1
|
Liu H, Tan S, Han S, Liu X, Li Z, Wang N, Wu Z, Ma J, Shi K, Wang W, Sha Z. Effects of miR-722 on gene expression and alternative splicing in the liver of half-smooth tongue sole after infection with Vibrio anguillarum. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109275. [PMID: 38081443 DOI: 10.1016/j.fsi.2023.109275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/22/2023] [Accepted: 12/04/2023] [Indexed: 12/31/2023]
Abstract
MicroRNAs play crucial roles in various biological processes, including but not limited to differentiation, development, disease, and immunity. However, their immunoregulatory roles in half-smooth tongue sole are lacking. Our previous studies indicated that miR-722 could target C5aR1 to modulate the complement pathway to alleviate inflammatory response and even affect the mortality after the bacterial infection with Vibrio anguillarum. Driven by the purpose of revealing the underlying mechanisms, in this study, we investigated the effects of miR-722 on the gene expression and alternative splicing (AS) in the liver of half-smooth tongue sole after Vibrio anguillarum infection, with the approach of miR-722 overexpression/silencing and subsequent RNA-seq. Among the different comparisons, the I group (miR-722 inhibitor and V. anguillarum) versus blank control (PBS) exhibited the highest number of differentially expressed genes (DEGs), suggesting that the immune response was overactivated after inhibiting the miR-722. In addition, enrichment analyses were performed to reveal the functions of DEGs and differential AS (DAS) genes, reflecting the enrichment of RNA splicing and immune-related pathways including NF-κB and T cell receptor signaling pathway. Comparing the M group (miR-722 mimic and V. anguillarum) with the negative control (random sequence and V. anguillarum), two immune-related genes, cd48 and mapk8, were differentially expressed, of which mapk8 was also differentially spliced, indicating their importance in the immune response. Furthermore, representative gene analysis was performed, suggesting their corresponding functional changes due to AS. To verify the RNA-seq data, quantitative real-time PCR was employed with twenty pairs of primers for DEGs and DAS events. Overall, our results demonstrated that miR-722 could mediate the transcriptome-wide changes of gene expression and AS in half-smooth tongue sole, and provided insights into the regulatory role of miR-722 in immune responses, laying the foundation for further functional analyses and practical applications in aquaculture.
Collapse
Affiliation(s)
- Hongning Liu
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Suxu Tan
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Sen Han
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Xinbao Liu
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Zhujun Li
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Ningning Wang
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China; College of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Zhendong Wu
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Jie Ma
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Kunpeng Shi
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Wenwen Wang
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Zhenxia Sha
- Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| |
Collapse
|
2
|
Dwivedi SL, Quiroz LF, Reddy ASN, Spillane C, Ortiz R. Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs. Int J Mol Sci 2023; 24:15205. [PMID: 37894886 PMCID: PMC10607462 DOI: 10.3390/ijms242015205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.
Collapse
Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053 Alnarp, SE, Sweden
| |
Collapse
|