An Integrated Database for Exploring Alternative Promoters in Animals
Abstract Alternative promoter (AP) events, as a major pre-transcriptional mechanism, can initiate different transcription start sites to generate distinct mRNA isoforms and regulate their expression. At present, hundreds of thousands of APs have been identified across human tissues, and a considerab...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-02-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04548-1 |
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| _version_ | 1823863272010416128 |
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| author | Feiyang Xue Yuqin Yan Weiwei Jin Haotian Zhu Yanbo Yang Zhanhui Yu Xuewen Xu Jing Gong Xiaohui Niu |
| author_facet | Feiyang Xue Yuqin Yan Weiwei Jin Haotian Zhu Yanbo Yang Zhanhui Yu Xuewen Xu Jing Gong Xiaohui Niu |
| author_sort | Feiyang Xue |
| collection | DOAJ |
| description | Abstract Alternative promoter (AP) events, as a major pre-transcriptional mechanism, can initiate different transcription start sites to generate distinct mRNA isoforms and regulate their expression. At present, hundreds of thousands of APs have been identified across human tissues, and a considerable number of APs have been demonstrated to be associated with complex traits and diseases. Recent researches have also proven important effects of APs on animals. However, the landscape of APs in animals has not been fully recognized. In this study, 102,349 AP profiles from 23,077 samples across 12 species were systematically characterized. We further identified tissue-specific APs and investigated trait-related promoters among various species. In addition, we analyzed the associations between APs and enhancer RNAs (eRNA)/transcription factors (TF) as a means of identifying potential regulatory factors. Integrating these findings, we finally developed Animal-APdb, a database for the searching, browsing, and downloading of information related to Animal APs. Animal-APdb is expected to serve as a valuable resource for exploring the functions and mechanisms of APs in animals. |
| format | Article |
| id | doaj-art-592913fd8b3b40378ef33d3fbff7ffae |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-592913fd8b3b40378ef33d3fbff7ffae2025-02-09T12:11:51ZengNature PortfolioScientific Data2052-44632025-02-011211810.1038/s41597-025-04548-1An Integrated Database for Exploring Alternative Promoters in AnimalsFeiyang Xue0Yuqin Yan1Weiwei Jin2Haotian Zhu3Yanbo Yang4Zhanhui Yu5Xuewen Xu6Jing Gong7Xiaohui Niu8Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural UniversityHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural UniversityHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural UniversityHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural UniversityHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural UniversityHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural UniversityKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural UniversityHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural UniversityHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural UniversityAbstract Alternative promoter (AP) events, as a major pre-transcriptional mechanism, can initiate different transcription start sites to generate distinct mRNA isoforms and regulate their expression. At present, hundreds of thousands of APs have been identified across human tissues, and a considerable number of APs have been demonstrated to be associated with complex traits and diseases. Recent researches have also proven important effects of APs on animals. However, the landscape of APs in animals has not been fully recognized. In this study, 102,349 AP profiles from 23,077 samples across 12 species were systematically characterized. We further identified tissue-specific APs and investigated trait-related promoters among various species. In addition, we analyzed the associations between APs and enhancer RNAs (eRNA)/transcription factors (TF) as a means of identifying potential regulatory factors. Integrating these findings, we finally developed Animal-APdb, a database for the searching, browsing, and downloading of information related to Animal APs. Animal-APdb is expected to serve as a valuable resource for exploring the functions and mechanisms of APs in animals.https://doi.org/10.1038/s41597-025-04548-1 |
| spellingShingle | Feiyang Xue Yuqin Yan Weiwei Jin Haotian Zhu Yanbo Yang Zhanhui Yu Xuewen Xu Jing Gong Xiaohui Niu An Integrated Database for Exploring Alternative Promoters in Animals Scientific Data |
| title | An Integrated Database for Exploring Alternative Promoters in Animals |
| title_full | An Integrated Database for Exploring Alternative Promoters in Animals |
| title_fullStr | An Integrated Database for Exploring Alternative Promoters in Animals |
| title_full_unstemmed | An Integrated Database for Exploring Alternative Promoters in Animals |
| title_short | An Integrated Database for Exploring Alternative Promoters in Animals |
| title_sort | integrated database for exploring alternative promoters in animals |
| url | https://doi.org/10.1038/s41597-025-04548-1 |
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