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Yu D, Liu S, Yu Y, Wang Y, Li L, Peijnenburg WJGM, Yuan Y, Peng X. Transcriptomic analysis reveals interactive effects of polyvinyl chloride microplastics and cadmium on Mytilus galloprovincialis: Insights into non-coding RNA responses and environmental implications. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 275:107062. [PMID: 39217792 DOI: 10.1016/j.aquatox.2024.107062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 09/04/2024]
Abstract
Despite increasing concerns regarding the interactions of microplastic and heavy metal pollution, there is limited knowledge on the molecular responses of marine organisms to these stressors. In this study, we used whole-transcriptome sequencing to investigate the molecular responses of the ecologically and economically important bivalve Mytilus galloprovincialis to individual and combined exposures of environmentally relevant concentrations of PVC microplastics and cadmium (Cd). Our results revealed distinct transcriptional changes in M. galloprovincialis, with significant overlap in the differentially expressed genes between the individual and combined exposure groups. Genes involved in cellular senescence, oxidative stress, and galactose metabolism were differentially expressed. Additionally, key signaling pathways related to apoptosis and drug metabolism were significantly modulated. Notably, the interaction of PVC microplastics and Cd resulted in differential expression of genes involved in drug metabolism and longevity regulating compared to single exposures. This suggests that the interaction between these two stressors may have amplified effects on mussel health. Overall, this comprehensive transcriptomic analysis provides valuable insights into the adaptive and detrimental responses of M. galloprovincialis to PVC microplastics and Cd in the environment.
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Affiliation(s)
- Deliang Yu
- Laoshan Laboratory, Qingdao 266237, PR China
| | - Shaochong Liu
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, PR China
| | - Yaqi Yu
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, PR China
| | - Yanhao Wang
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, PR China
| | - Lianzhen Li
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, PR China.
| | - Willie J G M Peijnenburg
- National Institute of Public Health and the Environment, Center for Safety of Substances and Products, Bilthoven, The Netherlands; Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands
| | - Yufeng Yuan
- School of Electronic Engineering and Intelligentization, Dongguan University of Technology, Dongguan, Guangdong 523808, PR China
| | - Xiao Peng
- State Key Laboratory of Radio Frequency Heterogeneous Integration (Shenzhen University), College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Shenzhen University, Shenzhen 518060, PR China.
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2
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Chen S, Nie H, Huo Z, Yan X. Comprehensive analysis of differentially expressed mRNA, lncRNA and miRNA, and their ceRNA networks in the regulation of shell color in the Manila clam (Ruditapes philippinarum). Int J Biol Macromol 2024; 256:128404. [PMID: 38016607 DOI: 10.1016/j.ijbiomac.2023.128404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/11/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
The regulatory mechanism of ceRNA network plays an important role in molecular function and biological processes, however, the molecular mechanism in the shell color of Ruditapes philippinarum has not yet been reported. In this study, we performed transcriptome sequencing on the mantle of R. philippinarum with different shell colors, and screened for mRNA, miRNA, and lncRNA. A total of 61 mRNAs, 3725 lncRNAs and 90 miRNAs were obtained from all the shell color comparison groups (all mRNAs, lncRNAs and miRNAs P < 0.05), and 7 mRNAs, 8 lncRNAs, and 4 miRNAs of the porphyrin pathway and melanin pathway were screened for competitive endogenous RNA (ceRNA) network construction. The results indicate that the ceRNA network composed of mRNA and lncRNA, centered around efu-miR-101, mle-bantam-3p, egr-miR-9-5p, and sma-miR-75p, may play a crucial regulatory role in shell color formation. This study reveals for the first time the mechanism of ceRNA regulatory networks in the shell color of R. philippinarum and providing important reference data for molecular breeding of shell color in R. philippinarum.
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Affiliation(s)
- Sitong Chen
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China.
| | - Zhongming Huo
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Xiwu Yan
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
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Hu Q, Xia X, Lian Z, Tian H, Li Z. Regulatory mechanism of LncRNAs in gonadal differentiation of hermaphroditic fish, Monopterus albus. Biol Sex Differ 2023; 14:74. [PMID: 37880697 PMCID: PMC10598917 DOI: 10.1186/s13293-023-00559-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Monopterus albus is a hermaphroditic fish with sex reversal from ovaries to testes via the ovotestes in the process of gonadal development, but the molecular mechanism of the sex reversal was unknown. METHODS We produced transcriptomes containing mRNAs and lncRNAs in the crucial stages of the gonad, including the ovary, ovotestis and testis. The expression of the crucial lncRNAs and their target genes was detected using qRT‒PCR and in situ hybridization. The methylation level and activity of the lncRNA promoter were analysed by applying bisulfite sequencing PCR and dual-luciferase reporter assays, respectively. RESULTS This effort revealed that gonadal development was a dynamic expression change. Regulatory networks of lncRNAs and their target genes were constructed through integrated analysis of lncRNA and mRNA data. The expression and DNA methylation of the lncRNAs MSTRG.38036 and MSTRG.12998 and their target genes Psmβ8 and Ptk2β were detected in developing gonads and sex reversal gonads. The results showed that lncRNAs and their target genes exhibited consistent expression profiles and that the DNA methylation levels were negatively regulated lncRNA expression. Furthermore, we found that Ptk2β probably regulates cyp19a1 expression via the Ptk2β/EGFR/STAT3 pathway to reprogram sex differentiation. CONCLUSIONS This study provides novel insight from lncRNA to explore the potential molecular mechanism by which DNA methylation regulates lncRNA expression to facilitate target gene transcription to reprogram sex differentiation in M. albus, which will also enrich the sex differentiation mechanism of teleosts.
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Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China.
| | - Xueping Xia
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China
| | - Zitong Lian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China.
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Zhou T, Zhang H, Chen M, Zhang Y, Chen G, Zou G, Liang H. Identification and Expression Analysis of Wnt2 Gene in the Sex Differentiation of the Chinese Soft-Shelled Turtle ( Pelodiscus sinensis). LIFE (BASEL, SWITZERLAND) 2023; 13:life13010188. [PMID: 36676139 PMCID: PMC9864750 DOI: 10.3390/life13010188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/28/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023]
Abstract
The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important freshwater aquaculture animal in China. The Wnt gene family plays important regulatory roles in the development and growth of mammals. However, the precise function of these family genes has not been well understood in the sex differentiation of Chinese soft-shelled turtles. Here, we cloned a member of the Wnt family, Wnt2, which obtained a 1077 bp open reading frame that encoded a 358-aa protein. The putative amino acid sequences of proteins are exceeded 80% identical to other turtles. The expression level of Wnt2 peaked at the 14th stage both in female and male embryos during the early gonadal differentiation period of Chinese soft-shelled turtles, which occurred before gonadal differentiation. Wnt2 mRNA was expressed at higher levels in the brains and gonads of mature P. sinensis females compared with those in mature males. Wnt agonists significantly affected the expression level of Wnt2 during the gonadal differentiation period. After Wnt agonists (1.0 μg/μL, 2.5 μg/μL, 5.0 μg/μL) treatment, the expression level of the Wnt2 generally appeared to have an inverted-V trend over time in female embryonic gonads. The results suggested that Wnt2 may participate in the regulation of gonad development in P. sinensis during the early embryonic stages. These results could provide a theoretical basis for the reproduction process of the Chinese soft-shelled turtle.
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Affiliation(s)
- Tong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Haiqi Zhang
- Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China
| | - Meng Chen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yingping Zhang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Guobin Chen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Guiwei Zou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
- Correspondence: (G.Z.); (H.L.)
| | - Hongwei Liang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
- Correspondence: (G.Z.); (H.L.)
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Wang P, Xiong G, Zeng D, Zhang J, Ge L, Liu L, Wang X, Hu Y. Comparative transcriptome and miRNA analysis of skin pigmentation during embryonic development of Chinese soft-shelled turtle (Pelodiscus sinensis). BMC Genomics 2022; 23:801. [PMID: 36471254 PMCID: PMC9721069 DOI: 10.1186/s12864-022-09029-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/21/2022] [Indexed: 12/10/2022] Open
Abstract
BACKGROUND Aquatic animals show diverse body coloration, and the formation of animal body colour is a complicated process. Increasing evidence has shown that microRNAs (miRNAs) play important regulatory roles in many life processes. The role of miRNAs in pigmentation has been investigated in some species. However, the regulatory patterns of miRNAs in reptile pigmentation remain to be elucidated. In this study, we performed an integrated analysis of miRNA and mRNA expression profiles to explore corresponding regulatory patterns in embryonic body colour formation in the soft-shelled turtle Pelodiscus sinensis. RESULTS We identified 8 866 novel genes and 9 061 mature miRNAs in the skin of Chinese soft-shelled turtles in three embryonic stages (initial period: IP, middle period: MP, final period: FP). A total of 16 563 target genes of the miRNAs were identified. Furthermore, we identified 2 867, 1 840 and 4 290 different expression genes (DEGs) and 227, 158 and 678 different expression miRNAs (DEMs) in IP vs. MP, MP vs. FP, and IP vs. FP, respectively. Among which 72 genes and 25 miRNAs may be related to turtle pigmentation in embryonic development. Further analysis of the novel miRNA families revealed that some novel miRNAs related to pigmentation belong to the miR-7386, miR-138, miR-19 and miR-129 families. Novel_miR_2622 and novel_miR_2173 belong to the miR-19 family and target Kit and Gpnmb, respectively. The quantification of novel_miR_2622 and Kit revealed negative regulation, indicating that novel_miR_2622 may participate in embryonic pigmentation in P. sinensis by negatively regulating the expression of Kit. CONCLUSIONS miRNA act as master regulators of biological processes by controlling the expression of mRNAs. Considering their importance, the identified miRNAs and their target genes in Chinese soft-shelled turtle might be useful for investigating the molecular processes involved in pigmentation. All the results of this study may aid in the improvement of P. sinensis breeding traits for aquaculture.
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Affiliation(s)
- Pei Wang
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
| | - Gang Xiong
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127 Hunan China
| | - Dan Zeng
- grid.440778.80000 0004 1759 9670College of Life and Environmental Science, Hunan University of Arts and Science, Changde, 415000 Hunan China
| | - Jianguo Zhang
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127 Hunan China
| | - Lingrui Ge
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China ,Hunan Biological and Electromechanical Polytechnic, Changsha, 410127 Hunan China
| | - Li Liu
- grid.449642.90000 0004 1761 026XSchool of Medical Technology, Shaoyang University, Shaoyang, 422000 Hunan China
| | - Xiaoqing Wang
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
| | - Yazhou Hu
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
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He Z, Ye L, Yang D, Ma Z, Deng F, He Z, Hu J, Chen H, Zheng L, Pu Y, Jiao Y, Chen Q, Gao K, Xiong J, Lai B, Gu X, Huang X, Yang S, Zhang M, Yan T. Identification, characterization and functional analysis of gonadal long noncoding RNAs in a protogynous hermaphroditic teleost fish, the ricefield eel (Monopterus albus). BMC Genomics 2022; 23:450. [PMID: 35725373 PMCID: PMC9208217 DOI: 10.1186/s12864-022-08679-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/09/2022] [Indexed: 11/11/2022] Open
Abstract
Background An increasing number of long noncoding RNAs (lncRNAs) have been found to play important roles in sex differentiation and gonad development by regulating gene expression at the epigenetic, transcriptional and posttranscriptional levels. The ricefield eel, Monopterus albus, is a protogynous hermaphroditic fish that undergoes a sequential sex change from female to male. However, the roles of lncRNA in the sex change is unclear. Results Herein, we performed RNA sequencing to analyse lncRNA expression patterns in five different stages of M. albus development to investigate the roles of lncRNAs in the sex change process. A total of 12,746 lncRNAs (1503 known lncRNAs and 11,243 new lncRNAs) and 2901 differentially expressed lncRNAs (DE-lncRNAs) were identified in the gonads. The target genes of the DE-lncRNAs included foxo1, foxm1, smad3, foxr1, camk4, ar and tgfb3, which were mainly enriched in signalling pathways related to gonadal development, such as the insulin signalling pathway, MAPK signalling pathway, and calcium signalling pathway. We selected 5 highly expressed DE-lncRNAs (LOC109952131, LOC109953466, LOC109954337, LOC109954360 and LOC109958454) for full length amplification and expression pattern verification. They were all expressed at higher levels in ovaries and intersex gonads than in testes, and exhibited specific time-dependent expression in ovarian tissue incubated with follicle-stimulating hormone (FSH) and human chorionic gonadotropin (hCG). The results of quantitative real-time PCR (qRT-PCR) analysis and a dual-luciferase assay showed that znf207, as the gene targeted by LOC109958454, was expressed in multiple tissues and gonadal developmental stages of M. albus, and its expression was also inhibited by the hormones FSH and hCG. Conclusions These results provide new insights into the role of lncRNAs in gonad development, especially regarding natural sex changes in fish, which will be useful for enhancing our understanding of sequential hermaphroditism and sex changes in the ricefield eel (M. albus) and other teleosts. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08679-2.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lijuan Ye
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhijun Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Faqiang Deng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhide He
- Luzhou Municipal Bureau of Agriculture and Rural Affairs, Luzhou, 646000, Sichuan, China
| | - Jiaxiang Hu
- Sichuan Water Conservancy Vocational College, Chengdu, 611231, Sichuan, China
| | - Hongjun Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Li Zheng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yong Pu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yuanyuan Jiao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiqi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Kuo Gao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jinxin Xiong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bolin Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaobin Gu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoli Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shiyong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Hu MY, Yu J, Lin JQ, Fang SG. Sex-Biased miRNAs in the Gonads of Adult Chinese Alligator ( Alligator sinensis) and Their Potential Roles in Sex Maintenance. Front Genet 2022; 13:843884. [PMID: 35432471 PMCID: PMC9008718 DOI: 10.3389/fgene.2022.843884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNA (miRNA) is a category of single-stranded non-coding small RNA (sRNA) that regulates gene expression by targeting mRNA. It plays a key role in the temperature-dependent sex determination of Chinese alligator (Alligator sinensis), a reptile whose sex is determined solely by the temperature during the incubation period and remains stable thereafter. However, the potential function of miRNAs in the gonads of adult Chinese alligators is still unclear. Here, we prepared and sequenced sRNA libraries of adult female and male alligator gonads, from breeding (in summer) and hibernating (in winter) animals. We obtained 130 conserved miRNAs and 683 novel miRNAs, which were assessed for sex bias in summer and winter; a total of 65 miRNAs that maintained sex bias in both seasons were identified. A regulatory network of sex-biased miRNAs and genes was constructed. Sex-biased miRNAs targeted multiple genes in the meiosis pathway of adult Chinese alligator oocytes and the antagonistic gonadal function maintenance pathway, such as MOS, MYT1, DMRT1, and GDF9. Our study emphasizes the function of miRNA in the epigenetic mechanisms of sex maintenance in crocodilians.
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Affiliation(s)
- Meng-Yuan Hu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jun Yu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian-Qing Lin
- MOE Key Laboratory of Biosystems Homeostasis and Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, China
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
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Micheel J, Safrastyan A, Wollny D. Advances in Non-Coding RNA Sequencing. Noncoding RNA 2021; 7:70. [PMID: 34842804 PMCID: PMC8628893 DOI: 10.3390/ncrna7040070] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.
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Affiliation(s)
| | | | - Damian Wollny
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, 07743 Jena, Germany; (J.M.); (A.S.)
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Zhou T, Sha H, Chen M, Chen G, Zou G, Liang H. MicroRNAs May Play an Important Role in Sexual Reversal Process of Chinese Soft-Shelled Turtle, Pelodiscus sinensis. Genes (Basel) 2021; 12:genes12111696. [PMID: 34828302 PMCID: PMC8620467 DOI: 10.3390/genes12111696] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 12/17/2022] Open
Abstract
The Chinese soft-shelled (Pelodiscus sinensis) turtle exhibits obvious sex dimorphism, which leads to the higher economic and nutritional value of male individuals. Exogenous hormones can cause the transformation from male to female phenotype during gonadal differentiation. However, the molecular mechanism related to the sexual reversal process is unclear. In this study, we compared the difference between the small RNAs of male, female, and pseudo-female turtles by small RNA-seq to understand the sexual reversal process of Chinese soft-shelled turtles. A certain dose of estrogen can cause the transformation of Chinese soft-shelled turtles from male to female, which are called pseudo-female individuals. The result of small RNA-seq has revealed that the characteristics of pseudo-females are very similar to females, but are strikingly different from males. The number of the microRNAs (miRNAs) of male individuals was significantly less than the number of female individuals or pseudo-female individuals, while the expression level of miRNAs of male individuals were significantly higher than the other two types. Furthermore, we found 533 differentially expressed miRNAs, including 173 up-regulated miRNAs and 360 down-regulated miRNAs, in the process of transformation from male to female phenotype. Cluster analysis of the total 602 differential miRNAs among females, males, and pseudo-females showed that miRNAs played a crucial role during the sexual differentiation. Among these differential miRNAs, we found 12 miRNAs related to gonadal development and verified their expression by qPCR. The TR-qPCR results confirmed the differential expression of 6 of the 12 miRNAs: miR-26a-5p, miR-212-5p, miR-202-5p, miR-301a, miR-181b-3p and miR-96-5p were involved in sexual reversal process, which was consistent with the results of omics. Using these six miRNAs and some of their target genes, we constructed a network diagram related to gonadal development. We suggest that these miRNAs may play an important role in the process of effective sex reversal, which would contribute to the breeding of all male strains of Chinese soft-shelled turtles.
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Affiliation(s)
- Tong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; (T.Z.); (H.S.); (M.C.); (G.C.); (G.Z.)
| | - Hang Sha
- Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; (T.Z.); (H.S.); (M.C.); (G.C.); (G.Z.)
| | - Meng Chen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; (T.Z.); (H.S.); (M.C.); (G.C.); (G.Z.)
| | - Guobin Chen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; (T.Z.); (H.S.); (M.C.); (G.C.); (G.Z.)
- College of Fisheries and Life, Shanghai Ocean University, Shanghai 201306, China
| | - Guiwei Zou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; (T.Z.); (H.S.); (M.C.); (G.C.); (G.Z.)
| | - Hongwei Liang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; (T.Z.); (H.S.); (M.C.); (G.C.); (G.Z.)
- Correspondence: ; Tel.: +27-81780097
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10
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Ma X, Wang G, Wu L, Liu H, Jiang H, Wang L, Liu Q, Wu Q, Tian X, Li X. Dynamic expression and functional analysis of circular RNA in the gonads of Chinese soft-shelled turtles (Pelodiscus sinensis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100863. [PMID: 34237608 DOI: 10.1016/j.cbd.2021.100863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
Circular RNA (circRNA) is a noncoding RNA that can regulate a variety of biological processes. CircRNAs can regulate gene expression posttranscriptionally by acting as microRNA sponges. Many turtle species are remarkable organisms due to their reproductive processes. However, information on circRNA in the gonads of turtles is limited. In this study, 6, 121 circRNAs were identified in the testes and ovaries of Chinese soft-shelled turtles (Pelodiscus sinensis) using the Illumina platform, and 710 circRNAs were significantly differentially expressed (DE). The DE circRNAs included 541 upregulated and 169 downregulated circRNAs in the testes. GO and KEGG pathway analysis indicated that the DE circRNAs were enriched in several signaling pathways, including GnRH, Wnt, FoxO, Progesterone mediated oocyte maturation, and mTOR signaling pathways. Five DE circRNAs were randomly selected, and their relative expression levels in ovaries and testes were detected by quantitative real-time PCR. All of these circRNAs were differentially expressed. In addition, 9, 883 interactions between circRNAs and miRNAs were predicted in the turtles. Target genes of the miRNAs include a range of genes regulating gonadal development. Seven ceRNA networks (DE circRNAs-DE miRNAs-DE mRNAs), including 7 DE circRNAs, 11 DE miRNAs and 20 DE mRNAs, were constructed. The networks included Cdc6, the miR-1 family, the miR-203 family, and the miR-302 family. The expression profile of gonadal circRNAs might help to elucidate the roles of nonprotein coding RNAs in turtle gonadal development.
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Affiliation(s)
- Xiao Ma
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Guiyu Wang
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Limin Wu
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Huifen Liu
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Hongxia Jiang
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Luming Wang
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Qian Liu
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Qisheng Wu
- Fisheries Research Institute of Fujian, Xiamen 361000, People's Republic of China.
| | - Xue Tian
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Xuejun Li
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
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He X, Kuang G, Zuo Y, Li S, Zhou S, Ou C. The Role of Non-coding RNAs in Diabetic Nephropathy-Related Oxidative Stress. Front Med (Lausanne) 2021; 8:626423. [PMID: 33959621 PMCID: PMC8093385 DOI: 10.3389/fmed.2021.626423] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/25/2021] [Indexed: 12/14/2022] Open
Abstract
Diabetic nephropathy (DN) is one of the main complications of diabetes and the main cause of diabetic end-stage renal disease, which is often fatal. DN is usually characterized by progressive renal interstitial fibrosis, which is closely related to the excessive accumulation of extracellular matrix and oxidative stress. Non-coding RNAs (ncRNAs) are RNA molecules expressed in eukaryotic cells that are not translated into proteins. They are widely involved in the regulation of biological processes, such as, chromatin remodeling, transcription, post-transcriptional modification, and signal transduction. Recent studies have shown that ncRNAs play an important role in the occurrence and development of DN and participate in the regulation of oxidative stress in DN. This review clarifies the functions and mechanisms of ncRNAs in DN-related oxidative stress, providing valuable insights into the prevention, early diagnosis, and molecular therapeutic targets of DN.
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Affiliation(s)
- Xiaoyun He
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Gaoyan Kuang
- Department of Orthopedics, The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Yi Zuo
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Shuangxi Li
- Department of Pathophysiology, Hunan University of Medicine, Huaihua, China
| | - Suxian Zhou
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Zuo Y, Chen L, He X, Ye Z, Li L, Liu Z, Zhou S. Atorvastatin Regulates MALAT1/miR-200c/NRF2 Activity to Protect Against Podocyte Pyroptosis Induced by High Glucose. Diabetes Metab Syndr Obes 2021; 14:1631-1645. [PMID: 33880049 PMCID: PMC8053520 DOI: 10.2147/dmso.s298950] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/18/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Diabetic nephropathy (DN) is one of the main complications of diabetes mellitus (DM), which leads to the long-term loss of kidney functions. Long noncoding RNAs (LncRNAs) can alleviate DN by interacting with microRNAs (miRNAs). In this work, we aimed to explore the effects of the MALAT1/miR-200c/NRF2 regulatory axis on the pyroptosis and oxidative stress (Oxidative stress, OS) of renal podocytes in high glucose (HG) environment and whether the lipid-lowering drug atorvastatin (AT) can relieve renal OS through this approach. METHODS MPC-5, a mouse podocyte cell line, was induced by HG as a cell model. The protein expressions of caspase-1, GSDMD, NLRP3, NRF2, etc. were detected by Western blotting and immunofluorescence, and the mRNA level of caspase-1, GSDMD, NLRP3, NRF2, MALAT1, miR-200c was tested by qRT-PCR. The cell pyroptosis of podocytes treated with AT was verified by CCK-8 or flow cytometry. The levels of Malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione (GSH) were measured by spectrophotometer, respectively. RESULTS The caspase-1 was upregulated in time-dependent manner and got the peak at 48 h and 30 mmol/L respectively in MPC-5 cells treated with HG. Further, the expression of GSDMD, MALAT1 and miR-200c were increased, while the level of NRF2, HO-1, OS-related indicators, were decreased simultaneously. Knockdown the MALAT1 protected MPC-5 cells from pyroptosis and OS induced by HG. However, overexpressing miR-200c in control-group cells increased pyroptosis and upregulated the OS level with HG culture medium. Further, atorvastatin protected MPC-5 cells from cell pyroptosis and downregulated the level of renal OS via attenuating the expression of MALAT1 and miR-200c. CONCLUSION Atorvastatin protects podocyte cells via MALAT1/miR-200c/NRF2 signal pathway from pyroptosis and OS induced by HG.
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Affiliation(s)
- Yi Zuo
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, People’s Republic of China
| | - Li Chen
- Guangxi Key Laboratory of Brain and Cognitive Neuroscience, Guilin, Guangxi, 541004, People’s Republic of China
| | - Xiaoyun He
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, 410008, People’s Republic of China
| | - Zhen Ye
- Guangxi Key Laboratory of Brain and Cognitive Neuroscience, Guilin, Guangxi, 541004, People’s Republic of China
| | - Ling Li
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, People’s Republic of China
| | - Zhanhong Liu
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, People’s Republic of China
| | - Suxian Zhou
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, People’s Republic of China
- Correspondence: Suxian Zhou Department of Endocrinology, Affiliated Hospital of Guilin Medical University, 15 Lequn Road, Guilin, Guangxi, 541001, People’s Republic of China Email
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