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Hu S, Chen L, Bai Y, He Q, Liu Y, Xu P. Epigenetic mechanisms of lncRNA in response to thermal stress during embryogenesis of allotetraploid Cyprinus carpio. Genomics 2023; 115:110698. [PMID: 37595932 DOI: 10.1016/j.ygeno.2023.110698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Embryogenesis and epigenetic mechanisms of lncRNA may play an important role in the formation of temperature tolerance in allotetraploid Cyprinus carpio. To investigate the response of lncRNA to thermal stress during embryogenesis of C. carpio, transcriptome sequencing was performed on 81 embryo or larva samples from different early development stages and temperatures. We identified 45,097 lncRNAs and analyzed transcriptome variation during embryogenesis. Stage-specific and temperature-specific DE lncRNAs and DEGs were screened. GO and KEGG analysis identified numerous pathways involved in thermal stress. Temperature-specific regulation of cis-/trans-/antisense lncRNAs was analyzed. Interaction network analysis identified 6 hub lncRNAs and many hub genes, such as cdk1 and hsf1. Decreased expression of many essential genes regulated by lncRNAs may lead to the death of embryos at 33 °C. Our findings provide new insights into the regulation of lncRNA in thermal stress response during embryogenesis and contribute to the understanding of environmental adaptation of allotetraploid species.
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Affiliation(s)
- Shuimu Hu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Lin Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yulin Bai
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Qian He
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yue Liu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Peng Xu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.
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Niu H, Pang Y, Xie L, Yu Q, Shen Y, Li J, Xu X. Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella). BMC Genomics 2023; 24:73. [PMID: 36782132 PMCID: PMC9926789 DOI: 10.1186/s12864-023-09159-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND A considerable fraction of microRNAs (miRNAs) are highly conserved, and certain miRNAs correspond to genomic clusters. The clustering of miRNAs can be advantageous, possibly by allowing coordinated expression. However, little is known about the evolutionary forces responsible for the loss and acquisition of miRNA and miRNA clusters. RESULTS The results demonstrated that several novel miRNAs arose throughout grass carp evolution. Duplication and de novo production were critical strategies for miRNA cluster formation. Duplicates accounted for a smaller fraction of the expansion in the grass carp miRNA than de novo creation. Clustered miRNAs are more conserved and change slower, whereas unique miRNAs usually have high evolution rates and low expression levels. The expression level of miRNA expression in clusters is strongly correlated. CONCLUSIONS This study examines the genomic distribution, evolutionary background, and expression regulation of grass carp miRNAs. Our findings provide novel insights into the genesis and development of miRNA clusters in teleost.
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Affiliation(s)
- Huiqin Niu
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yifan Pang
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Lingli Xie
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Qiaozhen Yu
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yubang Shen
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China. .,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China. .,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
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Zhang W, Ren W, Han D, Zhao G, Wang H, Guo H, Zheng Y, Ji Z, Gao W, Yuan B. LncRNA-m18as1 competitively binds with miR-18a-5p to regulate follicle-stimulating hormone secretion through the Smad2/3 pathway in rat primary pituitary cells. J Zhejiang Univ Sci B 2022; 23:502-514. [PMID: 35686528 DOI: 10.1631/jzus.b2101052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Long noncoding RNAs (lncRNAs) are expressed in different species and different tissues, and perform different functions, but little is known about their involvement in the synthesis or secretion of follicle-stimulating hormone (FSH). In general, we have revealed lncRNA‒microRNA (miRNA)‒messenger RNA (mRNA) interactions that may play important roles in rat primary pituitary cells. In this study, a new lncRNA was identified for the first time. First, we analyzed the gene expression of lncRNA-m18as1 in different tissues and different stages by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and observed the localization of lncRNA-m18as1 with fluorescence in situ hybridization, which indicated that this lncRNA was distributed mainly in the cytoplasm. Next, we used RT-qPCR and enzyme-linked immunosorbent assay (ELISA) to analyze the regulation of FSH synthesis and secretion after overexpression or knockdown of lncRNA-m18as1 and found that lncRNA-m18as1 was positively correlated with FSH synthesis and secretion. In addition, mothers against decapentaplegic homolog 2 (Smad2) was highly expressed in our sequencing results. We also screened miR-18a-5p from our sequencing results as a miRNA that may bind to lncRNA-m18as1 and Smad2. We used RNA immunoprecipitation-qPCR (RIP-qPCR) and/or dual luciferase assays to confirm that lncRNA-m18as1 interacted with miR-18a-5p and miR-18a-5p interacted with Smad2. Fluorescence in situ hybridization (FISH) showed that lncRNA-m18as1 and miR-18a-5p were localized mainly in the cytoplasm. Finally, we determined the relationship among lncRNA-m18as1, miR-18a-5p, and the Smad2/3 pathway. Overall, we found that lncRNA-m18as1 acts as a molecular sponge of miR-18a-5p to regulate the synthesis and secretion of FSH through the Smad2/3 pathway.
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Affiliation(s)
- Weidi Zhang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Wenzhi Ren
- Jilin Provincial Model Animal Engineering Research Center, Jilin University, Changchun 130062, China
| | - Dongxu Han
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Guokun Zhao
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Haoqi Wang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Haixiang Guo
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Yi Zheng
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Zhonghao Ji
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Wei Gao
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China.
| | - Bao Yuan
- Jilin Provincial Model Animal Engineering Research Center, Jilin University, Changchun 130062, China. ,
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Zhang X, Shi J, Sun Y, Wang Y, Zhang Z. The potential role of eyestalk in the immunity of Litopenaeus vannamei to Vibrio parahaemolyticus infection II. From the perspective of long non-coding RNA. FISH & SHELLFISH IMMUNOLOGY 2022; 124:300-312. [PMID: 35398223 DOI: 10.1016/j.fsi.2022.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been linked to immunological modulation. Unfortunately, little is known about the processes of immune control in shrimp. In crustaceans such as Litopenaeus vannamei, a prominent aquaculture species, the X-organ-sinus gland complex (XO-SG) in the eyestalk is an essential neuroendocrine regulatory organ. Eyestalk ablation is commonly employed in aquaculture to accelerate ovarian maturation in shrimp. It does, however, have a negative impact on the shrimps' immunocompetence and causes death. As a result, we used RNA-seq to profile the transcriptomes of L. vannamei hemocytes infected with Vibrio parahaemolyticus after the eyestalk ablation. Following strict transcript screening procedures, 2307 lncRNAs were identified from L. vannamei hemocytes in this study. Pearson correlation analysis was finally used to uncover 535 DElncRNAs and 1566 DEmRNA targets. According to the Venn diagram analysis, 326 non-eyestalk regulatory lncRNAs (NElncRNAs) with a target of 1014 non-eyestalk regulatory genes (NEmRNAs), 47 eyestalk negative regulatory lncRNAs (ENRlncRNAs) with a target of 95 eyestalk negative regulatory genes (ENRmRNAs), and 162 eyestalk positive regulatory lncRNAs (EPRlncRNAs) with a target of 457 eyestalk positive regulatory genes (EPRmRNAs) were screened. The bioinformatics analysis revealed that lncRNAs were associated with Axon regeneration, Rap1 signaling pathway, Thyroid hormone signaling pathway, TGF-beta signaling pathway, and PI3K-Akt signaling pathway, implying that lncRNAs may play a role in the regulation of the neuroendocrine-immune (NEI) system. Furthermore, several lncRNAs targeting HSP70, YWHAZ, FER2, HIF1α, and Notch were discovered and verified by qRT-PCR. These findings showed that regulation of lncRNAs in hemocytes which were controlled by the eyestalk might be one of the impact variables in controlling the differential expression of mRNAs associated with immune response in L. vannamei infected with V. parahaemolyticus.
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Affiliation(s)
- Xin Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Jialong Shi
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yulong Sun
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, 361021, China.
| | - Ziping Zhang
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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