biostudies-literatureSu FShandong Province Natural Science FoundationNational Natural Science Foundation of ChinaTaishan Scholar Foundation of Shandong Province1383-1393https://www.ebi.ac.uk/biostudies/studies/S-EPMC11999485biostudies-literatureUnknown27The sea cucumber <i>Apostichopus japonicus</i>, 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 <i>A. japonicus</i>, offering new insights into the underlying mechanisms and potential targets for enhancing regeneration.Computational and structural biotechnology journalLncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber &lt;i&gt;Apostichopus japonicus&lt;/i&gt;.PMC1199948542076093ZR2024YQ0504210613142276143202306279Yang HSun LWang TZhang LDolmatov IYDing KSu FfalseLncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber &lt;i&gt;Apostichopus japonicus&lt;/i&gt;.The sea cucumber <i>Apostichopus japonicus</i>, 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 <i>A. japonicus</i>, offering new insights into the underlying mechanisms and potential targets for enhancing regeneration.2025-01-01T00:00:00Z20252026-04-08T19:18:17.261Z2025-07-14T03:02:52.775ZS-EPMC119994854023563710.1016/j.csbj.2025.03.047