1
|
Zhou J, Li Q, Huang Z, Zhang L, Mou C, Zhao Z, Zhao H, Du J, Yang X, Liang X, Duan Y. Study on the Adaptive Regulation of Light on the Stress Response of Mandarin Fish ( Siniperca chuatsi) with Re-Feeding after Starvation. Animals (Basel) 2023; 13:2610. [PMID: 37627401 PMCID: PMC10451258 DOI: 10.3390/ani13162610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Light influences the stress response to environmental stimuli and feeding behaviors of Siniperca chuatsi and, thus, is an important regulator of normal growth and development. In this study, we first explored the important role of light on the digestive and stress capacity of S. chuatsi by studying the changes in physiological and biochemical indicators of S. chuatsi, taking the re-feeding after starvation as the constant environmental stimulus and the light intensity as the adjustable environmental stimulus. The activity of protease and lipase was generally higher in the stomach tissues than in the intestinal tissues, especially lipase, which was higher in stomach tissues under all light conditions, and the protease and lipase activity peaked in the stomach tissues of S. chuatsi at a light intensity of 18.44 ± 3.00 lx and in intestinal tissues at 11.15 ± 2.01 lx, respectively, indicating that greater light intensity increased the digestive capacity of stomach tissues, whereas lower light intensity facilitated the digestive capacity of intestinal tissues. The tissues of the gill, stomach, and intestine had relatively high activity of stress-related enzymes, whereas the tissues of the brain, kidney, liver, and plasma samples had relatively low activity of enzymes. Collectively, the results show that light intensity at 11.15 ± 2.01 lx promoted digestive capacity in the intestine and enhanced the anti-stress ability of S. chuatsi in response to stress induced by re-feeding after starvation. These findings should prove useful for artificial breeding of S. chuatsi.
Collapse
Affiliation(s)
- Jian Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China;
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China; (Q.L.); (Z.H.); (L.Z.); (C.M.); (Z.Z.); (H.Z.); (J.D.)
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China; (Q.L.); (Z.H.); (L.Z.); (C.M.); (Z.Z.); (H.Z.); (J.D.)
| | - Zhipeng Huang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China; (Q.L.); (Z.H.); (L.Z.); (C.M.); (Z.Z.); (H.Z.); (J.D.)
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China; (Q.L.); (Z.H.); (L.Z.); (C.M.); (Z.Z.); (H.Z.); (J.D.)
| | - Chengyan Mou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China; (Q.L.); (Z.H.); (L.Z.); (C.M.); (Z.Z.); (H.Z.); (J.D.)
| | - Zhongmeng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China; (Q.L.); (Z.H.); (L.Z.); (C.M.); (Z.Z.); (H.Z.); (J.D.)
| | - Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China; (Q.L.); (Z.H.); (L.Z.); (C.M.); (Z.Z.); (H.Z.); (J.D.)
| | - Jun Du
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China; (Q.L.); (Z.H.); (L.Z.); (C.M.); (Z.Z.); (H.Z.); (J.D.)
| | - Xiaojun Yang
- Western Aquatic Seed Industry Co., Ltd., Mianyang 621000, China
| | - Xufang Liang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China;
| | - Yuanliang Duan
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China; (Q.L.); (Z.H.); (L.Z.); (C.M.); (Z.Z.); (H.Z.); (J.D.)
| |
Collapse
|
2
|
Rbbani G, Nedoluzhko A, Siriyappagouder P, Sharko F, Galindo-Villegas J, Raeymaekers JAM, Joshi R, Fernandes JMO. The novel circular RNA CircMef2c is positively associated with muscle growth in Nile tilapia. Genomics 2023; 115:110598. [PMID: 36906188 PMCID: PMC7614353 DOI: 10.1016/j.ygeno.2023.110598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023]
Abstract
Muscle growth in teleosts is a complex biological process orchestrated by numerous protein-coding genes and non-coding RNAs. A few recent studies suggest that circRNAs are involved in teleost myogenesis, but the molecular networks involved remain poorly understood. In this study, an integrative omics approach was used to determine myogenic circRNAs in Nile tilapia by quantifying and comparing the expression profile of mRNAs, miRNAs, and circRNAs in fast muscle from full-sib fish with distinct growth rates. There were 1947 mRNAs, 9 miRNAs, and 4 circRNAs differentially expressed between fast- and slow-growing individuals. These miRNAs can regulate myogenic genes and have binding sites for the novel circRNA circMef2c. Our data indicate that circMef2c may interact with three miRNAs and 65 differentially expressed mRNAs to form multiple competing endogenous RNA networks that regulate growth, thus providing novel insights into the role of circRNAs in the regulation of muscle growth in teleosts.
Collapse
Affiliation(s)
- Golam Rbbani
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Artem Nedoluzhko
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; Paleogenomics laboratory, European University at Saint Petersburg, 191187 Saint-Petersburg, Russia
| | | | | | - Jorge Galindo-Villegas
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Joost A M Raeymaekers
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | | | - Jorge M O Fernandes
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
| |
Collapse
|
3
|
Cao Q, Zhang H, Li T, He L, Zong J, Shan H, Huang L, Zhang Y, Liu H, Jiang J. Profiling miRNAs of Teleost Fish in Responses to Environmental Stress: A Review. BIOLOGY 2023; 12:biology12030388. [PMID: 36979079 PMCID: PMC10045198 DOI: 10.3390/biology12030388] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/11/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
miRNAs are a class of endogenous and evolutionarily conserved noncoding short RNA molecules that post-transcriptionally regulate gene expression through sequence-specific interactions with mRNAs and are capable of controlling gene expression by binding to miRNA targets and interfering with the final protein output. The miRNAs of teleost were firstly reported in zebrafish development, but there are recent studies on the characteristics and functions of miRNAs in fish, especially when compared with mammals. Environmental factors including salinity, oxygen concentration, temperature, feed, pH, environmental chemicals and seawater metal elements may affect the transcriptional and posttranscriptional regulators of miRNAs, contributing to nearly all biological processes. The survival of aquatic fish is constantly challenged by the changes in these environmental factors. Environmental factors can influence miRNA expression, the functions of miRNAs and their target mRNAs. Progress of available information is reported on the environmental effects of the identified miRNAs, miRNA targets and the use of miRNAs in fish.
Collapse
Affiliation(s)
- Quanquan Cao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- MARBEC, University Montpellier, CNRS, IFREMER, IRD, 34090 Montpellier, France
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
| | - Hailong Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lingjie He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiali Zong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongying Shan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lishi Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yupeng Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Haifeng Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
| | - Jun Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
| |
Collapse
|
4
|
Genome-wide DNA methylation profiles provide insight into epigenetic regulation of red and white muscle development in Chinese perch Siniperca chuatsi. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110647. [PMID: 34271193 DOI: 10.1016/j.cbpb.2021.110647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/04/2021] [Accepted: 07/09/2021] [Indexed: 12/19/2022]
Abstract
Fish skeletal muscles are composed of spatially well-separated fiber types, namely, red and white muscles with different physiological functions and metabolism. To compare the DNA methylation profiles of the two types of muscle tissues and identify potential candidate genes for the muscle growth and development under epigenetic regulation, genome-wide DNA methylation of the red and white muscle in Chinese perch Siniperca chuatsi were comparatively analyzed using bisulfate sequencing methods. An average of 0.9 billion 150-bp paired-end reads were obtained, of which 86% were uniquely mapped to the genome. Methylation mostly occurred at CG sites at a ratio of 94.43% in the red muscle and 93.16% in the white muscle. The mean methylation levels at C-sites were 5.95% in red muscle and 5.83% in white muscle, whereas the mean methylation levels of CG, CHG, and CHH were 73.23%, 0.62%, and 0.67% in red muscle, and 71.01%, 0.62%, and 0.67% in white muscle, respectively. A total of 4192 differentially methylated genes (DMGs) were identified significantly enriched in cell signaling pathways related to skeletal muscle differentiation and growth. Various muscle-related genes, including myosin gene isoforms and regulatory factors, are differentially methylated in the promoter region between the red and white muscles. Further analysis of the transcriptional expression of these genes showed that the muscle regulatory factors (myf5, myog, pax3, pax7, and twitst2) and myosin genes (myh10, myh16, myo18a, myo7a, myo9a, and myl3) were differentially expressed between the two kinds of muscles, consistent with the DNA methylation analysis results. ELISA assays confirmed that the level of 5mC in red muscle was significantly higher than in white muscle (P < 0.05). The RT-qPCR assays revealed that the expression levels of the three DNA methylation transferase (dnmt) subtypes, dnmt1, dnmt3ab, and dnmt3bb1, were significantly higher in red muscle than in white muscle. The higher DNA methylation levels in the red muscle may result from higher DNA methylation transferase expression in the red muscles. Thus, this study might provide a theoretical foundation to better understand epigenetic regulation in the growth and development of red and white muscles in animals, at least in Chinese perch fish.
Collapse
|
5
|
Zhou W, Xie Y, Li Y, Xie M, Zhang Z, Yang Y, Zhou Z, Duan M, Ran C. Research progress on the regulation of nutrition and immunity by microRNAs in fish. FISH & SHELLFISH IMMUNOLOGY 2021; 113:1-8. [PMID: 33766547 DOI: 10.1016/j.fsi.2021.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/17/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs) are a class of highly conserved, endogenous non-coding single-stranded small RNA molecules with a length of 18-25 nucleotides. MiRNAs can negatively regulate the target gene through complementary pairing with the mRNA. It has been more than 20 years since the discovery of miRNA molecules, and many achievements have been made in fish research. This paper reviews the research progress in the regulation of fish nutrition and immunity by miRNAs in recent years. MiRNAs regulate the synthesis of long-chain polyunsaturated fatty acids, and are involved in the metabolism of glucose, lipids, as well as cholesterol in fish. Moreover, miRNAs play various roles in antibacterial and antiviral immunity of fish. They can promote the immune response of fish, but may also participate in the immune escape mechanism of bacteria or viruses. One important aspect of miRNAs regulation on fish immunity is mediated by targeting pattern recognition receptors and downstream signaling factors. Together, current results indicate that miRNAs are widely involved in the complex regulatory network of fish. Further studies on fish miRNAs may deepen our understanding of the regulatory network of fish nutrition and immunity, and have the potential to promote the development of microRNA-based products and detection reagents that can be applied in aquaculture industry.
Collapse
Affiliation(s)
- Wei Zhou
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Yadong Xie
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Yu Li
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Mingxu Xie
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Zhen Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yalin Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Zhigang Zhou
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Ming Duan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Chao Ran
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
| |
Collapse
|
6
|
Xu T, Xu Z, Lu L, Zeng T, Gu L, Huang Y, Zhang S, Yang P, Wen Y, Lin D, Xing M, Huang L, Liu G, Chao Z, Sun W. Transcriptome-wide study revealed m6A regulation of embryonic muscle development in Dingan goose (Anser cygnoides orientalis). BMC Genomics 2021; 22:270. [PMID: 33853538 PMCID: PMC8048326 DOI: 10.1186/s12864-021-07556-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The number of myofiber is determined during the embryonic stage and does not increase during the postnatal period for birds, including goose. Thus, muscle production of adult goose is pre-determined during embryogenesis. Previous studies show N6-methyladenosine (m6A) is an important regulator for skeletal muscle development of birds and miRNAs play as a co-regulator for the skeletal muscle development in birds. Herein, we sequenced m6A and miRNA transcriptomes to investigate the profiles of m6A and their potential mechanism of regulating breast muscle development in Dingan Goose. RESULTS We selected embryonic 21th day (E21) and embryonic 30th day (E30) to investigate the roles of transcriptome-wide m6A modification combining with mRNAs and miRNAs in goose breast muscle development. In this study, m6A peaks were mainly enriched in coding sequence (CDS) and start codon and397 genes were identified as differentially methylated genes (DMGs). GO and KEGG analysis showed that DMGs were highly related to cellular and metabolic process and that most DMGs were enriched in muscle-related pathways including Wnt signaling pathway, mTOR signaling and FoxO signaling pathway. Interestingly, a negative correlation between m6A methylation level and mRNA abundance was found through the analysis of m6A-RNA and RNA-seq data. Besides, we found 26 muscle-related genes in 397 DMGs. We also detected 228 differentially expressed miRNAs (DEMs), and further found 329 genes shared by the target genes of DEMs and DMGs (m6A-miRNA-genes), suggesting a tightly relationship between DEMs and DMGs. Among the m6A-miRNA-genes, we found 10 genes are related to breast muscle development. We further picked out an m6A-miRNA-gene, PDK3, from the 10 genes to visualize it and the result showed differentially methylated peaks on the mRNA transcript consistent with our m6A-seq results. CONCLUSION GO and KEGG of DMGs between E21 and E30 showed most DMGs were muscle-related. In total, 228 DEMs were found, and the majority of DMGs were overlapped with the targets of DEGs. The differentially methylated peaks along with an m6A-miRNA-gene, PDK3, showed the similar results with m6A-seq results. Taken together, the results presented here provide a reference for further investigation of embryonic skeletal muscle development mechanism in goose.
Collapse
Affiliation(s)
- Tieshan Xu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100 People’s Republic of China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 People’s Republic of China
| | - Zijie Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100 People’s Republic of China
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Tao Zeng
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100 People’s Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100 People’s Republic of China
| | - Shunjin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100 People’s Republic of China
| | - Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100 People’s Republic of China
| | - Yifan Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100 People’s Republic of China
| | - Dajie Lin
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100 People’s Republic of China
| | - Manping Xing
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100 People’s Republic of China
- Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou, 571100 People’s Republic of China
| | - Lili Huang
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100 People’s Republic of China
- Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou, 571100 People’s Republic of China
| | - Guojun Liu
- Institute of Animal Husbandry of Heilongjiang Academy of Agricultural Sciences, Haerbin, Heilongjiang 150086 People’s Republic of China
| | - Zhe Chao
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100 People’s Republic of China
| | - Weiping Sun
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 People’s Republic of China
| |
Collapse
|
7
|
Koganti P, Yao J, Cleveland BM. Molecular Mechanisms Regulating Muscle Plasticity in Fish. Animals (Basel) 2020; 11:ani11010061. [PMID: 33396941 PMCID: PMC7824542 DOI: 10.3390/ani11010061] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 12/12/2022] Open
Abstract
Growth rates in fish are largely dependent on genetic and environmental factors, of which the latter can be highly variable throughout development. For this reason, muscle growth in fish is particularly dynamic as muscle structure and function can be altered by environmental conditions, a concept referred to as muscle plasticity. Myogenic regulatory factors (MRFs) like Myogenin, MyoD, and Pax7 control the myogenic mechanisms regulating quiescent muscle cell maintenance, proliferation, and differentiation, critical processes central for muscle plasticity. This review focuses on recent advancements in molecular mechanisms involving microRNAs (miRNAs) and DNA methylation that regulate the expression and activity of MRFs in fish. Findings provide overwhelming support that these mechanisms are significant regulators of muscle plasticity, particularly in response to environmental factors like temperature and nutritional challenges. Genetic variation in DNA methylation and miRNA expression also correlate with variation in body weight and growth, suggesting that genetic markers related to these mechanisms may be useful for genomic selection strategies. Collectively, this knowledge improves the understanding of mechanisms regulating muscle plasticity and can contribute to the development of husbandry and breeding strategies that improve growth performance and the ability of the fish to respond to environmental challenges.
Collapse
Affiliation(s)
- Prasanthi Koganti
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506-6108, USA; (P.K.); (J.Y.)
| | - Jianbo Yao
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506-6108, USA; (P.K.); (J.Y.)
| | - Beth M. Cleveland
- USDA ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430, USA
- Correspondence: ; Tel.: +1-304-724-8340 (ext. 2133)
| |
Collapse
|
8
|
Sun JJ, Zheng LG, Chen CY, Zhang JY, You CH, Zhang QH, Ma HY, Monroig Ó, Tocher DR, Wang SQ, Li YY. MicroRNAs Involved in the Regulation of LC-PUFA Biosynthesis in Teleosts: miR-33 Enhances LC-PUFA Biosynthesis in Siganus canaliculatus by Targeting insig1 which in Turn Upregulates srebp1. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:475-487. [PMID: 31020472 DOI: 10.1007/s10126-019-09895-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
Post-transcriptional regulatory mechanisms play important roles in the regulation of LC-PUFA biosynthesis. Our previous study revealed that miR-33 could increase the expression of fatty acyl desaturases (fads2) in the rabbitfish Siganus canaliculatus, but the specific mechanism is unknown. Here, we confirmed that miR-33 could target the 3'UTR of insulin-induced gene 1 (insig1), resulting in downregulation of its protein level in the rabbitfish hepatocyte line (SCHL). In vitro overexpression of miR-33 inhibited the mRNA level of insig1 and increased the mRNA levels of Δ6Δ5 fads2 and elovl5, as well as srebp1. In SCHL cells, proteolytic activation of sterol-regulatory-element-binding protein-1 (Srebp1) was blocked by Insig1, with overexpression of insig1 decreasing mature Srebp1 level, while inhibition of insig1 led to the opposite effect. Srebp1 could enhance the promoter activity of Δ6Δ5 fads2 and elovl5, whose expression levels decreased with knockdown of srebp1 in SCHL. Overexpression of miR-33 also resulted in a higher conversion of 18:3n-3 to 18:4n-3 and 20:5n-3 to 22:5n-3, linked to desaturation and elongation via Δ6Δ5 Fads2 and Elovl5, respectively. The results suggested that the mechanism by which miR-33 regulates LC-PUFA biosynthesis in rabbitfish is through enhancing the expression of srebp1 by targeting insig1. The findings here provide more insight to the mechanism of miRNAs involvement in the regulation of LC-PUFA biosynthesis in teleosts.
Collapse
Affiliation(s)
- Jun Jun Sun
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Li Guo Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Cui Ying Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Jin Ying Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Cui Hong You
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Qing Hao Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Hong Yu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Óscar Monroig
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain
| | - Douglas R Tocher
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Shu Qi Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China.
| | - Yuan You Li
- School of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
9
|
He Y, Li Z, Zhang H, Hu S, Wang Q, Li J. Genome-wide identification of Chinese shrimp (Fenneropenaeus chinensis) microRNA responsive to low pH stress by deep sequencing. Cell Stress Chaperones 2019; 24:689-695. [PMID: 31209725 PMCID: PMC6629735 DOI: 10.1007/s12192-019-00989-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 03/01/2019] [Accepted: 03/11/2019] [Indexed: 10/26/2022] Open
Abstract
pH has a great impact on the distribution, growth, behavior, and physiology in many aquatic animals. Here, we analyzed miRNA expression profiles of Chinese shrimp (Fenneropenaeus chinensis) from control pH (8.2) and low pH (6.5)-treated shrimp. Expression analysis identified 6 known miRNAs and 23 novel miRNAs with significantly different expression between control pH 8.2 and low pH 6.5; the predicted target genes of differentially expressed miRNAs were significantly enriched in organic acid metabolic process, oxidoreductase activity, coenzyme binding, cofactor binding, and collagen trimer. Moreover, target genes were significantly enriched in several Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including citrate cycle, pyruvate metabolism, cytokine-cytokine receptor interaction, tight junction, carbon metabolism, etc. Our survey expanded the number of known shrimp miRNAs and provided comprehensive information about miRNA response to low pH stress.
Collapse
Affiliation(s)
- Yuying He
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, People's Republic of China
| | - Zhaoxia Li
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Haien Zhang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Shuo Hu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Qingyin Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, People's Republic of China.
| |
Collapse
|
10
|
Masouminia M, Gelfand R, Kovanecz I, Vernet D, Tsao J, Salas R, Castro K, Loni L, Rajfer J, Gonzalez-Cadavid NF. Dyslipidemia Is a Major Factor in Stem Cell Damage Induced by Uncontrolled Long-Term Type 2 Diabetes and Obesity in the Rat, as Suggested by the Effects on Stem Cell Culture. J Sex Med 2018; 15:1678-1697. [PMID: 30527052 PMCID: PMC6645779 DOI: 10.1016/j.jsxm.2018.09.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/04/2018] [Accepted: 09/28/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Previous work showed that muscle-derived stem cells (MDSCs) exposed long-term to the milieu of uncontrolled type 2 diabetes (UC-T2D) in male obese Zucker (OZ) rats, were unable to correct the associated erectile dysfunction and the underlying histopathology when implanted into the corpora cavernosa, and were also imprinted with a noxious gene global transcriptional signature (gene-GTS), suggesting that this may interfere with their use as autografts in stem cell therapy. AIM To ascertain the respective contributions of dyslipidemia and hyperglycemia to this MDSC damage, clarify its mechanism, and design a bioassay to identify the damaged stem cells. METHODS Early diabetes MDSCs and late diabetes MDSCs were respectively isolated from nearly normal young OZ rats and moderately hyperglycemic and severely dyslipidemic/obese aged rats with erectile dysfunction. Monolayer cultures of early diabetic MDSCs were incubated 4 days in DMEM/10% fetal calf serum + or - aged OZ or lean Zucker serum from non-diabetic lean Zucker rats (0.5-5%) or with soluble palmitic acid (PA) (0.5-2 mM), cholesterol (CHOL) (50-400 mg/dL), or glucose (10-25 mM). MAIN OUTCOME MEASURE Fat infiltration was estimated by Oil red O, apoptosis by TUNEL, protein expression by Western blots, and gene-GTS and microRNA (miR)-GTS were determined in these stem cells' RNA. RESULTS Aged OZ serum caused fat infiltration, apoptosis, myostatin overexpression, and impaired differentiation. Some of these changes, and also a proliferation decrease occurred with PA and CHOL. The gene-GTS changes by OZ serum did not resemble the in vivo changes, but some occurred with PA and CHOL. The miR-GTS changes by OZ serum, PA, and CHOL resembled most of the in vivo changes. Hyperglycemia did not replicate most alterations. CLINICAL IMPLICATIONS MDSCs may be damaged in long-term UC-T2D/obese patients and be ineffective in autologous human stem cell therapy, which may be prevented by excluding the damaged MDSCs. STRENGTH & LIMITATIONS The in vitro test of MDSCs is innovative and fast to define dyslipidemic factors inducing stem cell damage, its mechanism, prevention, and counteraction. Confirmation is required in other T2D/obesity rat models and stem cells (including human), as well as miR-GTS biomarker validation as a stem cell damage biomarker. CONCLUSION Serum from long-term UC-T2D/obese rats or dyslipidemic factors induces a noxious phenotype and miR-GTS on normal MDSCs, which may lead in vivo to the repair inefficacy of late diabetic MDSCs. This suggests that autograft therapy with MDSCs in long-term UT-T2D obese patients may be ineffective, albeit this may be predictable by prior stem cell miR-GTS tests. Masouminia M, Gelfand R, Kovanecz I, et al. Dyslipidemia Is a Major Factor in Stem Cell Damage Induced by Uncontrolled Long-Term Type 2 Diabetes and Obesity in the Rat, as Suggested by the Effects on Stem Cell Culture. J Sex Med 2018;15:1678-1697.
Collapse
Affiliation(s)
- Maryam Masouminia
- Division of Urology, Department of Surgery, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA, USA
| | - Robert Gelfand
- Division of Urology, Department of Surgery, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA, USA
| | - Istvan Kovanecz
- Division of Urology, Department of Surgery, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA, USA; Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Dolores Vernet
- Division of Urology, Department of Surgery, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA, USA
| | - James Tsao
- Department of Medicine, Charles Drew University of Medicine and Science, Los Angeles, CA, USA
| | - Ruben Salas
- Division of Urology, Department of Surgery, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA, USA
| | - Kenny Castro
- Division of Urology, Department of Surgery, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA, USA
| | - Leila Loni
- Division of Urology, Department of Surgery, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA, USA
| | - Jacob Rajfer
- Division of Urology, Department of Surgery, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA, USA
| | - Nestor F Gonzalez-Cadavid
- Division of Urology, Department of Surgery, Harbor-UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, CA, USA; Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Department of Medicine, Charles Drew University of Medicine and Science, Los Angeles, CA, USA.
| |
Collapse
|
11
|
Zhu T, Corraze G, Plagnes-Juan E, Skiba-Cassy S. Circulating miRNA measurements are reflective of cholesterol-based changes in rainbow trout (Oncorhynchus mykiss). PLoS One 2018; 13:e0206727. [PMID: 30395627 PMCID: PMC6218197 DOI: 10.1371/journal.pone.0206727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs which are known to posttranscriptionally regulate the expression of most genes in both animals and plants. Meanwhile, studies have shown that numbers of miRNAs are present in body fluids including the plasma. Despite the mode of action of these circulating miRNAs still remains unknown, they have been found to be promising biomarkers for disease diagnosis, prognosis and response to treatment. In order to evaluate the potential of miRNAs as non-invasive biomarkers in aquaculture, a time-course experiment was implemented to investigate the postprandial regulation of miRNAs levels in liver and plasma as well as the hepatic expression of genes involved in cholesterol metabolism. We showed that miR-1, miR-33a, miR-122, miR-128 and miR-223 were expressed in the liver of rainbow trout and present at detectable level in the plasma. We also demonstrated that hepatic expression of miR-1, miR-122 and miR-128 were regulated by feed intake and reached their highest levels 12 hours after the meal. Interestingly, we observed that circulating levels of miR-128 and miR-223 are subjected to postprandial regulations similar to that observed in their hepatic counterparts. Statistical correlations were observed between liver and plasma for miR-128 and miR-223 and between hepatic and circulating miR-122, miR-128 and miR-223 and expression of genes related to cholesterol synthesis and efflux or glucose phosphorylation. These results demonstrated that circulating miR-122, miR-128 and miR-223 are potential biomarkers of cholesterol metabolism in rainbow trout.
Collapse
Affiliation(s)
- Tengfei Zhu
- INRA, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition Métabolisme Aquaculture, Saint Pée sur Nivelle, France
| | - Geneviève Corraze
- INRA, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition Métabolisme Aquaculture, Saint Pée sur Nivelle, France
| | - Elisabeth Plagnes-Juan
- INRA, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition Métabolisme Aquaculture, Saint Pée sur Nivelle, France
| | - Sandrine Skiba-Cassy
- INRA, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition Métabolisme Aquaculture, Saint Pée sur Nivelle, France
- * E-mail:
| |
Collapse
|
12
|
Zhang F, Li Y, Chen L, Cheng J, Wu P, Chu W, Zhang J. Characterization of the Ubiquitin Specific Protease (USP) family members in the fast and slow muscle fibers from Chinese perch (Siniperca chuatsi). Gene 2018; 677:1-9. [PMID: 30030202 DOI: 10.1016/j.gene.2018.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 11/16/2022]
Abstract
Skeletal muscle atrophy results from fasting, disuse and other systemic diseases. Muscle atrophy is associated with increased muscle protein degradation via the Ubiquitin proteasome system (UPS). The Ubiquitin Specific Proteases (USPs), also known as deubiquitinating enzymes, regulates a wide variety of cellular processes in skeletal muscle. In our study, among the 41 members of the USP family identified in the skeletal muscle transcriptome of Chinese perch, 24 USPs were differentially expressed between the fast and slow muscle fibers. The expressional profile of 4 muscle-related USPs (USP10, USP14, USP19, USP45) was investigated in the fast and slow muscle in response to fasting at 4 and 7 days. The results showed that the expression of USP10, USP14 and USP19 was significantly increased in the fast muscle after fasting for 4 days and 7 days. But only the USP10 and USP14 had significantly increased at 7 days of fasting in the slow muscle. The expression of MAFbx and MuRF1 up-regulated and major myofibrillar genes down-regulated, indicating that all of these four USPs are involved in the protein degradation of the fast and slow muscle.
Collapse
Affiliation(s)
- FangLiang Zhang
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China.
| | - YuLong Li
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - Lin Chen
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - Jia Cheng
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - Ping Wu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - WuYing Chu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China; Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde 415000, China.
| | - JianShe Zhang
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China; Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde 415000, China.
| |
Collapse
|
13
|
Proteomic and microRNA Transcriptome Analysis revealed the microRNA-SmyD1 network regulation in Skeletal Muscle Fibers performance of Chinese perch. Sci Rep 2017; 7:16498. [PMID: 29184116 PMCID: PMC5705591 DOI: 10.1038/s41598-017-16718-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 11/16/2017] [Indexed: 12/14/2022] Open
Abstract
Fish myotomes are comprised of anatomically segregated fast and slow muscle fibers that possess different metabolic and contractile properties. Although the expression profile properties in fast and slow muscle fibers had been investigated at the mRNA levels, a comprehensive analysis at proteomic and microRNA transcriptomic levels is limited. In the present study, we first systematically compared the proteomic and microRNA transcriptome of the slow and fast muscles of Chinese perch (Siniperca chuatsi). Total of 2102 proteins were identified in muscle tissues. Among them, 99 proteins were differentially up-regulated and 400 were down-regulated in the fast muscle compared with slow muscle. MiRNA microarrays revealed that 199 miRNAs identified in the two types of muscle fibers. Compared with the fast muscle, the 32 miRNAs was up-regulated and 27 down-regulated in the slow muscle. Specifically, expression of miR-103 and miR-144 was negatively correlated with SmyD1a and SmyD1b expression in fast and slow muscles, respectively. The luciferase reporter assay further verified that the miR-103 and miR-144 directly regulated the SmyD1a and SmyD1b expression by targeting their 3′-UTR. The constructed miRNA-SmyD1 interaction network might play an important role in controlling the development and performance of different muscle fiber types in Chinese perch.
Collapse
|
14
|
Gao K, Wang Z, Zhou X, Wang H, Kong D, Jiang C, Wang X, Jiang Z, Qiu X. Comparative transcriptome analysis of fast twitch muscle and slow twitch muscle in Takifugu rubripes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 24:79-88. [PMID: 28886574 DOI: 10.1016/j.cbd.2017.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 12/26/2022]
Abstract
Fast twitch muscle and slow twitch muscle are two important organs of Takifugu rubripes. Both tissues are of ectodermic origin, and the differences between the two muscle fibers reflect the differences in their myofibril protein composition and molecular structure. In order to identify and characterize the gene expression profile in the two muscle fibers of T. rubripes, we generated 54 million and 44 million clean reads from the fast twitch muscle and slow twitch muscle, respectively, using RNA-Seq and identified a total of 580 fast-muscle-specific genes, 1533 slow-muscle-specific genes and 11,806 genes expressed by both muscles. Comparative transcriptome analysis of fast and slow twitch muscles allowed the identification of 1508 differentially expressed genes, of which 34 myosin and 30 ubiquitin family genes were determined. These differentially expressed genes (DEGs) were also analyzed by Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. In addition, alternative splicing analysis was also performed. The generation of larger-scale transcriptomic data presented in this work would enrich the genetic resources of Takifugu rubripes, which could be valuable to comparative studies of muscles.
Collapse
Affiliation(s)
- Kailun Gao
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Zhicheng Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Xiaoxu Zhou
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Haoze Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Derong Kong
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Chen Jiang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Xiuli Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Zhiqiang Jiang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Xuemei Qiu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China.
| |
Collapse
|
15
|
Qiang J, Bao WJ, Tao FY, He J, Li XH, Xu P, Sun LY. The expression profiles of miRNA-mRNA of early response in genetically improved farmed tilapia (Oreochromis niloticus) liver by acute heat stress. Sci Rep 2017; 7:8705. [PMID: 28821885 PMCID: PMC5562739 DOI: 10.1038/s41598-017-09264-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 07/17/2017] [Indexed: 12/16/2022] Open
Abstract
Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are commercially important fish that are cultured in China. GIFT are highly susceptible to diseases when exposed to high temperatures in summer. Better understanding the GIFT regulatory response to heat stress will not only help in determining the relationship between heat stress signalling pathways and adaption mechanisms, but will also contribute to breeding new high-temperature tolerant strains of GIFT. In this study, we built control (28 °C) and heat-treated (37.5 °C) groups, and extracted RNA from the liver tissues for high-throughput next-generation sequencing to study the miRNA and mRNA expression profiles. We identified 28 differentially expressed (DE) miRNAs and 744 DE mRNAs between the control and heat-treated groups and annotated them using the KEGG database. A total of 38 target genes were predicted for 21 of the DE miRNAs, including 64 negative miRNA-mRNA interactions. We verified 15 DE miRNA-mRNA pairs and 16 other DE mRNAs by quantitative real-time PCR. Important regulatory pathways involved in the early response of GIFT to heat stress included organism system, metabolism, and diseases. Our findings will facilitate the understanding of regulatory pathways affected by acute heat stress, which will help to better prevent heat damage to GIFT.
Collapse
Affiliation(s)
- Jun Qiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Wen J Bao
- Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Fan Y Tao
- Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Jie He
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Xia H Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.
| | - Lan Y Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| |
Collapse
|
16
|
Zavala E, Reyes D, Deerenberg R, Vidal R. Selection of reference genes for microRNA analysis associated to early stress response to handling and confinement in Salmo salar. Sci Rep 2017; 7:1756. [PMID: 28496155 PMCID: PMC5431957 DOI: 10.1038/s41598-017-01970-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/05/2017] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs are key non-coding RNA molecules that play a relevant role in the regulation of gene expression through translational repression and/or transcript cleavage during normal development and physiological adaptation processes like stress. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) has become the approach normally used to determine the levels of microRNAs. However, this approach needs the use of endogenous reference. An improper selection of endogenous references can result in confusing interpretation of data. The aim of this study was to identify and validate appropriate endogenous reference miRNA genes for normalizing RT-qPCR survey of miRNAs expression in four different tissues of Atlantic salmon, under handling and confinement stress conditions associated to early or primary stress response. Nine candidate reference normalizers, including microRNAs and nuclear genes, normally used in vertebrate microRNA expression studies were selected from literature, validated by RT-qPCR and analyzed by the algorithms geNorm and NormFinder. The results revealed that the ssa-miR-99-5p gene was the most stable overall and that ssa-miR-99-5p and ssa-miR-23a-5p genes were the best combination. Moreover, the suitability of ssa-miR-99-5p and ssa-miR-23a-5p as endogeneuos reference genes was demostrated by the expression analysis of ssa-miR-193-5p gene.
Collapse
Affiliation(s)
- Eduardo Zavala
- Department of Biology, Universidad de Santiago de Chile. Av. Libertador Bernardo O'Higgins 3363, Santiago, Chile
| | - Daniela Reyes
- Department of Biology, Universidad de Santiago de Chile. Av. Libertador Bernardo O'Higgins 3363, Santiago, Chile
| | | | - Rodrigo Vidal
- Department of Biology, Universidad de Santiago de Chile. Av. Libertador Bernardo O'Higgins 3363, Santiago, Chile.
| |
Collapse
|
17
|
Zhang Y, Yu B, He J, Chen D. From Nutrient to MicroRNA: a Novel Insight into Cell Signaling Involved in Skeletal Muscle Development and Disease. Int J Biol Sci 2016; 12:1247-1261. [PMID: 27766039 PMCID: PMC5069446 DOI: 10.7150/ijbs.16463] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/19/2016] [Indexed: 12/17/2022] Open
Abstract
Skeletal muscle is a remarkably complicated organ comprising many different cell types, and it plays an important role in lifelong metabolic health. Nutrients, as an external regulator, potently regulate skeletal muscle development through various internal regulatory factors, such as mammalian target of rapamycin (mTOR) and microRNAs (miRNAs). As a nutrient sensor, mTOR, integrates nutrient availability to regulate myogenesis and directly or indirectly influences microRNA expression. MiRNAs, a class of small non-coding RNAs mediating gene silencing, are implicated in myogenesis and muscle-related diseases. Meanwhile, growing evidence has emerged supporting the notion that the expression of myogenic miRNAs could be regulated by nutrients in an epigenetic mechanism. Therefore, this review presents a novel insight into the cell signaling network underlying nutrient-mTOR-miRNA pathway regulation of skeletal myogenesis and summarizes the epigenetic modifications in myogenic differentiation, which will provide valuable information for potential therapeutic intervention.
Collapse
Affiliation(s)
- Yong Zhang
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, Sichuan 625014, P. R. China.; Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, China
| | - Bing Yu
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, Sichuan 625014, P. R. China.; Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, China
| | - Jun He
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, Sichuan 625014, P. R. China.; Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, China
| | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an, Sichuan 625014, P. R. China.; Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, China
| |
Collapse
|
18
|
Mu C, Wang R, Li T, Li Y, Tian M, Jiao W, Huang X, Zhang L, Hu X, Wang S, Bao Z. Long Non-Coding RNAs (lncRNAs) of Sea Cucumber: Large-Scale Prediction, Expression Profiling, Non-Coding Network Construction, and lncRNA-microRNA-Gene Interaction Analysis of lncRNAs in Apostichopus japonicus and Holothuria glaberrima During LPS Challenge and Radial Organ Complex Regeneration. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:485-499. [PMID: 27392411 DOI: 10.1007/s10126-016-9711-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 05/16/2016] [Indexed: 06/06/2023]
Abstract
Long non-coding RNA (lncRNA) structurally resembles mRNA but cannot be translated into protein. Although the systematic identification and characterization of lncRNAs have been increasingly reported in model species, information concerning non-model species is still lacking. Here, we report the first systematic identification and characterization of lncRNAs in two sea cucumber species: (1) Apostichopus japonicus during lipopolysaccharide (LPS) challenge and in heathy tissues and (2) Holothuria glaberrima during radial organ complex regeneration, using RNA-seq datasets and bioinformatics analysis. We identified A. japonicus and H. glaberrima lncRNAs that were differentially expressed during LPS challenge and radial organ complex regeneration, respectively. Notably, the predicted lncRNA-microRNA-gene trinities revealed that, in addition to targeting protein-coding transcripts, miRNAs might also target lncRNAs, thereby participating in a potential novel layer of regulatory interactions among non-coding RNA classes in echinoderms. Furthermore, the constructed coding-non-coding network implied the potential involvement of lncRNA-gene interactions during the regulation of several important genes (e.g., Toll-like receptor 1 [TLR1] and transglutaminase-1 [TGM1]) in response to LPS challenge and radial organ complex regeneration in sea cucumbers. Overall, this pioneer systematic identification, annotation, and characterization of lncRNAs in echinoderm pave the way for similar studies and future genetic, genomic, and evolutionary research in non-model species.
Collapse
Affiliation(s)
- Chuang Mu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Ruijia Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
| | - Tianqi Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Yuqiang Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Meilin Tian
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Wenqian Jiao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Xiaoting Huang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Lingling Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Xiaoli Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Shi Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
| |
Collapse
|
19
|
Wu P, Li Y, Cheng J, Chen L, Zeng M, Wu Y, Wang J, Zhang J, Chu W. Transcriptome Analysis and Postprandial Expression of Amino Acid Transporter Genes in the Fast Muscles and Gut of Chinese Perch (Siniperca chuatsi). PLoS One 2016; 11:e0159533. [PMID: 27463683 PMCID: PMC4963124 DOI: 10.1371/journal.pone.0159533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/04/2016] [Indexed: 01/09/2023] Open
Abstract
The characterization of the expression and regulation of growth-related genes in the muscles of Chinese perch is of great interest to aquaculturists because of the commercial value of the species. The transcriptome annotation of the skeletal muscles is a crucial step in muscle growth-related gene analysis. In this study, we generated 52 504 230 reads of mRNA sequence data from the fast muscles of the Chinese perch by using Solexa/Illumina RNA-seq. Twenty-one amino acid transporter genes were annotated by searching protein and gene ontology databases, and postprandial changes in their transcript abundance were assayed after administering a single satiating meal to Chinese perch juveniles (body mass, approximately 100 g), following fasting for 1 week. The gut content of the Chinese perch increased significantly after 1 h and remained high for 6 h following the meal and emptied within 48-96 h. Expression of eight amino acid transporter genes was assayed in the fast muscles through quantitative real-time polymerase chain reaction at 0, 1, 3, 6, 12, 24, 48, and 96 h. Among the genes, five transporter transcripts were markedly up-regulated within 1 h of refeeding, indicating that they may be potential candidate genes involved in the rapid-response signaling system regulating fish myotomal muscle growth. These genes display coordinated regulation favoring the resumption of myogenesis responding to feeding.
Collapse
Affiliation(s)
- Ping Wu
- Department of Bioengneering and Environmental Science, Changsha University, Changsha, 410003, China
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, 415000, China
| | - Yulong Li
- Department of Bioengneering and Environmental Science, Changsha University, Changsha, 410003, China
| | - Jia Cheng
- Department of Bioengneering and Environmental Science, Changsha University, Changsha, 410003, China
| | - Lin Chen
- Department of Bioengneering and Environmental Science, Changsha University, Changsha, 410003, China
| | - Ming Zeng
- Institute of Hunan Aquaculture and Fishes, Changsha, 410005, China
| | - Yuanan Wu
- Institute of Hunan Aquaculture and Fishes, Changsha, 410005, China
| | - Jianhua Wang
- Department of Bioengneering and Environmental Science, Changsha University, Changsha, 410003, China
| | - Jianshe Zhang
- Department of Bioengneering and Environmental Science, Changsha University, Changsha, 410003, China
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, 415000, China
- * E-mail: (JSZ); (WYC)
| | - Wuying Chu
- Department of Bioengneering and Environmental Science, Changsha University, Changsha, 410003, China
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, 415000, China
- * E-mail: (JSZ); (WYC)
| |
Collapse
|
20
|
Molecular characterization and expression regulation of Smyd1a and Smyd1b in skeletal muscle of Chinese perch (Siniperca chuatsi). Comp Biochem Physiol B Biochem Mol Biol 2016; 194-195:25-31. [DOI: 10.1016/j.cbpb.2016.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 12/16/2015] [Accepted: 01/06/2016] [Indexed: 11/22/2022]
|
21
|
Zhu X, Li YL, Liu L, Wang JH, Li HH, Wu P, Chu WY, Zhang JS. Molecular characterization of Myf5 and comparative expression patterns of myogenic regulatory factors in Siniperca chuatsi. Gene Expr Patterns 2015; 20:1-10. [PMID: 26547039 DOI: 10.1016/j.gep.2015.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/28/2015] [Accepted: 10/30/2015] [Indexed: 01/20/2023]
Abstract
Myogenic regulatory factors (MRFs) are muscle-specific basic helix-loop-helix (bHLH) transcription factor that plays an essential role in regulating skeletal muscle development and growth. To investigate molecular characterization of Myf5 and compare the expressional patterns of the four MRFs, we cloned the Myf5 cDNA sequence and analyzed the MRFs expressional patterns using quantitative real-time polymerase chain reaction in Chinese perch (Siniperca chuatsi). Sequence analysis indicated that Chinese perch Myf5 and other MRFs shared a highly conserved bHLH domain with those of other vertebrates. Sequence alignment and phylogenetic tree showed that Chinese perch MRFs had the highest identity with the MRFs of Epinephelus coioides. Spatio-temporal expressional patterns revealed that the MRFs were primarily expressed in muscle, especially in white muscle. During embryonic development period, Myf5, MyoD and MyoG mRNAs had a steep increase at neurula stage, and their highest expressional level was predominantly observed at hatching period. Whereas the highest expressional level of the MRF4 was observed at the muscular effect stage. The expressional patterns of post-embryonic development showed that the Myf5, MyoD and MyoG mRNAs were highest at 90 days post-hatching (dph). Furthermore, starvation and refeeding results showed that the transcription of the MRFs in the fast skeletal muscle of Chinese perch responded quickly to a single meal after 7 days of fasting. It indicated that the MRFs might contribute to muscle recovery after refeeding in Chinese perch.
Collapse
Affiliation(s)
- Xin Zhu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yu-Long Li
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - Li Liu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - Jian-Hua Wang
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - Hong-Hui Li
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - Ping Wu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China
| | - Wu-Ying Chu
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China.
| | - Jian-She Zhang
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, Hunan 410003, China.
| |
Collapse
|
22
|
Luo W, Li E, Nie Q, Zhang X. Myomaker, Regulated by MYOD, MYOG and miR-140-3p, Promotes Chicken Myoblast Fusion. Int J Mol Sci 2015; 16:26186-201. [PMID: 26540045 PMCID: PMC4661805 DOI: 10.3390/ijms161125946] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 10/16/2015] [Accepted: 10/22/2015] [Indexed: 12/21/2022] Open
Abstract
The fusion of myoblasts is an important step during skeletal muscle differentiation. A recent study in mice found that a transmembrane protein called Myomaker, which is specifically expressed in muscle, is critical for myoblast fusion. However, the cellular mechanism of its roles and the regulatory mechanism of its expression remain unclear. Chicken not only plays an important role in meat production but is also an ideal model organism for muscle development research. Here, we report that Myomaker is also essential for chicken myoblast fusion. Forced expression of Myomaker in chicken primary myoblasts promotes myoblast fusion, whereas knockdown of Myomaker by siRNA inhibits myoblast fusion. MYOD and MYOG, which belong to the family of myogenic regulatory factors, can bind to a conserved E-box located proximal to the Myomaker transcription start site and induce Myomaker transcription. Additionally, miR-140-3p can inhibit Myomaker expression and myoblast fusion, at least in part, by binding to the 3ʹ UTR of Myomaker in vitro. These findings confirm the essential roles of Myomaker in avian myoblast fusion and show that MYOD, MYOG and miR-140-3p can regulate Myomaker expression.
Collapse
Affiliation(s)
- Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Erxin Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
23
|
Mennigen JA. Micromanaging metabolism-a role for miRNAs in teleost energy metabolism. Comp Biochem Physiol B Biochem Mol Biol 2015; 199:115-125. [PMID: 26384523 DOI: 10.1016/j.cbpb.2015.09.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/08/2015] [Accepted: 09/08/2015] [Indexed: 10/23/2022]
Abstract
MicroRNAs (miRNAs) are small, non-protein coding RNA sequences, which are found in most eukaryotes. Since their initial discovery, miRNAs have emerged as important regulators of many biological processes. One of the most important processes profoundly regulated by miRNAs is energy metabolism. Traditionally, metabolic functions of miRNAs have been studied in genome-sequenced mammalian organisms, especially the mouse model. However, partially driven by commercial interest in aquaculture, increasingly feasible large-scale molecular techniques have resulted in the characterization of miRNA repertoires, and importantly, several genome sequences of several (commercially important) teleost species, which also hold important roles as research models in the comparative physiology of energy metabolism. This review aims to introduce the recent advances in miRNA research in teleost fish and to describe the current knowledge of miRNA function in teleost energy metabolism. The most pressing research needs and questions to determine metabolic roles of miRNAs in teleost models are presented, as well as applicable technical approaches and current bottlenecks. Rainbow trout, which possess the advantages of newly available molecular tools and a long history as comparative research model in teleost energy metabolism, are discussed as a promising research model to address these questions.
Collapse
Affiliation(s)
- Jan A Mennigen
- College of Pharmacy, Department of Toxicology and Pharmacology, University of Austin at Texas, 107 W Dean Keeton, Austin, TX 78712, USA
| |
Collapse
|