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Hubert JN, Perret M, Riquet J, Demars J. Livestock species as emerging models for genomic imprinting. Front Cell Dev Biol 2024; 12:1348036. [PMID: 38500688 PMCID: PMC10945557 DOI: 10.3389/fcell.2024.1348036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 03/20/2024] Open
Abstract
Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.
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Affiliation(s)
| | | | | | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
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2
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Setti PG, Borra RC, Sassi FDMC, Cioffi MDB, Fukushima HCS. Zebrafish ( Danio rerio) Gynogenetic Production by Heat Shock: Comparison Between Mitotic and Meiotic Treatment. Zebrafish 2023; 20:181-188. [PMID: 37527193 DOI: 10.1089/zeb.2023.0013] [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] [Indexed: 08/03/2023] Open
Abstract
Inbred species are useful resources for a variety of biomedical research applications. To create isogenic zebrafish, it is feasible to stop meiosis II (repeatedly) or mitosis (two times) in a haploid embryo by applying pressure or by delivering a heat shock, respectively. In this study, to improve the repeatability, we suggest a less complicated approach based on sperm ultraviolet-C (UV-C) exposure for a shorter period followed by heat shock at various temperatures, eliminating the use of pressure in meiotic therapy since heat shock is more accessible to laboratories. In this study, the survivability rates of meiotic (Mei) and mitotic (Mit) gynogenesis offspring produced by various combinations of irradiation (28.5, 105, and 210 mJ/cm2) and temperature (Mei: 40.40°C, 40.60°C, or 40.90°C; Mt: 41.40°C, 41.90°C, or 42.45°C) were compared with diploid (C) and haploid (H) controls. Our findings demonstrated that 40.60°C and 41.90°C were the most suitable temperatures to produce meiotic and mitotic gynogenesis, respectively, whereas 28.5 mJ/cm2 was more successful in ensuring haploid embryos. As a result, we deduced that meiotic gynogenesis produces more viable offspring than the mitotic approach and requires a lower temperature to maintain the second polar body.
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Affiliation(s)
- Príncia Grejo Setti
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Ricardo Carneiro Borra
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, Brazil
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3
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Yu F, Li JL, Feng WR, Tang YK, Su SY, Xu P, Zhong H. Heat Shock Procedure Affects Cell Division-Associated Genes in Gynogenetic Manipulation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:354-365. [PMID: 35305189 DOI: 10.1007/s10126-022-10112-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Heat shock procedure is crucial for gynogenetic manipulation leading to diploidization of the maternal genomes; however, the underlying molecular mechanism especially the transcriptomic changes during this procedure has still not been unveiled yet. Here, the artificial gynogenesis of zebrafish (Danio rerio) using inactivated sperm from rare minnow (Gobiocypris rarus) was conducted. We found that artificial gynogenetic manipulation, including pseudo-fertilization and heat shock, decreased hatching rates, whereas heat shock treatment alone had medium hatching rates. The first cleavage changed the expression of genes associated with RNA transcription and protein synthesis. A co-expression network regulated by hub genes GIT1, Sepsecs, and FLNB was significantly correlated with heat shock procedure. The cyclin family and cyclin-dependent kinase-related genes were lowly expressed in embryos from gynogenetic zebrafish, and genes involved in controlling the cell cycle and genomic stability were significantly altered by the gynogenetic treatment. Our results show the effects of artificial gynogenesis on embryos and describe changes in gene expression that suggest drastic changes take place in cell division by heat shock procedure. These findings will contribute to an understanding of the molecular basis for germplasm improving, including the purifying effect and allogynogenetic biological effect by gynogenesis.
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Affiliation(s)
- Fan Yu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Jian-Lin Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wen-Rong Feng
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Yong-Kai Tang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Sheng-Yan Su
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Huan Zhong
- Hunan Research Center of Engineering Technology for Utilization of Distinctive Aquatic Resource, Hunan Agricultural University, Changsha, 410128, China.
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4
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Wang L, Wu Z, Zou C, Liang S, Zou Y, Liu Y, You F. Sex-Dependent RNA Editing and N6-adenosine RNA Methylation Profiling in the Gonads of a Fish, the Olive Flounder ( Paralichthys olivaceus). Front Cell Dev Biol 2020; 8:751. [PMID: 32850855 PMCID: PMC7419692 DOI: 10.3389/fcell.2020.00751] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/17/2020] [Indexed: 12/20/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) editing and N6-methyladenosine (m6A) are two of the most abundant RNA modifications. Here, we examined the characteristics of the RNA editing and transcriptome-wide m6A modification profile in the gonads of the olive flounder, Paralichthys olivaceus, an important maricultured fish in Asia. The gonadal differentiation and development of the flounder are controlled by genetic as well as environmental factors, and the epigenetic mechanism may play an important role. In total, 742 RNA editing events were identified, 459 of which caused A to I conversion. Most A-to-I sites were located in 3′UTRs, while 61 were detected in coding regions (CDs). The number of editing sites in the testis was higher than that in the ovary. Transcriptome-wide analyses showed that more than one-half of the transcribed genes presented an m6A modification in the flounder gonads, and approximately 60% of the differentially expressed genes (DEGs) between the testis and ovary appeared to be negatively correlated with m6A methylation enrichment. Further analyses revealed that the mRNA expression of some sex-related genes (e.g., dmrt1 and amh) in the gonads may be regulated by changes in mRNA m6A enrichment. Functional enrichment analysis indicated that the RNA editing and m6A modifications were enriched in several canonical pathways (e.g., Wnt and MAPK signaling pathways) in fish gonads and in some pathways whose roles have not been investigated in relation to fish sex differentiation and gonadal development (e.g., PPAR and RNA degradation pathways). There were 125 genes that were modified by both A-to-I editing and m6A, but the two types of modifications mostly occurred at different sites. Our results suggested that the presence of sex-specific RNA modifications may be involved in the regulation of gonadal development and gametogenesis.
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Affiliation(s)
- Lijuan Wang
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Zhihao Wu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Congcong Zou
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shaoshuai Liang
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Yuxia Zou
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Yan Liu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Feng You
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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5
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Wang B, Wang H, Song H, Jin C, Peng M, Gao C, Yang F, Du X, Qi J, Zhang Q, Cheng J. Evolutionary significance and regulated expression of Tdrd family genes in gynogenetic Japanese flounder (Paralichthys olivaceus). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100593. [PMID: 31125834 DOI: 10.1016/j.cbd.2019.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 11/29/2022]
Abstract
Tudor domain-containing proteins (TDRDs) are highly conserved among organisms and have a function in gonads to regulate gametogenesis and genome stability through the piwi-interacting RNA (piRNA) pathway. With diverse sexual development patterns in teleost species, the evolution and function of Tdrd genes among teleosts remain unclear. Here, we identified and characterized 12 Tdrd genes (PoTdrds) in Japanese flounder (Paralichthys olivaceus) which represents dramatic sexual dimorphic metrics and sex reversal during sex differentiation. Phylogenetic and comparative synteny indicated the gain and loss of Tdrd genes after teleost-specific whole-genome duplication (3R-WGD). Tdrd1, Tdrd5, Tdrd6 and Ecat8 were abundantly expressed in their gonads. Four PoTdrds (Tdrd6, Tdrd7b, Tdrd9 and Ecat8) represented significant male-biased expression in gynogenetic and wild-type Japanese flounder gonads (p < .01). This finding indicated their important roles in spermatogenesis of P. olivaceus. Some PoTdrds were either highly up-regulated in gynogenetic testis (Tdrd3, Tdrd5, Tdrd7b and Ecat8) or down-regulated in gynogenetic ovary (Tdrkh, Tdrd3, Tdrd6l) compared with wild-type gonads (p < .05). Molecular evolution tests revealed that the selective pressure of Tdrd6/6l differed between ancestral aquatic and terrestrial organisms with 13 positively selected sites found in the ancestral lineages of teleost Tdrd6. Expression profile analysis suggested that PoTdrd6 differed significantly from PoTdrd6l, indicating sub-functionalization after 3R-WGD. All these results are important for the functional annotation of Tdrd genes and can benefit the further deciphering of Tdrd functions during gonadal development and gametogenesis of teleost fish.
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Affiliation(s)
- Bo Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Huizhen Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Haofei Song
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Chaofan Jin
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Meiting Peng
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Chen Gao
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Fan Yang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Xinxin Du
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Jie Qi
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jie Cheng
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China.
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Wang Z, Cui J, Song J, Gou M, Wang H, Gao K, Qiu X, Wang X, Chang Y. Integration of small RNAs and mRNAs by high-throughput sequencing reveals a complex regulatory network in Chinese sea cucumber, Russian sea cucumber and their hybrids. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:1-13. [DOI: 10.1016/j.cbd.2018.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 10/13/2018] [Indexed: 11/30/2022]
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7
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Jung JH, Moon YS, Kim BM, Lee YM, Kim M, Rhee JS. Comparative analysis of distinctive transcriptome profiles with biochemical evidence in bisphenol S- and benzo[a]pyrene-exposed liver tissues of the olive flounder Paralichthys olivaceus. PLoS One 2018; 13:e0196425. [PMID: 29715276 PMCID: PMC5929548 DOI: 10.1371/journal.pone.0196425] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/12/2018] [Indexed: 02/06/2023] Open
Abstract
Flounder is a promising model species for environmental monitoring of coastal regions. To assess the usefulness of liver transcriptome profiling, juvenile olive flounder Paralichthys olivaceus were exposed to two pollutants, bisphenol S (BPS) and benzo[a]pyrene (BaP), which have different chemical characteristics and have distinct modes of metabolic action in teleost. Six hours after intraperitoneal injection with BPS (50 mg/kg bw) or BaP (20 mg/kg bw), liver transcriptomes were analyzed using the Illumina Hiseq 3000 platform. Interestingly, the transcriptome was highly sensitive and was distinctively expressed in response to each chemical. The primary effect of BPS was significantly increased transcription of egg process and vitellogenesis related genes, including vitellogenins (vtg1, vtg2), zona pellucida sperm-binding proteins (zp3, zp4), and estrogen receptors (erα, erβ), with increases in plasma 17β-estradiol (E2) and vitellogenin (VTG) concentrations. Following BaP treatment, detoxification- and biotransformation-related genes such as cyp1a1 and UDP-glucuronosyltransferase (ugt1a1) were significantly increased, with an increase in EROD activity. In both transcriptomes, mRNA expression of genes involved in antioxidant defense systems was increased, while genes involved in innate immunity were decreased upon BPS or BaP exposure with a decrease in complement activity. This study provides useful insight into the chemical-specific hepatic transcriptional response of P. olivaceus and suggests a basis for further studies examining biomarker application of liver transcriptomes for environmental pollution.
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Affiliation(s)
- Jee-Hyun Jung
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology, Geoje, South Korea
- Department of Marine Environmental Science, Korea University of Science and Technology, Daejeon, South Korea
- * E-mail: (JHJ); (JSR)
| | - Young-Sun Moon
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology, Geoje, South Korea
| | - Bo-Mi Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Young-Mi Lee
- Department of Life Science, College of Natural Sciences, Sangmyung University, Seoul, South Korea
| | - Moonkoo Kim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology, Geoje, South Korea
- Department of Marine Environmental Science, Korea University of Science and Technology, Daejeon, South Korea
| | - Jae-Sung Rhee
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, South Korea
- Research Institute of Basic Sciences, Incheon National University, Incheon, South Korea
- * E-mail: (JHJ); (JSR)
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Wang Z, Cui J, Song J, Wang H, Gao K, Qiu X, Gou M, Li X, Hu Z, Wang X, Chang Y. Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:193-205. [PMID: 29492749 DOI: 10.1007/s10126-018-9796-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 01/24/2018] [Indexed: 06/08/2023]
Abstract
Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.
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Affiliation(s)
- Zhicheng Wang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Jun Cui
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China
| | - Haoze Wang
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Kailun Gao
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Xuemei Qiu
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Meng Gou
- School of Life Science, Liaoning Normal University, Dalian, 116081, China
| | - Xin Li
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Ziwen Hu
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Xiuli Wang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China.
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China.
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China.
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China.
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Oomen RA, Hutchings JA. Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing. Facets (Ott) 2017. [DOI: 10.1139/facets-2017-0015] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short- and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.
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Affiliation(s)
- Rebekah A. Oomen
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Institute of Marine Research, Flødevigen Research Station, 4817 His, Norway
| | - Jeffrey A. Hutchings
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Institute of Marine Research, Flødevigen Research Station, 4817 His, Norway
- Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway
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Transcriptome Analysis Reveals Increases in Visceral Lipogenesis and Storage and Activation of the Antigen Processing and Presentation Pathway during the Mouth-Opening Stage in Zebrafish Larvae. Int J Mol Sci 2017; 18:ijms18081634. [PMID: 28758957 PMCID: PMC5578024 DOI: 10.3390/ijms18081634] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 12/11/2022] Open
Abstract
The larval phase of the fish life cycle has the highest mortality, particularly during the transition from endogenous to exogenous feeding. However, the transcriptional events underlying these processes have not been fully characterized. To understand the molecular mechanisms underlying mouth-opening acclimation, RNA-seq was used to investigate the transcriptional profiles of the endogenous feeding, mixed feeding and exogenous feeding stages of zebrafish larvae. Differential expression analysis showed 2172 up-regulated and 2313 down-regulated genes during this stage. Genes associated with the assimilation of exogenous nutrients such as the arachidonic acid metabolism, linoleic acid metabolism, fat digestion and absorption, and lipogenesis were activated significantly, whereas dissimilation including the cell cycle, homologous recombination, and fatty acid metabolism were inhibited, indicating a physiological switch for energy storage occurred during the mouth-opening stage. Moreover, the immune recognition involved in the antigen processing and presentation pathway was activated and nutritional supply seemed to be required in this event confirmed by qPCR. These results suggested the energy utilization during the mouth-opening stage is more tended to be reserved or used for some important demands, such as activity regulation, immune defense, and lipid deposition, instead of rapid growth. The findings of this study are important for understanding the physiological switches during the mouth-opening stage.
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