Comprehensive profiling of lncRNAs in the immune response of largemouth bass to Nocardia Seriolae infection
Long noncoding RNAs (lncRNAs) are crucial regulators of various biological processes. However, it remains unclear how lncRNAs can be involved in the immune response to Nocardia seriolae invasion in largemouth bass (Micropterus salmoides). Here we leveraged the whole transcriptome RNA-seq technique t...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-12-01
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| Series: | Comparative Immunology Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2950311624000326 |
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| author | Xiaona Fu Longsheng Zhang Keqi Li Zhigang Liu Jikui Wu Junling Zhang |
| author_facet | Xiaona Fu Longsheng Zhang Keqi Li Zhigang Liu Jikui Wu Junling Zhang |
| author_sort | Xiaona Fu |
| collection | DOAJ |
| description | Long noncoding RNAs (lncRNAs) are crucial regulators of various biological processes. However, it remains unclear how lncRNAs can be involved in the immune response to Nocardia seriolae invasion in largemouth bass (Micropterus salmoides). Here we leveraged the whole transcriptome RNA-seq technique to screen lncRNAs associated with the head kidney infected with Nocardia seriolae. A total of 5,661 lncRNAs were identified, comprising 2,427 known lncRNAs and 3,234 novel lncRNAs. Among these, 531 lncRNAs were found to be differentially expressed, with 213 showing increased expression and 318 showing reduced expression. In these differentially expressed lncRNAs, 176 lncRNAs may have cis-regulatory relationships with 243 protein-coding genes. For example, MSTRG.17818.1, MSTRG.10160.1 target mapk1 and rela, respectively, thereby regulating gene expression. We then exploited Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to analyze the enrichment of target genes of lncRNAs. These target genes were found to be significantly enriched in immune signaling pathways, including RIG-I-like receptor signaling and Toll-like receptor signaling. Furthermore, we harnessed a total of 12 mRNAs, 33 miRNAs, and 167 lncRNAs to construct two lncRNA-miRNA-mRNA network maps. CeRNA maps revealed that some lncRNAs can competitively bind to the same miRNA and affect the expression of immune-related genes. For instance, MSTRG.13668.1 and MSTRG.5180.1 can simultaneously bind to mir-155–5p to increase irak4 expression. These findings suggest that lncRNAs may participate in the immune response process of infected largemouth bass with Nocardia seriolae. Overall, this work presents a thorough lncRNAs expression profile of Nocardia seriolae-infected largemouth bass and offers insights into the ceRNA regulatory processes that influence fish's immune response to bacterial infections. |
| format | Article |
| id | doaj-art-ad94e06c4a9e44109bade2a66b603e55 |
| institution | Kabale University |
| issn | 2950-3116 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Comparative Immunology Reports |
| spelling | doaj-art-ad94e06c4a9e44109bade2a66b603e552024-12-18T08:56:02ZengElsevierComparative Immunology Reports2950-31162024-12-017200165Comprehensive profiling of lncRNAs in the immune response of largemouth bass to Nocardia Seriolae infectionXiaona Fu0Longsheng Zhang1Keqi Li2Zhigang Liu3Jikui Wu4Junling Zhang5Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, PR ChinaKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, PR ChinaKey Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, PR ChinaKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380, PR ChinaLaboratory of Quality and Safety Risk Assessment for Aquatic Product on Storage and Preservation, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, PR China; Corresponding authors.Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, PR China; Corresponding authors.Long noncoding RNAs (lncRNAs) are crucial regulators of various biological processes. However, it remains unclear how lncRNAs can be involved in the immune response to Nocardia seriolae invasion in largemouth bass (Micropterus salmoides). Here we leveraged the whole transcriptome RNA-seq technique to screen lncRNAs associated with the head kidney infected with Nocardia seriolae. A total of 5,661 lncRNAs were identified, comprising 2,427 known lncRNAs and 3,234 novel lncRNAs. Among these, 531 lncRNAs were found to be differentially expressed, with 213 showing increased expression and 318 showing reduced expression. In these differentially expressed lncRNAs, 176 lncRNAs may have cis-regulatory relationships with 243 protein-coding genes. For example, MSTRG.17818.1, MSTRG.10160.1 target mapk1 and rela, respectively, thereby regulating gene expression. We then exploited Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to analyze the enrichment of target genes of lncRNAs. These target genes were found to be significantly enriched in immune signaling pathways, including RIG-I-like receptor signaling and Toll-like receptor signaling. Furthermore, we harnessed a total of 12 mRNAs, 33 miRNAs, and 167 lncRNAs to construct two lncRNA-miRNA-mRNA network maps. CeRNA maps revealed that some lncRNAs can competitively bind to the same miRNA and affect the expression of immune-related genes. For instance, MSTRG.13668.1 and MSTRG.5180.1 can simultaneously bind to mir-155–5p to increase irak4 expression. These findings suggest that lncRNAs may participate in the immune response process of infected largemouth bass with Nocardia seriolae. Overall, this work presents a thorough lncRNAs expression profile of Nocardia seriolae-infected largemouth bass and offers insights into the ceRNA regulatory processes that influence fish's immune response to bacterial infections.http://www.sciencedirect.com/science/article/pii/S2950311624000326Largemouth bassNocardia seriolaeHead kidneylncRNACERNA, Immune response |
| spellingShingle | Xiaona Fu Longsheng Zhang Keqi Li Zhigang Liu Jikui Wu Junling Zhang Comprehensive profiling of lncRNAs in the immune response of largemouth bass to Nocardia Seriolae infection Comparative Immunology Reports Largemouth bass Nocardia seriolae Head kidney lncRNA CERNA, Immune response |
| title | Comprehensive profiling of lncRNAs in the immune response of largemouth bass to Nocardia Seriolae infection |
| title_full | Comprehensive profiling of lncRNAs in the immune response of largemouth bass to Nocardia Seriolae infection |
| title_fullStr | Comprehensive profiling of lncRNAs in the immune response of largemouth bass to Nocardia Seriolae infection |
| title_full_unstemmed | Comprehensive profiling of lncRNAs in the immune response of largemouth bass to Nocardia Seriolae infection |
| title_short | Comprehensive profiling of lncRNAs in the immune response of largemouth bass to Nocardia Seriolae infection |
| title_sort | comprehensive profiling of lncrnas in the immune response of largemouth bass to nocardia seriolae infection |
| topic | Largemouth bass Nocardia seriolae Head kidney lncRNA CERNA, Immune response |
| url | http://www.sciencedirect.com/science/article/pii/S2950311624000326 |
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