A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse
Abstract Background The post-anal tail is a common physical feature of vertebrates including mammals. Although it exhibits rich phenotypic diversity, its development has been evolutionarily conserved as early as the embryonic period. Genes participating in embryonic tail morphogenesis have hitherto...
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BMC
2025-03-01
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| Series: | BMC Biology |
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| Online Access: | https://doi.org/10.1186/s12915-025-02192-0 |
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| author | Yong-Xuan Chen Xiu-Ping Zhang David N. Cooper Dong-Dong Wu Wan-Dong Bao |
| author_facet | Yong-Xuan Chen Xiu-Ping Zhang David N. Cooper Dong-Dong Wu Wan-Dong Bao |
| author_sort | Yong-Xuan Chen |
| collection | DOAJ |
| description | Abstract Background The post-anal tail is a common physical feature of vertebrates including mammals. Although it exhibits rich phenotypic diversity, its development has been evolutionarily conserved as early as the embryonic period. Genes participating in embryonic tail morphogenesis have hitherto been widely explored on the basis of experimental discovery, whereas the associated cis-regulatory elements (CREs) have not yet been systematically investigated for vertebrate/mammalian tail development. Results Here, utilizing high-throughput sequencing schemes pioneered in mice, we profiled the dynamic transcriptome and CREs marked by active histone modifications during embryonic tail morphogenesis. Temporal and spatial disparity analyses revealed the genes specific to tail development and their putative CREs, which facilitated the identification of novel molecular expression features and potential regulatory influence of non-coding loci including long non-coding RNA (lncRNA) genes and CREs. Moreover, these identified sets of multi-omics data supply genetic clues for understanding the regulatory effects of relevant signaling pathways (such as Fgf, Wnt) dominating embryonic tail morphogenesis. Conclusions Our work brings new insights and provides exploitable fundamental datasets for the elucidation of the complex genetic mechanisms responsible for the formation of the vertebrate/mammalian tail. |
| format | Article |
| id | doaj-art-c4ce6b521d5f49c791b2f6da0ddd338d |
| institution | OA Journals |
| issn | 1741-7007 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj-art-c4ce6b521d5f49c791b2f6da0ddd338d2025-08-20T02:10:14ZengBMCBMC Biology1741-70072025-03-0123112010.1186/s12915-025-02192-0A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouseYong-Xuan Chen0Xiu-Ping Zhang1David N. Cooper2Dong-Dong Wu3Wan-Dong Bao4State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of SciencesState Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of SciencesInstitute of Medical Genetics, School of Medicine, Cardiff UniversityState Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of SciencesState Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of SciencesAbstract Background The post-anal tail is a common physical feature of vertebrates including mammals. Although it exhibits rich phenotypic diversity, its development has been evolutionarily conserved as early as the embryonic period. Genes participating in embryonic tail morphogenesis have hitherto been widely explored on the basis of experimental discovery, whereas the associated cis-regulatory elements (CREs) have not yet been systematically investigated for vertebrate/mammalian tail development. Results Here, utilizing high-throughput sequencing schemes pioneered in mice, we profiled the dynamic transcriptome and CREs marked by active histone modifications during embryonic tail morphogenesis. Temporal and spatial disparity analyses revealed the genes specific to tail development and their putative CREs, which facilitated the identification of novel molecular expression features and potential regulatory influence of non-coding loci including long non-coding RNA (lncRNA) genes and CREs. Moreover, these identified sets of multi-omics data supply genetic clues for understanding the regulatory effects of relevant signaling pathways (such as Fgf, Wnt) dominating embryonic tail morphogenesis. Conclusions Our work brings new insights and provides exploitable fundamental datasets for the elucidation of the complex genetic mechanisms responsible for the formation of the vertebrate/mammalian tail.https://doi.org/10.1186/s12915-025-02192-0Vertebrate/mammal/mouseEmbryonic tail morphogenesisTranscriptomeEpigenomic histone modificationCis-regulatory element |
| spellingShingle | Yong-Xuan Chen Xiu-Ping Zhang David N. Cooper Dong-Dong Wu Wan-Dong Bao A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse BMC Biology Vertebrate/mammal/mouse Embryonic tail morphogenesis Transcriptome Epigenomic histone modification Cis-regulatory element |
| title | A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse |
| title_full | A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse |
| title_fullStr | A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse |
| title_full_unstemmed | A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse |
| title_short | A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse |
| title_sort | combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse |
| topic | Vertebrate/mammal/mouse Embryonic tail morphogenesis Transcriptome Epigenomic histone modification Cis-regulatory element |
| url | https://doi.org/10.1186/s12915-025-02192-0 |
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