1
|
Zheng W, Chen Y, Wang Y, Chen S, Xu XW. Genome-Wide Identification and Involvement in Response to Biotic and Abiotic Stresses of lncRNAs in Turbot ( Scophthalmus maximus). Int J Mol Sci 2023; 24:15870. [PMID: 37958851 PMCID: PMC10648414 DOI: 10.3390/ijms242115870] [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: 10/07/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in a variety of biological processes, including stress response. However, the number, characteristics and stress-related expression of lncRNAs in turbot are still largely unknown. In this study, a total of 12,999 lncRNAs were identified at the genome-wide level of turbot for the first time using 24 RNA-seq datasets. Sequence characteristic analyses of transcripts showed that lncRNA transcripts were shorter in average length, lower in average GC content and in average expression level as compared to the coding genes. Expression pattern analyses of lncRNAs in 12 distinct tissues showed that lncRNAs, especially lincRNA, exhibited stronger tissue-specific expression than coding genes. Moreover, 612, 1351, 1060, 875, 420 and 1689 differentially expressed (DE) lncRNAs under Vibrio anguillarum, Enteromyxum scophthalmi, and Megalocytivirus infection and heat, oxygen, and salinity stress conditions were identified, respectively. Among them, 151 and 62 lncRNAs showed differential expression under various abiotic and biotic stresses, respectively, and 11 lncRNAs differentially expressed under both abiotic and biotic stresses were selected as comprehensive stress-responsive lncRNA candidates. Furthermore, expression pattern analysis and qPCR validation both verified the comprehensive stress-responsive functions of these 11 lncRNAs. In addition, 497 significantly co-expressed target genes (correlation coefficient (R) > 0.7 and q-value < 0.05) for these 11 comprehensive stress-responsive lncRNA candidates were identified. Finally, GO and KEGG enrichment analyses indicated that these target genes were enriched mainly in molecular function, such as cytokine activity and active transmembrane transporter activity, in biological processes, such as response to stimulus and immune response, and in pathways, such as protein families: signaling and cellular processes, transporters and metabolism. These findings not only provide valuable reference resources for further research on the molecular basis and function of lncRNAs in turbot but also help to accelerate the progress of molecularly selective breeding of stress-resistant turbot strains or varieties.
Collapse
Affiliation(s)
- Weiwei Zheng
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
| | - Yadong Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Yaning Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- College of Life Science, Qingdao University, Qingdao 266071, China
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Xi-wen Xu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| |
Collapse
|
2
|
Identification and characterization of long non-coding RNAs in juvenile and adult skeletal muscle of largemouth bass (Micropterus salmoides). Comp Biochem Physiol B Biochem Mol Biol 2022; 261:110748. [PMID: 35460873 DOI: 10.1016/j.cbpb.2022.110748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a class of transcriptional RNA molecules, which play critical roles in diverse biological processes. However, little is known about the overall expression pattern and roles of lncRNAs in skeletal muscle of largemouth bass (LMB). Here, we constructed two skeletal muscle RNA libraries to find lncRNAs that may involve in the regulation of skeletal muscle development between juvenile and adult LMB. A total of 16,147 lncRNAs and 4611 differentially expressed lncRNAs were identified. Among these identified lncRNAs, 10 lncRNAs were randomly selected to confirm their expression by real-time qPCR both in libraries, which were consistent with the RNA sequencing results. The target mRNAs of lncRNAs were predicted for GO enrichment analysis. Results showed that these targets associated with growth and development of muscle, such as skeletal muscle fiber development, myoblast proliferation and differentiation. Importantly, correlation analysis of lncRNA-miRNA-mRNA regulatory network revealed that several lncRNAs targeted miRNAs which are closely involved in the regulation of muscle development. It is the first time to identify a number of lncRNA that correlate with skeletal muscle development in LMB. Our results not only provide a comprehensive expression profile of muscle lncRNAs in this species, but also provide a theoretical basis for further elaborating genetic regulation mechanism of muscle growth and development, and pave the way for the future molecular assisted breeding in carnivorous fishes.
Collapse
|
3
|
Hou X, Wang L, Zhao F, Liu X, Gao H, Shi L, Yan H, Wang L, Zhang L. Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds. Animals (Basel) 2021; 11:ani11113169. [PMID: 34827901 PMCID: PMC8614396 DOI: 10.3390/ani11113169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Variation exists in muscle-related traits, such as muscle growth and meat quality, between obese and lean pigs. In this study, the transcriptome profiles of skeletal muscle between Beijing Blackand Yorkshire pigs were characterized to explore the molecular mechanism underlying skeletal muscle-relatedtraits. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that differentially expressed mRNAs, lncRNAs, and circRNAs involved in skeletal muscle development and fatty acid metabolism played a key role in the determination of muscle-related traits between different pig breeds. These results provide candidate genes responsible for muscle phenotypic variation and are valuable for pig breeding. Abstract RNA-Seq technology is widely used to analyze global changes in the transcriptome and investigate the influence on relevant phenotypic traits. Beijing Black pigs show differences in growth rate and meat quality compared to western pig breeds. However, the molecular mechanisms responsible for such phenotypic differences remain unknown. In this study, longissimus dorsi muscles from Beijing Black and Yorkshire pigs were used to construct RNA libraries and perform RNA-seq. Significantly different expressions were observed in 1051 mRNAs, 322 lncRNAs, and 82 circRNAs. GO and KEGG pathway annotation showed that differentially expressed mRNAs participated in skeletal muscle development and fatty acid metabolism, which determined the muscle-related traits. To explore the regulatory role of lncRNAs, the cis and trans-target genes were predicted and these lncRNAswere involved in the biological processes related to skeletal muscle development and fatty acid metabolismvia their target genes. CircRNAs play a ceRNA role by binding to miRNAs. Therefore, the potential miRNAs of differentially expressed circRNAs were predicted and interaction networks among circRNAs, miRNAs, and key regulatory mRNAs were constructed to illustrate the function of circRNAs underlying skeletal muscle development and fatty acid metabolism. This study provides new clues for elucidating muscle phenotypic variation in pigs.
Collapse
|
4
|
Real MV, Rocha MJ, Gonçalves JF, Rocha E. Histology and design-based estimation of hepatocellularity and volumes of hepatocytes in control and ethynylestradiol exposed males of platyfish (Xiphophorus maculatus). Tissue Cell 2020; 63:101327. [DOI: 10.1016/j.tice.2019.101327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 12/27/2019] [Accepted: 12/29/2019] [Indexed: 02/06/2023]
|
5
|
Aedo JE, Zuloaga R, Bastías-Molina M, Meneses C, Boltaña S, Molina A, Valdés JA. Early transcriptomic responses associated with the membrane-initiated action of cortisol in the skeletal muscle of rainbow trout (Oncorhynchus mykiss). Physiol Genomics 2019; 51:596-606. [DOI: 10.1152/physiolgenomics.00042.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cortisol is a critical neuroendocrine regulator of the stress response in fish. Cortisol practically affects all tissues by interacting with an intracellular receptor and modulating target gene expression. However, cortisol also interacts with components of the plasma membrane in a nongenomic process that activates rapid signaling. Until now, the implication of this novel cortisol signaling for the global transcriptional response has not been explored. In the present work, we evaluated the effects of the membrane-initiated actions of cortisol on the in vivo transcriptome of rainbow trout ( Oncorhynchus mykiss) skeletal muscle. RNA-Seq analyses were performed to examine the transcriptomic changes in rainbow trout stimulated by physiological concentrations of cortisol and cortisol coupled with bovine serum albumin (cortisol-BSA), a membrane-impermeable analog of cortisol. A total of 660 million paired-ends reads were generated. Reads mapped onto the reference genome revealed that 1,737; 897; and 1,012 transcripts were differentially expressed after 1, 3, and 9 h of cortisol-BSA treatment, respectively. Gene Ontology analysis showed that this novel action of cortisol modulates several biological processes, such as mRNA processing, ubiquitin-dependent protein catabolic processes, and transcription regulation. In addition, a KEGG analysis revealed that focal adhesion was the main signaling pathway that was upregulated at all the times tested. Taking these results together, we propose that the membrane-initiated cortisol action contributes significantly in the regulation of stress-mediated gene expression.
Collapse
Affiliation(s)
- Jorge E. Aedo
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
| | - Rodrigo Zuloaga
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Macarena Bastías-Molina
- Universidad Andrés Bello, Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Claudio Meneses
- Universidad Andrés Bello, Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Sebastián Boltaña
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
- Universidad de Concepción, ThermoFish Lab, Biotechnology Center, Concepción, Chile
| | - Alfredo Molina
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, Santiago, Chile
- Universidad de Concepción, ThermoFish Lab, Biotechnology Center, Concepción, Chile
| | - Juan Antonio Valdés
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, Santiago, Chile
- Universidad de Concepción, ThermoFish Lab, Biotechnology Center, Concepción, Chile
| |
Collapse
|
6
|
Miao Z, Wei P, Khan MA, Zhang J, Guo L, Liu D, Zhang X, Bai Y, Wang S. Transcriptome analysis reveals differential gene expression in intramuscular adipose tissues of Jinhua and Landrace pigs. J Vet Med Sci 2018; 80:953-959. [PMID: 29709900 PMCID: PMC6021883 DOI: 10.1292/jvms.18-0074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Meat is a rich source of protein, fatty acids and carbohydrates for human needs. In
addition to necessary nutrients, high fat contents in pork increase the tenderness and
juiciness of the meat, featuring diverse application in various dishes. This study
investigated the transcriptomic profiles of intramuscular adipose tissues in Jinhua and
Landrace pigs by employing advanced RNA sequencing. Results showed significant interesting
to note that there were significant differences in the expression of genes. 1,632 genes
showed significant differential expression, 837 genes were up-regulated and 195 genes were
down-regulated. Variations in genes responsible for cell aggregation, extracellular matrix
formation, cellular lipid catabolic process, and fatty acid binding strongly supported
that both pig breeds feature variable fat and muscle metabolism. Certain differentially
expressed genes are included in the pathway of mitogen-activated protein kinase signaling
pathway, Ras signaling pathway and insulin pathway. Results from real-time quantitative
polymerase chain reaction also validated the differential expression of 17 mRNAs between
meats of the two pig breeds. Overall, these findings reveal significant differences in fat
and protein metabolism of intramuscular adipose tissues of two pig breeds at the
transcriptomic level and suggest diversification at the genetic level between breeds of
the same species.
Collapse
Affiliation(s)
- Zhiguo Miao
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Panpeng Wei
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Muhammad Akram Khan
- Department of Pathobiology, Faculty of Veterinary and Animal Sciences, PMAS- Arid Agriculture University Rawalpindi, 46000, Pakistan
| | - Jinzhou Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Liping Guo
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Dongyang Liu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Xiaojian Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Yueyu Bai
- Animal Health Supervision of Henan Province, Bureau of Animal Husbandry of Henan province, Zhengzhou, 450000, P.R. China
| | - Shan Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| |
Collapse
|