Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals
Summary: Alternative splicing (AS) as one of the important post-transcriptional regulatory mechanisms has been poorly studied during embryogenesis. In this study, we comprehensively collected and analyzed the transcriptome data of early embryos from human and mouse. We found that AS plays an importa...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-03-01
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| Series: | iScience |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004224003250 |
| _version_ | 1797295746760835072 |
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| author | Jianhua Chen Yanni He Liangliang Chen Tian Wu Guangping Yang Hui Luo Saifei Hu Siyue Yin Yun Qian Hui Miao Na Li Congxiu Miao Ruizhi Feng |
| author_facet | Jianhua Chen Yanni He Liangliang Chen Tian Wu Guangping Yang Hui Luo Saifei Hu Siyue Yin Yun Qian Hui Miao Na Li Congxiu Miao Ruizhi Feng |
| author_sort | Jianhua Chen |
| collection | DOAJ |
| description | Summary: Alternative splicing (AS) as one of the important post-transcriptional regulatory mechanisms has been poorly studied during embryogenesis. In this study, we comprehensively collected and analyzed the transcriptome data of early embryos from human and mouse. We found that AS plays an important role in this process and predicted candidate RNA binding protein (RBP) regulators that are associated with reproductive development. The predicted RBPs such as EIF4A3, MAK16, SRSF2, and UTP23 were found to be associated with reproductive disorders. By Smart-seq2 sequencing analysis, we identified 5445 aberrant alternative splicing events in Eif4a3-knockdown embryos. These events were preferentially associated with RNA processing. In conclusion, our work on the landscape and potential function of alternative splicing events will boost further investigation of detailed mechanisms and key factors regulating mammalian early embryo development and promote the inspiration of pharmaceutical approaches for disorders in this crucial biology process. |
| first_indexed | 2024-03-07T21:53:23Z |
| format | Article |
| id | doaj.art-844b6f2ed4d44b50af0947e41b65ce34 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-03-07T21:53:23Z |
| publishDate | 2024-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-844b6f2ed4d44b50af0947e41b65ce342024-02-25T04:36:16ZengElsevieriScience2589-00422024-03-01273109104Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammalsJianhua Chen0Yanni He1Liangliang Chen2Tian Wu3Guangping Yang4Hui Luo5Saifei Hu6Siyue Yin7Yun Qian8Hui Miao9Na Li10Congxiu Miao11Ruizhi Feng12State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, ChinaState Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, ChinaState Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, ChinaState Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, ChinaState Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, ChinaState Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, ChinaState Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, ChinaState Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, ChinaReproductive Medical Center of Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, ChinaDepartment of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, ChinaDepartment of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, ChinaDepartment of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, China; Corresponding authorState Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China; Reproductive Medical Center of Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, China; Corresponding authorSummary: Alternative splicing (AS) as one of the important post-transcriptional regulatory mechanisms has been poorly studied during embryogenesis. In this study, we comprehensively collected and analyzed the transcriptome data of early embryos from human and mouse. We found that AS plays an important role in this process and predicted candidate RNA binding protein (RBP) regulators that are associated with reproductive development. The predicted RBPs such as EIF4A3, MAK16, SRSF2, and UTP23 were found to be associated with reproductive disorders. By Smart-seq2 sequencing analysis, we identified 5445 aberrant alternative splicing events in Eif4a3-knockdown embryos. These events were preferentially associated with RNA processing. In conclusion, our work on the landscape and potential function of alternative splicing events will boost further investigation of detailed mechanisms and key factors regulating mammalian early embryo development and promote the inspiration of pharmaceutical approaches for disorders in this crucial biology process.http://www.sciencedirect.com/science/article/pii/S2589004224003250Molecular biologyEmbryologySystems biology |
| spellingShingle | Jianhua Chen Yanni He Liangliang Chen Tian Wu Guangping Yang Hui Luo Saifei Hu Siyue Yin Yun Qian Hui Miao Na Li Congxiu Miao Ruizhi Feng Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals iScience Molecular biology Embryology Systems biology |
| title | Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals |
| title_full | Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals |
| title_fullStr | Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals |
| title_full_unstemmed | Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals |
| title_short | Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals |
| title_sort | differential alternative splicing landscape identifies potentially functional rna binding proteins in early embryonic development in mammals |
| topic | Molecular biology Embryology Systems biology |
| url | http://www.sciencedirect.com/science/article/pii/S2589004224003250 |
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