LncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber Apostichopus japonicus
The sea cucumber Apostichopus japonicus, renowned for its remarkable ability to expel and regenerate its internal organs within weeks, serves as a model organism for regeneration research. However, studies on the role of non-coding RNAs, particularly long non-coding RNA (lncRNA), in intestinal regen...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037025001163 |
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| author | Fang Su Igor Yu. Dolmatov Tianming Wang Hongsheng Yang Kui Ding Libin Zhang Lina Sun |
| author_facet | Fang Su Igor Yu. Dolmatov Tianming Wang Hongsheng Yang Kui Ding Libin Zhang Lina Sun |
| author_sort | Fang Su |
| collection | DOAJ |
| description | The sea cucumber Apostichopus japonicus, renowned for its remarkable ability to expel and regenerate its internal organs within weeks, serves as a model organism for regeneration research. However, studies on the role of non-coding RNAs, particularly long non-coding RNA (lncRNA), in intestinal regeneration remain limited. In this study, we identified and performed differential expression analysis of lncRNAs in both normal intestines and intestines at 3 days post evisceration (dpe). A total of 2361 lncRNAs were identified, 183 of which were differentially expressed (DE-lncRNAs). The genes targeted by these lncRNAs, either cis- or trans-acting, were involved in oxidative stress, immune response, extracellular matrix remodeling, and energy metabolism during intestinal regeneration. Notably, MSTRG.6200/miR-7847–3p and MSTRG.18440/miR-4220–5p have been confirmed as interacting lncRNA-miRNA pairs. These results suggest that lncRNAs are key regulators of intestinal regeneration in A. japonicus, offering new insights into the underlying mechanisms and potential targets for enhancing regeneration. |
| format | Article |
| id | doaj-art-e2c03a490d8e4120ac4b0a0c6da84e59 |
| institution | DOAJ |
| issn | 2001-0370 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj-art-e2c03a490d8e4120ac4b0a0c6da84e592025-08-20T03:17:51ZengElsevierComputational and Structural Biotechnology Journal2001-03702025-01-01271383139310.1016/j.csbj.2025.03.047LncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber Apostichopus japonicusFang Su0Igor Yu. Dolmatov1Tianming Wang2Hongsheng Yang3Kui Ding4Libin Zhang5Lina Sun6CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, ChinaA.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, RussiaNational Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, ChinaCAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaCAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, ChinaCAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Corresponding author at: CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.The sea cucumber Apostichopus japonicus, renowned for its remarkable ability to expel and regenerate its internal organs within weeks, serves as a model organism for regeneration research. However, studies on the role of non-coding RNAs, particularly long non-coding RNA (lncRNA), in intestinal regeneration remain limited. In this study, we identified and performed differential expression analysis of lncRNAs in both normal intestines and intestines at 3 days post evisceration (dpe). A total of 2361 lncRNAs were identified, 183 of which were differentially expressed (DE-lncRNAs). The genes targeted by these lncRNAs, either cis- or trans-acting, were involved in oxidative stress, immune response, extracellular matrix remodeling, and energy metabolism during intestinal regeneration. Notably, MSTRG.6200/miR-7847–3p and MSTRG.18440/miR-4220–5p have been confirmed as interacting lncRNA-miRNA pairs. These results suggest that lncRNAs are key regulators of intestinal regeneration in A. japonicus, offering new insights into the underlying mechanisms and potential targets for enhancing regeneration.http://www.sciencedirect.com/science/article/pii/S2001037025001163Long non-coding RNA (lncRNA)Intestinal regenerationEchinodermApostichopus japonicus |
| spellingShingle | Fang Su Igor Yu. Dolmatov Tianming Wang Hongsheng Yang Kui Ding Libin Zhang Lina Sun LncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber Apostichopus japonicus Computational and Structural Biotechnology Journal Long non-coding RNA (lncRNA) Intestinal regeneration Echinoderm Apostichopus japonicus |
| title | LncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber Apostichopus japonicus |
| title_full | LncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber Apostichopus japonicus |
| title_fullStr | LncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber Apostichopus japonicus |
| title_full_unstemmed | LncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber Apostichopus japonicus |
| title_short | LncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber Apostichopus japonicus |
| title_sort | lncrna mirna interplay regulate intestinal regeneration in the sea cucumber apostichopus japonicus |
| topic | Long non-coding RNA (lncRNA) Intestinal regeneration Echinoderm Apostichopus japonicus |
| url | http://www.sciencedirect.com/science/article/pii/S2001037025001163 |
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