and 3′UTRs. The organization of miRNA BS into clusters leads to competition among miRNAs to bind mRNAs. Differences in the binding characteristics of miRNAs to the mRNAs of genes expressed at different rates were identified. Single miRNA BS, polysites for the binding for one miRNA, and multiple BS for two or more miRNAs in one mRNA were identified. Evolutionary changes in the BS of miRNAs and their clusters in 5′UTRs, CDSs and 3′UTRs of mRNA of orthologous candidate PD genes were established. Based on the quantitative characteristics of the interactions between miRNAs and mRNAs candidate PD genes, several associations recommended as markers for the diagnosis of PD. |
| first_indexed | 2024-12-17T22:10:45Z |
| format | Article |
| id | doaj.art-c629054b403f4c289353dfb9941afa19 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-17T22:10:45Z |
| publishDate | 2021-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-c629054b403f4c289353dfb9941afa192022-12-21T21:30:45ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-03-011210.3389/fgene.2021.647288647288Evolutionary Changes in the Interaction of miRNA With mRNA of Candidate Genes for Parkinson’s DiseaseSaltanat Kamenova0Assel Aralbayeva1Aida Kondybayeva2Aigul Akimniyazova3Aigul Akimniyazova4Anna Pyrkova5Anatoliy Ivashchenko6Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, KazakhstanDepartment of Neurology, Kazakh Medical University, Almaty, KazakhstanFaculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, KazakhstanFaculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, KazakhstanFaculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, KazakhstanFaculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, KazakhstanFaculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, KazakhstanParkinson’s disease (PD) exhibits the second-highest rate of mortality among neurodegenerative diseases. PD is difficult to diagnose and treat due to its polygenic nature. In recent years, numerous studies have established a correlation between this disease and miRNA expression; however, it remains necessary to determine the quantitative characteristics of the interactions between miRNAs and their target genes. In this study, using novel bioinformatics approaches, the quantitative characteristics of the interactions between miRNAs and the mRNAs of candidate PD genes were established. Of the 6,756 miRNAs studied, more than one hundred efficiently bound to mRNA of 61 candidate PD genes. The miRNA binding sites (BS) were located in the 5′-untranslated region (5′UTR), coding sequence (CDS) and 3′-untranslated region (3′UTR) of the mRNAs. In the mRNAs of many genes, the locations of miRNA BS with overlapping nucleotide sequences (clusters) were identified. Such clusters substantially reduced the proportion of nucleotide sequences of miRNA BS in the 5′UTRs, CDSs, and 3′UTRs. The organization of miRNA BS into clusters leads to competition among miRNAs to bind mRNAs. Differences in the binding characteristics of miRNAs to the mRNAs of genes expressed at different rates were identified. Single miRNA BS, polysites for the binding for one miRNA, and multiple BS for two or more miRNAs in one mRNA were identified. Evolutionary changes in the BS of miRNAs and their clusters in 5′UTRs, CDSs and 3′UTRs of mRNA of orthologous candidate PD genes were established. Based on the quantitative characteristics of the interactions between miRNAs and mRNAs candidate PD genes, several associations recommended as markers for the diagnosis of PD.https://www.frontiersin.org/articles/10.3389/fgene.2021.647288/fullgenephylogenyParkinson’s diseasemiRNAmRNAassociation |
| spellingShingle | Saltanat Kamenova Assel Aralbayeva Aida Kondybayeva Aigul Akimniyazova Aigul Akimniyazova Anna Pyrkova Anatoliy Ivashchenko Evolutionary Changes in the Interaction of miRNA With mRNA of Candidate Genes for Parkinson’s Disease Frontiers in Genetics gene phylogeny Parkinson’s disease miRNA mRNA association |
| title | Evolutionary Changes in the Interaction of miRNA With mRNA of Candidate Genes for Parkinson’s Disease |
| title_full | Evolutionary Changes in the Interaction of miRNA With mRNA of Candidate Genes for Parkinson’s Disease |
| title_fullStr | Evolutionary Changes in the Interaction of miRNA With mRNA of Candidate Genes for Parkinson’s Disease |
| title_full_unstemmed | Evolutionary Changes in the Interaction of miRNA With mRNA of Candidate Genes for Parkinson’s Disease |
| title_short | Evolutionary Changes in the Interaction of miRNA With mRNA of Candidate Genes for Parkinson’s Disease |
| title_sort | evolutionary changes in the interaction of mirna with mrna of candidate genes for parkinson s disease |
| topic | gene phylogeny Parkinson’s disease miRNA mRNA association |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.647288/full |
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