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Wang X, Chen X, Sun X, Ao J. Comparative analysis of miRNAs and mRNAs in large yellow croaker head kidney cells (LYCK) provided novel insights into the redox regulation of fish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170503. [PMID: 38301776 DOI: 10.1016/j.scitotenv.2024.170503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/21/2023] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
Reactive oxygen species (ROS) over-production and oxidative stress resulted from climate change and environmental pollution seriously endangered global fish populations and healthy development of marine aquaculture. Peroxiredoxins (Prxs), a highly conserved family of thiol-specific antioxidants, can mitigate ROS and protect cells from oxidative stress. We previously demonstrated that large yellow croaker PrxIV (LcPrxIV) could not only regulate the pro-inflammatory responses, but also scavenge ROS. However, the underlying mechanism how LcPrxIV regulated immune response and redox homeostasis remains unknown. MicroRNAs (miRNAs) are non-coding RNAs that play important roles in the regulation of various biological processes. In this study, mRNA and miRNA expression profiles from LYCK-pcDNA3.1 and LYCK-PrxIV cells, with or without oxidative stress stimulated by H2O2 were evaluated using high-throughput sequencing. A series of differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs), as well as DEM-DEG pairs were identified from each two-group comparison, respectively. GO and KEGG functional analyses indicated that most significant DEGs were associated with signaling pathways related to oxidative stress and immune response. Subsequent DEM-DEG interaction analysis revealed that miR-731 and miR-1388 may be involved in both redox regulation and immune response via synergistic effect with LcPrxIV. Interestingly, miR-731 could regulate the expression of different down-stream DEGs under different stimulations of LcPrxIV over-expression, H2O2, or both. Moreover, miR-731 could cause the DEG, γ-glutamyl hydrolase (GGH), to be expressed in opposite ways under different stimulations. On the other hand, the expression of miR-1388 could be negatively or positively regulated under the stimulation of LcPrxIV over-expression with or without oxidative stress, thus regulating gene expression of different mRNAs. Based on these results, we speculate that LcPrxIV may participate in immune response or redox regulation by regulating the expression of different down-stream genes through controlling the expression level of a certain miRNA or by regulating the varieties of expressed miRNAs.
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Affiliation(s)
- Xianhui Wang
- Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China
| | - Xinhua Chen
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoming Sun
- Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China; School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China.
| | - Jingqun Ao
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Ojo OE, Hajek L, Johanns S, Pacífico C, Sener-Aydemir A, Ricci S, Rivera-Chacon R, Castillo-Lopez E, Reisinger N, Zebeli Q, Kreuzer-Redmer S. Evaluation of circulating microRNA profiles in blood as potential candidate biomarkers in a subacute ruminal acidosis cow model - a pilot study. BMC Genomics 2023; 24:333. [PMID: 37328742 DOI: 10.1186/s12864-023-09433-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Subacute ruminal acidosis (SARA) is a metabolic disorder often observed in high-yielding dairy cows, that are fed diets high in concentrates. We hypothesized that circulating miRNAs in blood of cows could serve as potential candidate biomarkers to detect animals with metabolic dysbalances such as SARA. MicroRNAs (miRNAs) are a class of small non-coding RNAs, serving as regulators of a plethora of molecular processes. To test our hypothesis, we performed a pilot study with non-lactating Holstein-Friesian cows fed a forage diet (FD; 0% concentrate, n = 4) or a high-grain diet (HG; 65% concentrate, n = 4) to induce SARA. Comprehensive profiling of miRNA expression in plasma and leucocytes were performed by next generation sequencing (NGS). The success of our model to induce SARA was evaluated based on ruminal pH and was evidenced by increased time spent with a pH threshold of 5.8 for an average period of 320 min/d. RESULTS A total of 520 and 730 miRNAs were found in plasma and leucocytes, respectively. From these, 498 miRNAs were shared by both plasma and leucocytes, with 22 miRNAs expressed exclusively in plasma and 232 miRNAs expressed exclusively in leucocytes. Differential expression analysis revealed 10 miRNAs that were up-regulated and 2 that were down-regulated in plasma of cows when fed the HG diet. A total of 63 circulating miRNAs were detected exclusively in the plasma of cows with SARA, indicating that these animals exhibited a higher number and diversity of circulating miRNAs. Considering the total read counts of miRNAs expressed when fed the HG diet, differentially expressed miRNAs ( log2 fold change) and known function, we have identified bta-miR-11982, bta-miR-1388-5p, bta-miR-12034, bta-miR-2285u, and bta-miR-30b-3p as potential candidates for SARA-biomarker in cows by NGS. These were further subjected to validation using small RNA RT-qPCR, confirming the promising role of bta-miR-30b-3p and bta-miR-2285. CONCLUSION Our data demonstrate that dietary change impacts the release and expression of miRNAs in systemic circulation, which may modulate post-transcriptional gene expression in cows undergoing SARA. Particularly, bta-miR-30b-3p and bta-miR-2285 might serve as promising candidate biomarker predictive for SARA and should be further validated in larger cohorts.
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Affiliation(s)
- O E Ojo
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - L Hajek
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - S Johanns
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - C Pacífico
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
- Biome Diagnostics GmbH, Vienna, Austria
| | - A Sener-Aydemir
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - S Ricci
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - R Rivera-Chacon
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - E Castillo-Lopez
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - N Reisinger
- DSM, BIOMIN Research Center, Tulln an Der Donau, Austria
| | - Q Zebeli
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - S Kreuzer-Redmer
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria.
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria.
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Huang Y, Chen H, Gao X, Ren H, Gao S. Identification and functional analysis of miRNAs in skeletal muscle of juvenile and adult largemouth bass, Micropterus salmoides. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100985. [PMID: 35381488 DOI: 10.1016/j.cbd.2022.100985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/20/2022] [Accepted: 03/25/2022] [Indexed: 11/28/2022]
Abstract
MicroRNAs (miRNAs) are considered key regulators to post-transcriptionally regulate gene expression affecting multiple biological activities. However, the developmental process of fish skeletal muscles is regulated by complicated molecular mechanism that has not been completely well-described. In this study, two small RNAs libraries from skeletal muscle of juvenile as well as adult largemouth bass (LMB) were obtained and sequenced using deep sequencing to investigate the development-related miRNAs. We identified an overall number of 486 already recognized miRNAs in addition to 43 novel miRNAs. Comparison of two different skeletal muscle development stages led to the identification of 220 differently expressed miRNAs between juvenile and adult LMB containing 116 up-regulated as well as 104 down-regulated miRNAs. Of them, confirmation of some differently expressed miRNAs was performed via a stem-loop qRT-PCR, which exhibited differently expressed level in juvenile and adult LMB. Furthermore, GO and KEGG enrichment analyses of targets of differently-expressed miRNAs were carried out. Additionally, the analysis of miRNAs-targets interaction network showed that miR-181b-5p_R-1, miR-725 and miR-103 as the nodal miRNAs has over 20 target genes. Moreover, miR-103 could bind the 3'-UTR of actr8, which was validated via dual-luciferase reporter assay. It has been reasonably hypothesized that miR-103 may play a crucial role, which regulate skeletal muscle development of LMB. The present study provides the first identification of miRNA expression profiles at two different skeletal muscle development stages in LMB. Results may be valuable in interpreting the regulatory role miRNAs plays in the growth and developmental process of skeletal muscle and its possible use in LMB breeding.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China.
| | - Haigang Chen
- Guangdong Province Key Laboratory of Fish Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Xiaochan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Hongtao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Shiyang Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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Huang JS, Li HJ, Guo ZX, Zhang JD, Wang WZ, Wang ZL, Amenyogbe E, Chen G. Identification and expression analysis of cobia (Rachycentron canadum) liver-related miRNAs under hypoxia stress. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:1951-1967. [PMID: 34633578 DOI: 10.1007/s10695-021-01017-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
At present, due to the influence of global warming, seasonal change, diurnal variation, and eutrophication of the water body, hypoxia has become one of the major factors limiting the stable development of cobia (Rachycentron canadum) culture. In this study, the miRNAs involved in hypoxia stress were screened, and the target genes of miRNAs were annotated and analyzed. The results showed that a total of 184 conservative microRNA (miRNA) and 121 newly predicted miRNA were obtained by sequencing the liver of control (C) and hypoxic (dissolved oxygen, DO (2.64 ± 0.25) mg/L; 3 h) (S) groups. The pathways involved in energy metabolism included starch and sucrose metabolism (ko00500), glycosaminoglycan degradation (ko00531), and galactose metabolism (ko00052). The results indicate that the body maintains physiological activities by regulating some important pathways at the transcriptional level under hypoxia stress, such as the conversion of aerobic metabolism and anaerobic metabolism, the reduction of energy consumption, and the promotion of red blood cell proliferation to maintain the homeostasis of the body.
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Affiliation(s)
- Jian-Sheng Huang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524025, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China
| | - Hong-Juan Li
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Zhi-Xiong Guo
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Jian-Dong Zhang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524025, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China
| | - Wei-Zheng Wang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Zhong-Liang Wang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Eric Amenyogbe
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China.
| | - Gang Chen
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524025, China.
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China.
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5
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Yong Huang, Chen H, Gao X, Sun X. Identification and Сharacteristics of Conserved miRNA in Testis Tissue from Chinese Giant Salamander (Andrias davidianus) by Deep Sequencing. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s106816201902016x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Identification and comparative analysis of the miRNA expression profiles from four tissues of Micropterus salmoides using deep sequencing. Genomics 2018; 110:414-422. [DOI: 10.1016/j.ygeno.2018.09.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 09/21/2018] [Accepted: 09/27/2018] [Indexed: 01/05/2023]
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7
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Huang Y, Gong WB. Identification and Characterization of MicroRNAs in Skin of Chinese Giant Salamander (Andrias davidianus) by the Deep Sequencing Approach. BIOCHEMISTRY (MOSCOW) 2018; 83:766-777. [PMID: 30195333 DOI: 10.1134/s0006297918060147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNA) play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. However, the miRNAs from skin of Andrias davidianus have not been reported. In this study, a small-RNA cDNA library was constructed and sequenced from skin of A. davidianus. A total of 513 conserved miRNAs belonging to 174 families were identified. The remaining 108 miRNAs we identified were novel and likely to be skin tissue-specific but were expressed at low levels. The presence of randomly selected 15 miRNAs identified and their expression in eight different tissues from A. davidianus were validated by stem-loop qRT-PCR. For better understanding the functions of miRNAs, 129,791 predicated target genes were analyzed by GO and their pathways illustrated by KEGG pathway analyses. The results show that these identified miRNAs from A. davidianus skin are involved in a broad range of physiological functions including metabolism, growth, development, and immune responses. This study exhaustively identifies miRNAs and their target genes, which will ultimately pave the way for understanding their role in skin of A. davidianus and other amphibians. Further studies are necessary to better understand miRNA-mediated gene regulation.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Wang Bao Gong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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8
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Huang Y, Gao XC, Ren HT, Xiong JL, Sun XH. Characterization of conserved and novel miRNAs using deep sequencing and prediction of miRNA targets in Crucian carp (Carassius auratus). Gene 2017; 635:61-68. [PMID: 28890379 DOI: 10.1016/j.gene.2017.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/03/2017] [Accepted: 09/06/2017] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs of -22 nucleotides that can base pair with their target mRNAs, which represses their translation or induces their degradation in various biological processes. However, little is known about identification of miRNAs and their target genes in C. auratus. In the present study, a small RNA library from pooled tissue of C. auratus was constructed and sequenced using the deep sequencing. A total of 320 conserved miRNAs (belonging to 105 families) as well as 11 potentially novel miRNAs were identified. Stem-loop qRT-PCR analysis confirmed that both conserved and novel miRNAs were expressed in C. auratus, and some of them were preferentially expressed in certain tissues. Subsequently, a total of 1668 potential target genes were predicted for these identified miRNAs and GO analysis showed that most of the targets were involved in lots of physiological actions. This study represents a first large-scale identification and characterization of C. auratus miRNAs and their potential target genes. Taken together, our results add new information to existing data on C. auratus miRNAs and should be useful for investigating the biological functions of miRNAs in fishes and other aquatic species.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Hong Tao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Jian Li Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xi Hong Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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9
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Huang Y, Yang YB, Gao XC, Ren HT, Xiong JL, Sun XH. Genome-wide identification and characterization of microRNAs and target prediction by computational approaches in common carp. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Identification of the conserved and novel microRNAs by deep sequencing and prediction of their targets in Topmouth culter. Gene 2017; 626:298-304. [DOI: 10.1016/j.gene.2017.05.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 05/21/2017] [Accepted: 05/24/2017] [Indexed: 01/28/2023]
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11
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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Paul S. Identification and characterization of microRNAs and their targets in high-altitude stress-adaptive plant maca (Lepidium meyenii Walp). 3 Biotech 2017; 7:103. [PMID: 28560642 DOI: 10.1007/s13205-017-0734-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/19/2017] [Indexed: 11/26/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous, short (~21-nucleotide), non-coding RNA molecules that play pivotal roles in plant growth, development, and stress response signaling. In this study using recently published draft genome sequence of a high-altitude plant maca (Lepidium meyenii Walp) and applying genome-wide computational-based approaches, a total of 62 potentially conserved miRNAs belonging to 28 families were identified and four (lme-miR160a, lme-miR164c, lme-miR 166a, and lme-miR 319a) of them further validated by RT-PCR. Deploying psRNATarget tool a total of 99 potential miRNA target transcripts were also identified in maca. Targets include a number of transcription factors like Squamosa promoter-binding, NAC, MYB, auxin response factor, APETALA, WRKY, and F-box protein. To the best of my knowledge, this is the first genome-based miRNA profiling of a high-altitude plant.
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Affiliation(s)
- Sujay Paul
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India.
- Laboratorio de Micología y Biotecnología, Universidad Nacional Agraria La Molina, Av. La Molina s/n, 12, Lima, Peru.
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Genome-wide identification and characterization of conserved and novel microRNAs in grass carp ( Ctenopharyngodon idella ) by deep sequencing. Comput Biol Chem 2017; 68:92-100. [DOI: 10.1016/j.compbiolchem.2017.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/14/2017] [Accepted: 02/26/2017] [Indexed: 12/20/2022]
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14
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Huang Y, Ren HT, Xiong JL, Gao XC, Sun XH. Identification and characterization of known and novel microRNAs in three tissues of Chinese giant salamander base on deep sequencing approach. Genomics 2017; 109:258-264. [PMID: 28476431 DOI: 10.1016/j.ygeno.2017.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/27/2017] [Accepted: 04/30/2017] [Indexed: 01/06/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although animal miRNAs have been extensively studied in model systems, less is known in other animal with limited genome sequence data, including Chinese giant salamander (Andrias davidianus). The identification of the full repertoire of miRNAs expressed in the liver, spleen and muscle of A. davidianus would significantly increase our understanding for physiological function of A. davidianus, in this ancient and endangered urodele amphibian. In this study, three independent small RNA libraries were constructed from the liver, spleen and muscle of A. davidianus. The libraries were subjected to high-throughput sequencing by using the Illumina deep sequencing. As a result, a total of 12,831,239, 13,592,195 and 9,887,531 raw reads representing 2,240,771, 1,363,266 and 1,964,252 clean reads per library were obtained separately. Through bioinformatics analysis, we identified total of 553 known miRNAs and 44 putative novel miRNAs in our small RNA dataset from liver, spleen and muscle tissues. Five known miRNAs (gga-miR-10a-5p, pma-miR-29d-5p, aca-miR-338-3p, hsa-miR-455-3p and ssa-miR-2184-5p_R-1) and three novel miRNAs (PC-5p-891_1763, PC-5p-32538_50 and PC-3p-33645_48) showed different expression in eight different tissues as revealed by stem-loop qPCR analysis. This study characterized the miRNA of A. davidianus for the first time, which provides an opportunity for further understanding of miRNA regulation function in A. davidianus ranked as living fossils.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.
| | - Hong Tao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Jian Li Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xi Hong Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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15
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Transcriptome-wide identification and functional investigation of circular RNA in the teleost large yellow croaker (Larimichthys crocea). Mar Genomics 2017; 32:71-78. [PMID: 28089131 DOI: 10.1016/j.margen.2016.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 01/01/2023]
Abstract
Circular RNA (circRNA) was first reported over thirty years ago. With the development of high-throughput sequencing technologies, circRNA has been identified in an increasing number of species. However, few studies on circRNA have been reported in teleost fish. Accumulating transcriptome and phenotype data enable us to probe the biological functions of circRNA in fish species. Here, we report the identification of circRNAs from RNA sequencing (RNA-seq) data in large yellow croaker (Larimichthys crocea), a commercially important marine fish in China and East Asia. Using the computational identification, 975 circular RNAs were detected, of which three were validated by experiments. GO and KEGG analyses revealed the biological functions of genes hosting the circRNAs were enriched in the progression of translation initiation, macromolecule metabolism and binding. Notably, we found that many circRNAs in large yellow croaker had abundant microRNA-binding sites. A total of 363 the identified circRNAs had more than five miRNA-binding sites, among which twenty-two had more than ten binding sites for the miRNA-430 and the let-7 family. Our study confirmed the presence of circRNAs in large yellow croaker for the first time, providing a valuable reference for circRNA identification in fish species. Meanwhile, this work confirmed that the RNA-seq data from the traditional linear transcriptome library could be used for preliminary circRNA identification, which may offer an important reference for preliminary circRNA investigations in other species.
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16
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Improving classification of mature microRNA by solving class imbalance problem. Sci Rep 2016; 6:25941. [PMID: 27181057 PMCID: PMC4867574 DOI: 10.1038/srep25941] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/22/2016] [Indexed: 11/29/2022] Open
Abstract
MicroRNAs (miRNAs) are ~20–25 nucleotides non-coding RNAs, which regulated gene expression in the post-transcriptional level. The accurate rate of identifying the start sit of mature miRNA from a given pre-miRNA remains lower. It is noting that the mature miRNA prediction is a class-imbalanced problem which also leads to the unsatisfactory performance of these methods. We improved the prediction accuracy of classifier using balanced datasets and presented MatFind which is used for identifying 5′ mature miRNAs candidates from their pre-miRNA based on ensemble SVM classifiers with idea of adaboost. Firstly, the balanced-dataset was extract based on K-nearest neighbor algorithm. Secondly, the multiple SVM classifiers were trained in orderly using the balance datasets base on represented features. At last, all SVM classifiers were combined together to form the ensemble classifier. Our results on independent testing dataset show that the proposed method is more efficient than one without treating class imbalance problem. Moreover, MatFind achieves much higher classification accuracy than other three approaches. The ensemble SVM classifiers and balanced-datasets can solve the class-imbalanced problem, as well as improve performance of classifier for mature miRNA identification. MatFind is an accurate and fast method for 5′ mature miRNA identification.
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