Integrated co-expression analysis of regulatory elements (miRNA, lncRNA, and TFs) in bovine monocytes induced by Str. uberis
Abstract Non-coding RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), together with transcription factors, are critical pre-, co-, and post-transcriptional regulators. In addition to their criteria as ideal biomarkers, they have great potential in disease prognosis, diagnosis, a...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-09-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-42067-4 |
| _version_ | 1797452727888904192 |
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| author | Somayeh Sharifi Abbas Pakdel Mohammad Hossein Pakdel Raana Tabashiri Mohammad Reza Bakhtiarizadeh Ahmad Tahmasebi |
| author_facet | Somayeh Sharifi Abbas Pakdel Mohammad Hossein Pakdel Raana Tabashiri Mohammad Reza Bakhtiarizadeh Ahmad Tahmasebi |
| author_sort | Somayeh Sharifi |
| collection | DOAJ |
| description | Abstract Non-coding RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), together with transcription factors, are critical pre-, co-, and post-transcriptional regulators. In addition to their criteria as ideal biomarkers, they have great potential in disease prognosis, diagnosis, and treatment of complex diseases. Investigation of regulatory mechanisms in the context of bovine mastitis, as most common and economic disease in the dairy industry, to identify elements influencing the expression of candidate genes as key regulators of the mammary immune response is not yet fully understood. Transcriptome profiles (50 RNA-Seq and 50 miRNA-Seq samples) of bovine monocytes induced by Str. uberis were used for co-expression module detection and preservation analysis using the weighted gene co-expression network analysis (WGCNA) approach. Assigned mi-, lnc-, and m-modules used to construct the integrated regulatory networks and miRNA-lncRNA-mRNA regulatory sub-networks. Remarkably, we have identified 18 miRNAs, five lncRNAs, and seven TFs as key regulators of str. uberis-induced mastitis. Most of the genes introduced here, mainly involved in immune response, inflammation, and apoptosis, were new to mastitis. These findings may help to further elucidate the underlying mechanisms of bovine mastitis, and the discovered genes may serve as signatures for early diagnosis and treatment of the disease. |
| first_indexed | 2024-03-09T15:12:51Z |
| format | Article |
| id | doaj.art-8794f488a5bf4e7bb3359fc2cac404c0 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-09T15:12:51Z |
| publishDate | 2023-09-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-8794f488a5bf4e7bb3359fc2cac404c02023-11-26T13:15:40ZengNature PortfolioScientific Reports2045-23222023-09-0113111510.1038/s41598-023-42067-4Integrated co-expression analysis of regulatory elements (miRNA, lncRNA, and TFs) in bovine monocytes induced by Str. uberisSomayeh Sharifi0Abbas Pakdel1Mohammad Hossein Pakdel2Raana Tabashiri3Mohammad Reza Bakhtiarizadeh4Ahmad Tahmasebi5Department of Animal Science, College of Agriculture, Isfahan University of TechnologyDepartment of Animal Science, College of Agriculture, Isfahan University of TechnologyDepartment of Plant Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB)Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares UniversityDepartment of Animal and Poultry Science, College of Aburaihan, University of TehranInstitute of Biotechnology, Shiraz UniversityAbstract Non-coding RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), together with transcription factors, are critical pre-, co-, and post-transcriptional regulators. In addition to their criteria as ideal biomarkers, they have great potential in disease prognosis, diagnosis, and treatment of complex diseases. Investigation of regulatory mechanisms in the context of bovine mastitis, as most common and economic disease in the dairy industry, to identify elements influencing the expression of candidate genes as key regulators of the mammary immune response is not yet fully understood. Transcriptome profiles (50 RNA-Seq and 50 miRNA-Seq samples) of bovine monocytes induced by Str. uberis were used for co-expression module detection and preservation analysis using the weighted gene co-expression network analysis (WGCNA) approach. Assigned mi-, lnc-, and m-modules used to construct the integrated regulatory networks and miRNA-lncRNA-mRNA regulatory sub-networks. Remarkably, we have identified 18 miRNAs, five lncRNAs, and seven TFs as key regulators of str. uberis-induced mastitis. Most of the genes introduced here, mainly involved in immune response, inflammation, and apoptosis, were new to mastitis. These findings may help to further elucidate the underlying mechanisms of bovine mastitis, and the discovered genes may serve as signatures for early diagnosis and treatment of the disease.https://doi.org/10.1038/s41598-023-42067-4 |
| spellingShingle | Somayeh Sharifi Abbas Pakdel Mohammad Hossein Pakdel Raana Tabashiri Mohammad Reza Bakhtiarizadeh Ahmad Tahmasebi Integrated co-expression analysis of regulatory elements (miRNA, lncRNA, and TFs) in bovine monocytes induced by Str. uberis Scientific Reports |
| title | Integrated co-expression analysis of regulatory elements (miRNA, lncRNA, and TFs) in bovine monocytes induced by Str. uberis |
| title_full | Integrated co-expression analysis of regulatory elements (miRNA, lncRNA, and TFs) in bovine monocytes induced by Str. uberis |
| title_fullStr | Integrated co-expression analysis of regulatory elements (miRNA, lncRNA, and TFs) in bovine monocytes induced by Str. uberis |
| title_full_unstemmed | Integrated co-expression analysis of regulatory elements (miRNA, lncRNA, and TFs) in bovine monocytes induced by Str. uberis |
| title_short | Integrated co-expression analysis of regulatory elements (miRNA, lncRNA, and TFs) in bovine monocytes induced by Str. uberis |
| title_sort | integrated co expression analysis of regulatory elements mirna lncrna and tfs in bovine monocytes induced by str uberis |
| url | https://doi.org/10.1038/s41598-023-42067-4 |
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