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Pawlina-Tyszko K, Szmatoła T. Benchmarking of bioinformatics tools for NGS-based microRNA profiling with RT-qPCR method. Funct Integr Genomics 2023; 23:347. [PMID: 38030823 PMCID: PMC10687144 DOI: 10.1007/s10142-023-01276-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/03/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
MicroRNAs are vital gene expression regulators, extensively studied worldwide. The large-scale characterization of miRNAomes is possible using next-generation sequencing (NGS). This technology offers great opportunities, but these cannot be fully exploited without proper and comprehensive bioinformatics analysis. This may be achieved by the use of reliable dedicated software; however, different programs may generate divergent results, leading to additional discrepancies. Thus, the aim of this study was to compare three bioinformatic algorithms dedicated to NGS-based microRNA profiling and validate them using an alternative method, namely RT-qPCR. The comparison analysis revealed differences in the number and sets of identified miRNAs. The qPCR confirmed the expression of the investigated microRNAs. The correlation analysis of NGS and qPCR measurements showed strong and significant coefficients for a subset of the tested miRNAs, including those detected by all three algorithms. Single miRNA variants (isomiRs) showed different levels of correlation with the qPCR data. The obtained results revealed the good performance of all tested programs, despite the observed differences. Moreover, they implied that some specific miRNAs may be differentially estimated using NGS technology and the qPCR method, regardless of the used bioinformatics software. These discrepancies may stem from many factors, including the composition of the isomiR profile, their abundance, length, and investigated species. In conclusion, in this study, we shed light on the bioinformatics aspects of miRNAome profiling, elucidating its complexity and pinpointing potential features influencing validation. Thus, qPCR validation results should be open to interpretation when not fully concordant with NGS results until further, additional analyses are conducted.
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Affiliation(s)
- Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 st., 32-083, Balice, Poland.
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 st., 32-083, Balice, Poland
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, 30-248, Krakow, Poland
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2
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Shukla N, Vemula H, Raval I, Kumar S, Shrivastava V, Chaudhari A, Patel AK, Joshi CG. Integrative miRNA-mRNA network analysis to identify crucial pathways of salinity adaptation in brain transcriptome of Labeo rohita. Front Genet 2023; 14:1209843. [PMID: 37719712 PMCID: PMC10500595 DOI: 10.3389/fgene.2023.1209843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/17/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction: Brain being the master regulator of the physiology of animal, the current study focuses on the gene expression pattern of the brain tissue with special emphasis on regulation of growth, developmental process of an organism and cellular adaptation of Labeo rohita against unfavourable environmental conditions. Methods: RNA-seq study was performed on collected brain samples at 8ppt salt concentration and analyzed for differential gene expression, functional annotation and miRNA-mRNA regulatory network. Results: We found that 2450 genes were having significant differential up and down regulation. The study identified 20 hub genes based on maximal clique centrality algorithm. These hub genes were mainly involved in various signaling pathways, energy metabolism and ion transportation. Further, 326 up and 1214 down regulated genes were found to be targeted by 7 differentially expressed miRNAs i.e., oni-miR-10712, oni-miR-10736, ssa-miR-221-3p, ssa-miR-130d-1-5p, ssa-miR-144-5p and oni-miR-10628. Gene ontology analysis of these differentially expressed genes led to the finding that these genes were involved in signal transduction i.e., calcium, FOXO, PI3K-AKT, TGF-β, Wnt and p53 signalling pathways. Differentially expressed genes were also involved in regulation of immune response, environmental adaptation i.e., neuroactive ligand-receptor interaction, ECM-receptor interaction, cell adhesion molecules and circadian entrainment, osmoregulation and energy metabolism, which are critical for salinity adaptation. Discussion: The findings of whole transcriptomic study on brain deciphered the miRNA-mRNA interaction patterns and pathways associated with salinity adaptation of L. rohita.
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Affiliation(s)
- Nitin Shukla
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Harshini Vemula
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Ishan Raval
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Sujit Kumar
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Gandhinagar, Gujarat, India
| | - Vivek Shrivastava
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Gandhinagar, Gujarat, India
| | - Aparna Chaudhari
- Central Institute of Fisheries Education, Mumbai, Maharashtra, India
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Wu Y, Wang Y, Xue Y, Wu N, Wu J, Zhang J. cbx2 is a functional target of the let-7 family in the gonad of Japanese flounder (Paralichthys olivaceus). Comp Biochem Physiol B Biochem Mol Biol 2023; 263:110799. [PMID: 36155820 DOI: 10.1016/j.cbpb.2022.110799] [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: 07/21/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/18/2022]
Abstract
As a key member of the miRNA family, the role and target gene of the let-7 family in the gonad of Japanese flounder (Paralichthys olivaceus) is unclear. Chromobox homolog 2 (CBX2) is one of the core components of the polycomb group complex (PcG) and significantly influences gonadal development. The deletion of CBX2 can lead to sex reversal in mammals. Therefore, exploring the relationship between the let-7 family and cbx2 is crucial to clarify the role played by the let-7 family in the gonad of Japanese flounder. We predicted and verified the target interaction between the let-7 family and cbx2. The results showed that cbx2 was a direct target of let-7d, let-7e, let-7g, let-7j, and let-7b. Among them, let-7d, let-7e, let-7g, and let-7j exhibited an extremely significant targeting relationship with cbx2 (p < 0.001). Taking let-7g as an example, we further investigated the regulatory role between let-7g and cbx2 in the gonad by miRNA overexpression and inhibition experiments in primary testis cells. The results revealed that let-7g could negatively regulate cbx2 at the level of primary testis cells. And the expression of sf1 (steroidogenic factor 1) was also significantly decreased after the interference of cbx2 siRNA. This suggests that the let-7 family may be involved in the Japanese flounder gonadal development via targeting cbx2.
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Affiliation(s)
- Yahui Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yangyang Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yidong Xue
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Ningning Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Jikui Wu
- Laboratory of Quality and Safety Risk Assessment for Aquatic Product on Storage and Preservation, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China.
| | - Junling Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
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4
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Identification and Characterization of Sex-Biased miRNAs in the Golden Pompano ( Trachinotus blochii). Animals (Basel) 2022; 12:ani12233342. [PMID: 36496865 PMCID: PMC9739008 DOI: 10.3390/ani12233342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The golden pompano (Trachinotus blochii) is a marine fish of considerable commercial importance in China. It shows notable sexual size dimorphism; the growth rate of females is faster than that of males. Therefore, sex-biased research is of great importance in T. blochii breeding. However, there have been few studies on sex differentiation and mechanisms underlying sex determination in T. blochii. MicroRNAs (miRNAs) play crucial roles in sex differentiation and determination in animals. However, limited miRNA data are available on fish. In this study, two small RNA libraries prepared from the gonads of T. blochii were constructed and sequenced. The RNA-seq analysis yielded 1366 known and 69 novel miRNAs with 289 significantly differentially expressed miRNAs (p < 0.05). Gene ontology (GO) analysis confirmed that the TFIIA transcription factor complex (GO: 0005672) was the most significantly enriched GO term. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the differentially expressed miRNAs and target genes were mainly related to sex determination and gonadal developmental signaling pathways, specifically the Wnt signaling pathway, MAPK signaling pathway, and steroid biosynthetic pathway. MiRNA-mRNA co-expression network analysis strongly suggested a role for sex-biased miRNAs in sex determination/differentiation and gonadal development. For example, gata4, foxo3, wt1, and sf1 genes were found to be regulated by bta-miR-2898; esr2 and foxo3 by novel_176, and ar by oar-let-7b. Quantitative real-time polymerase chain reaction analysis of selected mRNAs and miRNAs validated the integrated analysis. This study established a set of sex-biased miRNAs that are potential regulatory factors in gonadal development in T. blochii. These results provide new insight into the function of miRNAs in sex differentiation and determination in T. blochii and highlight some key miRNAs for future studies.
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Fu J, Zhu W, Wang L, Luo M, Jiang B, Dong Z. Dynamic Expression and Gene Regulation of MicroRNAs During Bighead Carp (Hypophthalmichthys nobilis) Early Development. Front Genet 2022; 12:821403. [PMID: 35126475 PMCID: PMC8809360 DOI: 10.3389/fgene.2021.821403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
The early development of fish is regulated through dynamic and complex mechanisms involving the regulation of various genes. Many genes are subjected to post-transcriptional regulation by microRNAs (miRNAs). In the Chinese aquaculture industry, the native species bighead carp (Hypophthalmichthys nobilis) is important. However, the genetic regulation related to the early development of bighead carp is unknown. Here, we generated developmental profiles by miRNA sequencing to study the dynamic regulation of miRNAs during bighead carp early development. This study identified 1 046 miRNAs, comprising 312 known miRNAs and 734 uncharacterized miRNAs. Changes in miRNA expression were identified in the six early development stages. An obviously increased expression trend was detected during the development process, with the main burst of activity occurring after the earliest stage (early blastula, DS1). Investigations revealed that several miRNAs were dominantly expressed during the development process, especially in the later stages (e.g., miR-10b-5p, miR-21, miR-92a-3p, miR-206-3p, and miR-430a-3p), suggesting that these miRNAs exerted important functions during embryonic development. The differentially expressed miRNAs (DEMs) and time-serial analysis (profiles) of DEMs were analyzed. A total of 372 miRNAs were identified as DEMs (fold-change >2, and false discovery rate <0.05), and three expression profiles of the DEMs were detected to have co-expression patterns (r > 0.7, and p < 0.05). The broad negative regulation of target genes by miRNAs was speculated, and many development-related biological processes and pathways were enriched for the targets of the DEMs, which might be associated with maternal genome degradation and embryogenesis processes. In conclusion, we revealed the repertoire of miRNAs that are active during early development of bighead carp. These findings will increase our understanding of the regulatory mechanisms of early development of fish.
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Affiliation(s)
- Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
| | - Wenbin Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Lanmei Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
| | - Mingkun Luo
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
| | - Bingjie Jiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Zaijie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- *Correspondence: Zaijie Dong, ,
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Piferrer F. Epigenetic mechanisms in sex determination and in the evolutionary transitions between sexual systems. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200110. [PMID: 34247505 PMCID: PMC8273503 DOI: 10.1098/rstb.2020.0110] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The hypothesis that epigenetic mechanisms of gene expression regulation have two main roles in vertebrate sex is presented. First, and within a given generation, by contributing to the acquisition and maintenance of (i) the male or female function once during the lifetime in individuals of gonochoristic species; and (ii) the male and female function in the same individual, either at the same time in simultaneous hermaphrodites, or first as one sex and then as the other in sequential hermaphrodites. Second, if environmental conditions change, epigenetic mechanisms may have also a role across generations, by providing the necessary phenotypic plasticity to facilitate the transition: (i) from one sexual system to another, or (ii) from one sex-determining mechanism to another. Furthermore, if the environmental change lasts enough time, epimutations could facilitate assimilation into genetic changes that stabilize the new sexual system or sex-determining mechanism. Examples supporting these assertions are presented, caveats or difficulties and knowledge gaps identified, and possible ways to test this hypothesis suggested. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
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Affiliation(s)
- Francesc Piferrer
- Institut de Ciències del Mar (ICM), Spanish National Research Council (CSIC), Passeig Marítim, 37-49, 08003 Barcelona, Spain
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7
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Identification of sex differentiation-related microRNA and long non-coding RNA in Takifugu rubripes gonads. Sci Rep 2021; 11:7459. [PMID: 33811216 PMCID: PMC8018949 DOI: 10.1038/s41598-021-83891-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 01/14/2021] [Indexed: 02/01/2023] Open
Abstract
Although sex determination and differentiation are key developmental processes in animals, the involvement of non-coding RNA in the regulation of this process is still not clarified. The tiger pufferfish (Takifugu rubripes) is one of the most economically important marine cultured species in Asia, but analyses of miRNA and long non-coding RNA (lncRNA) at early sex differentiation stages have not been conducted yet. In our study, high-throughput sequencing technology was used to sequence transcriptome libraries from undifferentiated gonads of T. rubripes. In total, 231 (107 conserved, and 124 novel) miRNAs were obtained, while 2774 (523 conserved, and 2251 novel) lncRNAs were identified. Of these, several miRNAs and lncRNAs were predicted to be the regulators of the expression of sex-related genes (including fru-miR-15b/foxl2, novel-167, novel-318, and novel-538/dmrt1, novel-548/amh, lnc_000338, lnc_000690, lnc_000370, XLOC_021951, and XR_965485.1/gsdf). Analysis of differentially expressed miRNAs and lncRNAs showed that three mature miRNAs up-regulated and five mature miRNAs were down-regulated in male gonads compared to female gonads, while 79 lncRNAs were up-regulated and 51 were down-regulated. These findings could highlight a group of interesting miRNAs and lncRNAs for future studies and may reveal new insights into the function of miRNAs and lncRNAs in sex determination and differentiation.
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8
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Wang X, Song X, Bhandari RK. Distinct expression patterns of seven crucial microRNAs during early embryonic development in medaka (Oryzias latipes). Gene Expr Patterns 2020; 37:119133. [PMID: 32800847 DOI: 10.1016/j.gep.2020.119133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 07/18/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022]
Abstract
MicroRNAs (i.e. miRNAs) are small non-coding RNAs that play essential modulation roles in embryonic development in vertebrates. Paternal and maternal miRNAs contribute to the development of post-fertilization embryo and zygotic genome activation. The pattern of expression and their roles in embryonic development of medaka are not clearly understood. The present study, therefore, examined a temporal expression of seven miRNAs, ola-let-7a, ola-miR-202-3p, ola-miR-126-3p, ola-miR-122, ola-miR-92a, ola-miR-125a-3p and ola-miR-430a in sperm, oocytes, and embryos during early developmental stages. Three unique expression patterns of miRNAs were observed. ola-let7a, ola-miR-202-3p and ola-miR-126-3p showed both paternal and maternal expression, and ola-miR-122, ola-miR-92a, ola-miR-125a-3p showed maternal expression only. The expression of six out of seven miRNAs significantly decreased after maternal-zygotic transition (MZT), whereas ola-miR-430a expression initiated only after MZT. The temporal dynamic expression of these miRNAs suggests their potential roles in early embryogenesis and genome-zygotic activation in medaka.
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Affiliation(s)
- Xuegeng Wang
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, 27412, USA
| | - Xiaohong Song
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, 27412, USA; College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541004, China
| | - Ramji K Bhandari
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, 27412, USA.
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Yang F, Qi J. miR-430a regulates the development of left-right asymmetry by targeting sqt in the teleost. Gene 2020; 745:144628. [PMID: 32224271 DOI: 10.1016/j.gene.2020.144628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 10/24/2022]
Abstract
microRNAs (miRNAs) are short, endogenous non-coding RNAs that contain approximately 18-22 nucleotides. miRNAs are involved in gene regulation by recognizing and binding the 3'UTR of target gene. In our previous data, miR-430 family showed significant differential expression modes through metamorphosis in Japanese flounder. It was speculated that miR-430a plays a key role in left-right patterning. We predicted the targets of miR-430a and gene ontology (GO) was performed. We speculated miR-430a is involved in the basal molecular function and organ development. In Japanese flounder, sqt as a target of miR-430a was enriched into heart development term. Sqt has been reported to participate in mesendoderm formation and organ development. Cardiac morphogenesis is the first asymmetric development process, which breaks left-right symmetry in bilateria. It was used as a marker to detect L-R asymmetric effects of miR-430a. Overexpression and suppression of miR-430a resulted in abnormal KV (Kupffer's vesicles) development and disordered in nodal-related expression with consequent cardiac laterality. Squint mRNA of Japanese flounder (Posqt) as a target of miR-430a was overexpressed and caused similar phenotype with miR-430a suppression group, such as longer cilia in KV and high range of clmc2 and spaw ectopic expression. Moreover, rescue experiments were performed and suggested that cardiac and KV defections, induced by overexpressing miR-430a, could be rescued by injecting Posqt mRNA. These results suggested that miR-430a regulates the development of left-right asymmetry by targeting sqt in the teleost.
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Affiliation(s)
- Fan Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jie Qi
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
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Li X, Hu H, Li R, Wang Z, Qi J, Wang Z. The role of miR-92 in regulating early development and metamorphosis of Japanese flounder Paralichthys olivaceus. Genes Genet Syst 2019; 95:1-10. [PMID: 31839648 DOI: 10.1266/ggs.18-00047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs are a class of short non-coding RNAs that contain approximately 22 nucleotides and play a regulatory role in RNA silencing and translational repression. miR-92 belongs to the miR-17-92 family and has a regulatory effect on cell proliferation, apoptosis, and expression of proto-oncogenes and tumor suppressor genes. However, its function in flatfish is unclear. In this study, we used farmed Japanese flounder, Paralichthys olivaceus, and showed that gata5 is a target gene of miR-92. Experiments on miR-92 overexpression indicated that gata5 and sox17 were downregulated, while the transcription level of ntl increased. By contrast, depletion of miR-92 resulted in increased gata5 and sox17 levels and reduced ntl level. Moreover, thiourea treatment indicated that miR-92 may inhibit the metamorphic development of Japanese flounder. Our study suggests that miR-92 regulates the fate of endoderm and mesoderm by controlling gata5.
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Affiliation(s)
- Xuemei Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China
| | - Hongshuang Hu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China
| | - Rui Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China
| | - Zhenwei Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China
| | - Jie Qi
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China
| | - Zhigang Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China
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11
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Sarropoulou E, Kaitetzidou E, Papandroulakis N, Tsalafouta A, Pavlidis M. Inventory of European Sea Bass ( Dicentrarchus labrax) sncRNAs Vital During Early Teleost Development. Front Genet 2019; 10:657. [PMID: 31404269 PMCID: PMC6670005 DOI: 10.3389/fgene.2019.00657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/21/2019] [Indexed: 01/25/2023] Open
Abstract
During early animal ontogenesis, a plethora of small non-coding RNAs (sncRNAs) are greatly expressed and have been shown to be involved in several regulatory pathways vital to proper development. The rapid advancements in sequencing and computing methodologies in the last decade have paved the way for the production of sequencing data in a broad range of organisms, including teleost species. Consequently, this has led to the discovery of sncRNAs as well as the potentially novel roles of sncRNA in gene regulation. Among the several classes of sncRNAs, microRNAs (miRNAs) have, in particular, been shown to play a key role in development. The present work aims to identify the miRNAs that play important roles during early European sea bass (Dicentrarchus labrax) development. The European sea bass is a species of high commercial impact in European and especially Mediterranean aquaculture. This study reports, for the first time, the identification and characterization of small RNAs that play a part in the 10 developmental stages (from morula to all fins) of the European sea bass. From 10 developmental stages, more than 135 million reads, generated by next-generation sequencing, were retrieved from publicly available databases as well as newly generated. The analysis resulted in about 2,000 sample grouped reads, and their subsequently annotation revealed that the majority of transcripts belonged to the class of miRNAs followed by small nuclear RNAs and small nucleolar RNAs. The analysis of small RNA expression among the developmental stages under study revealed that miRNAs are active throughout development, with the main activity occurring after the earlier stages (morula and 50% epiboly) and at the later stages (first feeding, flexion, and all fins). Furthermore, investigating miRNAs exclusively expressed in one of the stages unraveled five miRNAs with a higher abundance only in the morula stage (miR-155, miR-430a, d1, d2, and miR-458), indicating possible important key roles of those miRNAs in further embryonic development. An additional target search showed putative miRNA-mRNA interactions with possible direct and indirect regulatory functions of the identified miRNAs.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
| | - Elizabet Kaitetzidou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
| | - Nikos Papandroulakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
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12
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Induced androgenetic development in rainbow trout and transcriptome analysis of irradiated eggs. Sci Rep 2019; 9:8084. [PMID: 31147623 PMCID: PMC6542805 DOI: 10.1038/s41598-019-44568-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 05/20/2019] [Indexed: 12/17/2022] Open
Abstract
Ionizing radiation is administered to damage nuclear genome in fish eggs during induced androgenesis. In this study, we examined whether 350 Gy of X-ray applied to damage chromosomes in the rainbow trout eggs affects maternal RNA. Shortly after irradiation, we did not find any symptoms of RNA degradation in the treated eggs. Significant (p < 0.01) differences between non-irradiated and irradiated eggs concerned only a few transcripts including increased expression of immediate early response 2 (IER2) and early growth response 1 (EGR1) genes observed in the irradiated eggs. Both genes belong to the group of “immediate early genes” that respond quickly to the diverse extracellular stimuli. Elevated expression of these genes was accompanied by decreased level of ssa-miR-10b-5p and ssa-miR-21b-5p (p < 0.05), for which IER2 and EGR1 are target genes. The level of RNA in the fertilized irradiated eggs was highly significantly lower than in the non-irradiated eggs (p < 0.001) and in the unfertilized irradiated eggs (p < 0.0001). However, transcriptome profiles of fertilized non-irradiated eggs and fertilized irradiated eggs did not differ significantly. Thus, we assume that reduced abundance of mRNA in the fertilized irradiated eggs was associated with post-translational degradation and clearance of the maternal transcripts rather than from the irradiation of eggs.
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13
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Hong X, Chen R, Yuan L, Zha J. Global microRNA and isomiR expression associated with liver metabolism is induced by organophosphorus flame retardant exposure in male Chinese rare minnow (Gobiocypris rarus). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 649:829-838. [PMID: 30176492 DOI: 10.1016/j.scitotenv.2018.08.305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/31/2018] [Accepted: 08/22/2018] [Indexed: 06/08/2023]
Abstract
To reveal the adverse effects of organophosphorus flame retardants (OPFRs) on aquatic organisms at the epigenetic level, male Chinese rare minnows were exposed to 0.24 mg/L tris(2‑butoxyethyl) phosphate (TBOEP), 0.04 mg/L tris(1,3‑dichloro‑2‑propyl) phosphate (TDCIPP), or 0.012 mg/L triphenyl phosphate (TPHP) for 14 days. The effects of sub-acute OPFR exposure on liver miRNA and the 3' isomiR expression profiles of Chinese rare minnows were investigated. Through small RNA sequencing and bioinformatics analysis, a total of 32, 84, and 19 differentially expressed miRNAs were detected for TBOEP, TDCIPP, and TPHP exposure, respectively (p < 0.05). Target prediction of the differentially expressed miRNAs and pathway enrichment analysis indicated that predicted altered mRNAs for all three OPFRs were associated with metabolic pathways, whereas base excision repair was only predicted to be perturbed by the TPHP treatment. In addition, 3' isomiR-Us were unexpectedly abundant in all groups (e.g., miR-143), and TDCIPP strongly increased the ratio of 3' isomiR-U expression. Finally, histological examination and metabolic enzyme activity analyses werein agreement with the predicted metabolic pathways. As such, our study indicates that the investigation of epigenetics changes in miRNA gene transcription is a considerable method for the assessment of aquatic toxicity.
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Affiliation(s)
- Xiangsheng Hong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100085, China
| | - Rui Chen
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lilai Yuan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jinmiao Zha
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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Abstract
Marine organisms' persistence hinges on the capacity for acclimatization and adaptation to the myriad of interacting environmental stressors associated with global climate change. In this context, epigenetics-mechanisms that facilitate phenotypic variation through genotype-environment interactions-are of great interest ecologically and evolutionarily. Our comprehensive review of marine environmental epigenetics guides our recommendations of four key areas for future research: the dynamics of wash-in and wash-out of epigenetic effects, the mechanistic understanding of the interplay of different epigenetic marks and the interaction with the microbiome, the capacity for and mechanisms of transgenerational epigenetic inheritance, and the evolutionary implications of the interaction of genetic and epigenetic features. Emerging insights in marine environmental epigenetics can be applied to critical issues such as aquaculture, biomonitoring, and biological invasions, thereby improving our ability to explain and predict the responses of marine taxa to global climate change.
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Affiliation(s)
- Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Center for Coastal Oceans Research, Institute for Water and Environment, Florida International University, North Miami, Florida 33181, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA;
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15
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Campbell-Tofte J, Vrahatis A, Josefsen K, Mehlsen J, Winther K. Investigating the aetiology of adverse events following HPV vaccination with systems vaccinology. Cell Mol Life Sci 2019; 76:67-87. [PMID: 30324425 PMCID: PMC11105185 DOI: 10.1007/s00018-018-2925-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/10/2018] [Accepted: 09/20/2018] [Indexed: 12/18/2022]
Abstract
In contrast to the insidious and poorly immunogenic human papillomavirus (HPV) infections, vaccination with the HPV virus-like particles (vlps) is non-infectious and stimulates a strong neutralizing-antibody response that protects HPV-naïve vaccinees from viral infection and associated cancers. However, controversy about alleged adverse events following immunization (AEFI) with the vlps have led to extensive reductions in vaccine acceptance, with countries like Japan dropping it altogether. The AEFIs are grouped into chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME). In this review, we present a hypothesis that the AEFIs might arise from malfunctions within the immune system when confronted with the unusual antigen. In addition, we outline how the pathophysiology of the AEFIs can be cost-effectively investigated with the holistic principles of systems vaccinology in a two-step process. First, comprehensive immunological profiles of HPV vaccinees exhibiting the AEFIs are generated by integrating the data derived from serological profiling for prominent HPV antibodies and serum cytokines, with data from serum metabolomics, peripheral white blood cells transcriptomics and gut microbiome profiling. Next, the immunological profiles are compared with corresponding profiles generated for matched (a) HPV vaccinees without AEFIs; (b) non-HPV-vaccinated individuals with CFS/ME-like symptoms; and (c) non-HPV-vaccinated individuals without CFS/ME. In these comparisons, any causal links between HPV vaccine and the AEFIs, as well as the underlying molecular basis for the links will be revealed. Such a study should provide an objective basis for evaluating HPV vaccine safety and for identifying biomarkers for individuals at risk of developing AEFI with HPV vaccination.
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Affiliation(s)
| | | | - Knud Josefsen
- Bartholin Institute, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark
| | - Jesper Mehlsen
- Coordinating Research Centre, Bispebjerg and Frederiksberg Hospital, Nordre Fasanvej 57, 2000, Frederiksberg, Denmark
| | - Kaj Winther
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Nørre Allé 51, DK-2200, Copenhagen N, Denmark
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16
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Zhu T, Corraze G, Plagnes-Juan E, Skiba-Cassy S. Circulating miRNA measurements are reflective of cholesterol-based changes in rainbow trout (Oncorhynchus mykiss). PLoS One 2018; 13:e0206727. [PMID: 30395627 PMCID: PMC6218197 DOI: 10.1371/journal.pone.0206727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs which are known to posttranscriptionally regulate the expression of most genes in both animals and plants. Meanwhile, studies have shown that numbers of miRNAs are present in body fluids including the plasma. Despite the mode of action of these circulating miRNAs still remains unknown, they have been found to be promising biomarkers for disease diagnosis, prognosis and response to treatment. In order to evaluate the potential of miRNAs as non-invasive biomarkers in aquaculture, a time-course experiment was implemented to investigate the postprandial regulation of miRNAs levels in liver and plasma as well as the hepatic expression of genes involved in cholesterol metabolism. We showed that miR-1, miR-33a, miR-122, miR-128 and miR-223 were expressed in the liver of rainbow trout and present at detectable level in the plasma. We also demonstrated that hepatic expression of miR-1, miR-122 and miR-128 were regulated by feed intake and reached their highest levels 12 hours after the meal. Interestingly, we observed that circulating levels of miR-128 and miR-223 are subjected to postprandial regulations similar to that observed in their hepatic counterparts. Statistical correlations were observed between liver and plasma for miR-128 and miR-223 and between hepatic and circulating miR-122, miR-128 and miR-223 and expression of genes related to cholesterol synthesis and efflux or glucose phosphorylation. These results demonstrated that circulating miR-122, miR-128 and miR-223 are potential biomarkers of cholesterol metabolism in rainbow trout.
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Affiliation(s)
- Tengfei Zhu
- INRA, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition Métabolisme Aquaculture, Saint Pée sur Nivelle, France
| | - Geneviève Corraze
- INRA, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition Métabolisme Aquaculture, Saint Pée sur Nivelle, France
| | - Elisabeth Plagnes-Juan
- INRA, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition Métabolisme Aquaculture, Saint Pée sur Nivelle, France
| | - Sandrine Skiba-Cassy
- INRA, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition Métabolisme Aquaculture, Saint Pée sur Nivelle, France
- * E-mail:
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17
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MiR-205 Mediated Cu-Induced Lipid Accumulation in Yellow Catfish Pelteobagrus fulvidraco. Int J Mol Sci 2018; 19:ijms19102980. [PMID: 30274304 PMCID: PMC6213235 DOI: 10.3390/ijms19102980] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/20/2018] [Accepted: 09/26/2018] [Indexed: 01/15/2023] Open
Abstract
The present working hypothesis is that the Cu-induced changes in lipid metabolism may be mediated by miRNAs. Here, we describe the miRNA profile of the liver tissues of yellow catfish exposed to waterborne Cu, based on larger-scale sequencing of small RNA libraries. We identified a total of 172 distinct miRNAs. Among these miRNAs, compared to the control, mRNA expression levels of 16 miRNAs (miR-203a, 205, 1788-3p, 375, 31, 196a, 203b-3p, 2187-5p, 196d, 459-3p, 153a and miR-725, and two novel-miRNAs: chr4-1432, chr-7684) were down-regulated, and mRNA levels of miR-212 and chr20-5274 were up-regulated in Cu-exposed group. The functions of their target genes mainly involved ether lipid metabolism, glycerophospholipid metabolism, linoleic acid metabolism and α-linolenic acid metabolism. Cu exposure inhibited the expression of miR-205, whose predicted target genes were enriched in the pathway of lipid metabolism, including fas, lxrα, ddit3, lamp2, casp3a and baxa. These potential target genes were further verified by Dual-luciferase reporter gene assay. Using primary hepatocytes of yellow catfish, Cu incubation down-regulated miR-205 expression, and increased TG contents and FAS activity. LXR antagonist effectively ameliorate the Cu-induced change of TG content and FAS activity. These data suggest that down-regulation of the miRNA-205 may be an important step in Cu-induced changes in lipid metabolism in yellow catfish.
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Gay S, Bugeon J, Bouchareb A, Henry L, Delahaye C, Legeai F, Montfort J, Le Cam A, Siegel A, Bobe J, Thermes V. MiR-202 controls female fecundity by regulating medaka oogenesis. PLoS Genet 2018; 14:e1007593. [PMID: 30199527 PMCID: PMC6147661 DOI: 10.1371/journal.pgen.1007593] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 09/20/2018] [Accepted: 07/26/2018] [Indexed: 12/12/2022] Open
Abstract
Female gamete production relies on coordinated molecular and cellular processes that occur in the ovary throughout oogenesis. In fish, as in other vertebrates, these processes have been extensively studied both in terms of endocrine/paracrine regulation and protein expression and activity. The role of small non-coding RNAs in the regulation of animal reproduction remains however largely unknown and poorly investigated, despite a growing interest for the importance of miRNAs in a wide variety of biological processes. Here, we analyzed the role of miR-202, a miRNA predominantly expressed in male and female gonads in several vertebrate species. We studied its expression in the medaka ovary and generated a mutant line (using CRISPR/Cas9 genome editing) to determine its importance for reproductive success with special interest for egg production. Our results show that miR-202-5p is the most abundant mature form of the miRNA and that it is expressed in granulosa cells and in the unfertilized egg. The knock out (KO) of mir-202 gene resulted in a strong phenotype both in terms of number and quality of eggs produced. Mutant females exhibited either no egg production or produced a dramatically reduced number of eggs that could not be fertilized, ultimately leading to no reproductive success. We quantified the size distribution of the oocytes in the ovary of KO females and performed a large-scale transcriptomic analysis approach to identified dysregulated molecular pathways. Together, cellular and molecular analyses indicate that the lack of miR-202 impairs the early steps of oogenesis/folliculogenesis and decreases the number of large (i.e. vitellogenic) follicles, ultimately leading to dramatically reduced female fecundity. This study sheds new light on the regulatory mechanisms that control the early steps of follicular development, including possible targets of miR-202-5p, and provides the first in vivo functional evidence that a gonad-predominant microRNA may have a major role in female reproduction. The role of small non-coding RNAs in the regulation of animal reproduction remains poorly investigated, despite a growing interest for the importance of miRNAs in a wide variety of biological processes. Here, we analyzed the role of miR-202, a miRNA predominantly expressed in gonads in vertebrate. We studied its expression in the medaka ovary and knocked out the mir-202 gene to study its importance for reproductive success. We showed that the lack of miR-202 results in the sterility of both females and males. In particular, it led to a drastic reduction of both the number and the quality of eggs produced by females. Mutant females exhibited either no egg production or produced a drastically reduced number of eggs that could not be fertilized, ultimately leading to no reproductive success. Quantitative histological and molecular analyses indicated that mir-202 KO impairs oocyte development and is also associated with the dysregulation of many genes that are critical for reproduction. This study sheds new light on the regulatory mechanisms that control oogenesis, including possible targets of miR-202-5p, and provides the first in vivo functional evidence that a gonad-predominant microRNA may have a major role in female reproduction.
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Affiliation(s)
| | | | | | | | - Clara Delahaye
- LPGP, INRA, Rennes, France
- Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Fabrice Legeai
- Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
- IGEPP, INRA BP35327, Le Rheu, France
| | | | | | - Anne Siegel
- Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
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Shigematsu M, Honda S, Kirino Y. Dumbbell-PCR for Discriminative Quantification of a Small RNA Variant. Methods Mol Biol 2018; 1680:65-73. [PMID: 29030841 DOI: 10.1007/978-1-4939-7339-2_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Cellular RNAs are often expressed as multiple isoforms of complex heterogeneity in both length and terminal sequences. IsomiRs, the isoforms of microRNAs, are such an example. Distinct quantification of each RNA variant is necessary to unravel the biogenesis mechanism and biological significance of heterogenetic RNA expression. Here we describe Dumbbell-PCR (Db-PCR), a TaqMan RT-PCR-based method that distinctively quantifies a specific small RNA variant with single-nucleotide resolution at terminal sequences. Db-PCR enables the quantitative analysis of RNA terminal heterogeneity without performing Next-Generation Sequencing.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Shozo Honda
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, JAH Suite #M77, Philadelphia, PA, 19107, USA.
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20
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Differential miRNA expression in the three-spined stickleback, response to environmental changes. Sci Rep 2017; 7:18089. [PMID: 29273769 PMCID: PMC5741757 DOI: 10.1038/s41598-017-18128-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 12/01/2017] [Indexed: 12/13/2022] Open
Abstract
miRNAs play important role in the various physiological and evolutionary processes, however, there is no data allowing comparison of evolutionary differences between various ecotypes adapted to different environmental conditions and specimen demonstrating immediate physiological response to the environmental changes. We compared miRNA expression profiles between marine and freshwater stickleback populations of the three-spined stickleback to identify the evolutionary differences. To study the immediate physiological response to foreign environment, we explored the changes induced by transfer of marine sticklebacks into freshwater environment and vice versa. Comparative analysis of changes in miRNA expression suggested that they are driven by three independent factors: (1) non-specific changes in miRNA expression under different environmental conditions; (2) specific response to freshwater conditions in the marine stickleback ecotype; (3) specific response to extreme osmotic conditions for both marine and freshwater ecotypes during the contact with non-native environment. Gene Ontology enrichment analysis of differential expressed miRNA targets supports our current hypothesis.
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21
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Tu J, Tian C, Zhao P, Sun J, Wang M, Fan Q, Yuan Y. Identification and profiling of growth-related microRNAs in Chinese perch (Siniperca chuatsi). BMC Genomics 2017; 18:489. [PMID: 28659132 PMCID: PMC5490230 DOI: 10.1186/s12864-017-3851-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 06/07/2017] [Indexed: 12/17/2022] Open
Abstract
Background MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in the regulation of diverse biological processes in eukaryotes. Chinese perch (Siniperca chuatsi) is one of the most economically important fish species widely cultured in China. Growth is an extremely important characteristic in fish. Individual differences in body size are common in Siniperca chuatsi, which significantly influence the aquaculture production of Siniperca chuatsi. However, the underline growth-related regulatory factors, such as miRNAs, are still unknown. Results To investigate the growth-related miRNAs in Siniperca chuatsi, two RNA libraries from four growth-related tissues (brain, pituitary, liver, and muscle) of Siniperca chuatsi at 6-month stage with relatively high or low growth rates (big-size group or small-size group) were obtained and sequenced using Solexa sequencing. A total of 252 known miRNAs and 12 novel miRNAs were identified. The expression patterns of these miRNAs in big-size group and small-size group were compared, and the results showed that 31 known and 5 novel miRNAs were differently expressed (DE). Furthermore, to verify the Solexa sequencing, five DE miRNAs were randomly selected and quantified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results showed that their expression patterns were consistent with those of Solexa sequencing. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of target genes of DE miRNAs was performed. It showed that the target genes were involved in multiple biological processes including metabolic process, suggesting that metabolic process played an important role in growth of fish. Conclusions Siniperca chuatsi is a popular and economically important species in aquaculture. In this study, miRNAs in Siniperca chuatsi with different growth rates were identified, and their expression profiles were compared. The data provides the first large-scale miRNA profiles related to growth of Siniperca chuatsi, which is expected to contribute to a better understanding of the role of miRNAs in regulating the biological processes of growth and possibly useful for Siniperca chuatsi breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3851-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiagang Tu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Changxu Tian
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Peiqi Zhao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junxiao Sun
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Min Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qixue Fan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongchao Yuan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. .,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, Hubei, 430070, China.
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22
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Chen R, Du J, Ma L, Wang LQ, Xie SS, Yang CM, Lan XY, Pan CY, Dong WZ. Comparative microRNAome analysis of the testis and ovary of the Chinese giant salamander. Reproduction 2017. [PMID: 28630098 DOI: 10.1530/rep-17-0109] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are 18-24 nucleotides non-coding RNAs that regulate gene expression by post-transcriptional suppression of mRNA. The Chinese giant salamander (CGS, Andrias davidianus), which is an endangered species, has become one of the important models of animal evolution; however, no miRNA studies on this species have been conducted. In this study, two small RNA libraries of CGS ovary and testis were constructed using deep sequencing technology. A bioinformatics pipeline was developed to distinguish miRNA sequences from other classes of small RNAs represented in the sequencing data. We found that many miRNAs and other small RNAs such as piRNA and tsRNA were abundant in CGS tissue. A total of 757 and 756 unique miRNAs were annotated as miRNA candidates in the ovary and testis respectively. We identified 145 miRNAs in CGS ovary and 155 miRNAs in CGS testis that were homologous to those in Xenopus laevis ovary and testis respectively. Forty-five miRNAs were more highly expressed in ovary than in testis and 21 miRNAs were more highly expressed in testis than in ovary. The expression profiles of the selected miRNAs (miR-451, miR-10c, miR-101, miR-202, miR-7a and miR-499) had their own different roles in other eight tissues and different development stages of testis and ovary, suggesting that these miRNAs play vital regulatory roles in sexual differentiation, gametogenesis and development in CGS. To our knowledge, this is the first study to reveal miRNA profiles that are related to male and female CGS gonads and provide insights into sex differences in miRNA expression in CGS.
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Affiliation(s)
- Rui Chen
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Jian Du
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Lin Ma
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Li-Qing Wang
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Sheng-Song Xie
- Key Lab of Agricultural Animal GeneticsBreeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Chang-Ming Yang
- Animal Husbandry and Veterinary Station of Chenggu CountyHanzhong, China
| | - Xian-Yong Lan
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Chuan-Ying Pan
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Wu-Zi Dong
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
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Pawlina K, Gurgul A, Szmatoła T, Koch C, Mählmann K, Witkowski M, Bugno-Poniewierska M. Comprehensive characteristics of microRNA expression profile of equine sarcoids. Biochimie 2017; 137:20-28. [DOI: 10.1016/j.biochi.2017.02.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/28/2017] [Indexed: 12/21/2022]
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Evolution of Fish Let-7 MicroRNAs and Their Expression Correlated to Growth Development in Blunt Snout Bream. Int J Mol Sci 2017; 18:ijms18030646. [PMID: 28300776 PMCID: PMC5372658 DOI: 10.3390/ijms18030646] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 03/12/2017] [Accepted: 03/13/2017] [Indexed: 12/12/2022] Open
Abstract
The lethal-7 (let-7) miRNA, known as one of the first founding miRNAs, is present in multiple copies in a genome and has diverse functions in animals. In this study, comparative genomic analysis of let-7 miRNAs members in fish species indicated that let-7 miRNA is a sequence conserved family in fish, while different species have the variable gene copy numbers. Among the ten members including let-7a/b/c/d/e/f/g/h/i/j, the let-7a precursor sequence was more similar to ancestral sequences, whereas other let-7 miRNA members were separate from the late differentiation of let-7a. The mostly predicted target genes of let-7 miRNAs are involved in biological process, especially developmental process and growth through Gene Ontology (GO) enrichment analysis. In order to identify the possible different functions of these ten miRNAs in fish growth development, their expression levels were quantified in adult males and females of Megalobrama amblycephala, as well as in 3-, 6-, and 12-months-old individuals with relatively slow- and fast-growth rates. These ten miRNAs had similar tissue expression patterns between males and females, with higher expression levels in the brain and pituitary than that in other tissues (p < 0.05). Among these miRNAs, the relative expression level of let-7a was the highest among almost all the tested tissues, followed by let-7b, let-7d and let-7c/e/f/g/h/i/j. As to the groups with different growth rates, the expression levels of let-7 miRNAs in pituitary and brain from the slow-growth group were always significantly higher than that in the fast-growth group (p < 0.05). These results suggest that let-7 miRNA members could play an important role in the regulation of growth development in M. amblycephala through negatively regulating expression of their target genes.
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25
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Dynamics of miRNA transcriptome during gonadal development of zebrafish. Sci Rep 2017; 7:43850. [PMID: 28262836 PMCID: PMC5338332 DOI: 10.1038/srep43850] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/31/2017] [Indexed: 12/28/2022] Open
Abstract
Studies in non-teleost vertebrates have found microRNAs (miRNAs) to be essential for proper gonadal development. However, comparatively little is known about their role during gonadal development in teleost fishes. So far in zebrafish, a model teleost, transcript profiling throughout gonadal development has not been established because of a tiny size of an organ in juvenile stages and its poor distinguishability from surrounding tissues. We performed small RNA sequencing on isolated gonads of See-Thru-Gonad line, from the undifferentiated state at 3 weeks post fertilization (wpf) to fully mature adults at 24 wpf. We identified 520 gonadal mature miRNAs; 111 of them had significant changes in abundance over time, while 50 miRNAs were either testis- or ovary-enriched significantly in at least one developmental stage. We characterized patterns of miRNA abundance over time including isomiR variants. We identified putative germline versus gonadal somatic miRNAs through differential small RNA sequencing of isolated gametes versus the whole gonads. This report is the most comprehensive analysis of the miRNA repertoire in zebrafish gonads during the sexual development to date and provides an important database from which functional studies can be performed.
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Gomes F, Watanabe L, Nozawa S, Oliveira L, Cardoso J, Vianez J, Nunes M, Schneider H, Sampaio I. Identification and characterization of the expression profile of the microRNAs in the Amazon species Colossoma macropomum by next generation sequencing. Genomics 2017; 109:67-74. [PMID: 28192178 DOI: 10.1016/j.ygeno.2017.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/06/2017] [Accepted: 02/08/2017] [Indexed: 01/20/2023]
Abstract
Colossoma macropomum is a resistant species native of Amazonas and Orinoco river basins. It is regarded as the second largest finfish of Solimões and Amazon rivers, representing a major fishery resource in Amazonas and an important species in tropical aquaculture. MicroRNAs are non-coding endogenous riboregulators of nearly 22 nucleotides that play a key role in post-transcriptional gene regulation of several organisms. We analyzed samples of liver and skin from specimens of C. macropomum using next generation sequencing. The dataset was evaluated using computational programs to check the quality of sequences, identification of miRNAs, as well as to evaluate the expression levels of these microRNAs and interaction of target genes. We identified 279 conserved miRNAs, being 257 from liver and 272 from skin, with several miRNAs shared between tissues, with divergence in the number of reads. The strands miR-5p and miR-3p were observed in 72 miRNAs, some of them presenting a higher number of 3p reads. The functional annotation of the most expressed miRNAs resulted in 27 pathways for the liver and skin mainly related to the "biological processes" domain. Based on the identified pathways, we visualized a large gene network, suggesting the regulation of selected miRNA over this interactive dataset. We were able to identify and characterize the expression levels of miRNAs in two tissues of great activity in C. macropomum, which stands out as the beginning of several studies that can be carried out to elucidate the influence of miRNAs in this species and their applicability as biotechnological tools.
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Affiliation(s)
- Fátima Gomes
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
| | - Luciana Watanabe
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
| | - Sérgio Nozawa
- Dow AgroSciences, Av Antonio Diederichsen, 400, - Ribeirão Preto, SP 14020-250, Brazil.
| | - Layanna Oliveira
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil.
| | - Jedson Cardoso
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil; Postgraduate Program in Virology (PPGV), Evandro Chagas Institute, Ministry of Health, Ananindeua, PA 67030-000, Brazil.
| | - João Vianez
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil.
| | - Márcio Nunes
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, 67030-000 Ananindeua, PA, Brazil.
| | - Horacio Schneider
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
| | - Iracilda Sampaio
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Federal University of Pará, Campus of Bragança, 68600-000 Bragança, PA, Brazil.
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Robledo D, Hermida M, Rubiolo JA, Fernández C, Blanco A, Bouza C, Martínez P. Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 21:41-55. [PMID: 28063346 DOI: 10.1016/j.cbd.2016.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022]
Abstract
Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes. In this work, we integrate all available genomic information of these species within a common framework, taking as reference the whole assembled genomes of turbot and tongue sole (>210× coverage). New insights related to the genetic basis of productive traits and new data useful to understand the evolutionary origin and diversification of this group were obtained. Despite a general 1:1 chromosome syntenic relationship between species, the comparison of turbot and tongue sole genomes showed huge intrachromosomic reorganizations. The integration of available mapping information supported specific chromosome fusions along flatfish evolution and facilitated the comparison between species of previously reported genetic associations for productive traits. When comparing transcriptomic resources of the six species, a common set of ~2500 othologues and ~150 common miRNAs were identified, and specific sets of putative missing genes were detected in flatfish transcriptomes, likely reflecting their evolutionary diversification.
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Affiliation(s)
- Diego Robledo
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Biology (CIBUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Juan A Rubiolo
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
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Illumina Sequencing Reveals Aberrant Expression of MicroRNAs and Their Variants in Whitefish (Coregonus lavaretus) Liver after Exposure to Microcystin-LR. PLoS One 2016; 11:e0158899. [PMID: 27391076 PMCID: PMC4938405 DOI: 10.1371/journal.pone.0158899] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/23/2016] [Indexed: 12/19/2022] Open
Abstract
Molecular analyses show that challenging fish with microcystin-LR (MC-LR) causes perturbations of microRNA (miRNA) signaling. However, the significance and scope of these alterations is currently unknown. To address this issue, we studied miRNA gene expression in the liver of juvenile whitefish, C. lavaretus, during 28 days of exposure to a subacute dose of MC-LR (100 μg·kg-1 body mass). Using genomic resources of Atlantic salmon (AGKD03), the mature miRNA library of Atlantic salmon (miRBase-21) and bioinformatics tools (sRNAbench), we discovered and annotated a total of 377 distinct mature miRNAs belonging to 93 families of evolutionary conserved miRNAs, as well as 24 novel mature miRNA candidates that were mapped to 14 distinct S. salar miRNA precursors. miRNA-Seq transcriptome profiling of liver tissues revealed differential miRNA expression in control and treated fish at 14 days (73 miRNAs were modulated) and at 28 days (83 miRNAs) of the treatment, subsequently validated by qPCR for nine selected differentially expressed miRNAs. Additional qPCR study confirmed the miRNA-Seq data and revealed consistent, aberrant miRNAs expression profile in the later phase of MC-LR hepatotoxicity (7–28 d). Functional annotation analysis revealed that the aberrantly expressed miRNAs have target genes involved in cytoskeletal remodeling, cell metabolism, cell cycle regulation and apoptosis; dysregulation of these processes in liver cells leads to cirrhosis and hepatocellular carcinoma in humans. To enable deeper insight into the molecular responses of liver cells in fish exposed to MC-LR, we expanded the miRNAome analysis by inclusion of miRNA variants (isomiRs) profiles, and we showed that the isomiR profiles of liver specific MiR122, and a few other miRNAs, correlated with MC-LR treatment. Given the importance of isomiRs for disease biology in mammals, we believe that further research focused on the miRNA isoforms will bring us closer to better understanding the molecular mechanisms of MC-LR hepatotoxicity.
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29
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Rastorguev SM, Nedoluzhko AV, Sharko FS, Boulygina ES, Sokolov AS, Gruzdeva NM, Skryabin KG, Prokhortchouk EB. Identification of novel microRNA genes in freshwater and marine ecotypes of the three-spined stickleback (Gasterosteus aculeatus). Mol Ecol Resour 2016; 16:1491-1498. [PMID: 27238497 DOI: 10.1111/1755-0998.12545] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/26/2016] [Accepted: 05/13/2016] [Indexed: 11/30/2022]
Abstract
The three-spined stickleback (Gasterosteus aculeatus L.) is an important model organism for studying the molecular mechanisms of speciation and adaptation to salinity. Despite increased interest to microRNA discovery and recent publication on microRNA prediction in the three-spined stickleback using bioinformatics approaches, there is still a lack of experimental support for these data. In this paper, high-throughput sequencing technology was applied to identify microRNA genes in gills of the three-spined stickleback. In total, 595 miRNA genes were discovered; half of them were predicted in previous computational studies and were confirmed here as microRNAs expressed in gill tissue. Moreover, 298 novel microRNA genes were identified. The presence of miRNA genes in selected 'divergence islands' was analysed and 10 miRNA genes were identified as not randomly located in 'divergence islands'. Regulatory regions of miRNA genes were found enriched with selective SNPs that may play a role in freshwater adaptation.
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Affiliation(s)
- S M Rastorguev
- National Research Center 'Kurchatov Institute', Kurchatov sq. 1, Moscow, 123182, Russia. .,Russian Federal Research Institute of Fisheries and Oceanography, (VNIRO) V. Krasnoselskaya str. 17, Moscow, 107140, Russia.
| | - A V Nedoluzhko
- National Research Center 'Kurchatov Institute', Kurchatov sq. 1, Moscow, 123182, Russia
| | - F S Sharko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, 119071, Russia
| | - E S Boulygina
- National Research Center 'Kurchatov Institute', Kurchatov sq. 1, Moscow, 123182, Russia
| | - A S Sokolov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, 119071, Russia
| | - N M Gruzdeva
- National Research Center 'Kurchatov Institute', Kurchatov sq. 1, Moscow, 123182, Russia
| | - K G Skryabin
- National Research Center 'Kurchatov Institute', Kurchatov sq. 1, Moscow, 123182, Russia.,Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, 119071, Russia.,Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow, 119991, Russia
| | - E B Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, 119071, Russia.,Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow, 119991, Russia
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30
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Wang S, Xu Y, Li M, Tu J, Lu Z. Dysregulation of miRNA isoform level at 5' end in Alzheimer's disease. Gene 2016; 584:167-72. [PMID: 26899870 DOI: 10.1016/j.gene.2016.02.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 01/09/2016] [Accepted: 02/15/2016] [Indexed: 01/10/2023]
Abstract
Alzheimer's disease (AD) is the most common form of dementia, whose mechanism is still not yet fully understood. A miRNA-based signature method, commonly according to the changes of expression levels, is widely used for AD analysis in previous studies. Recently, miRNA isoforms called as isomiR variants, which is considered to play important biological roles, have been demonstrated as the applications of high throughput sequencing platforms. Here, we presented an entropy-based model to detect the miRNA isoform level at the 5' end, and found many miRNAs with significant changes of isoform levels between the early stage and the late stage of AD by the application of this model to the public data. The statistical significance of the overlap between isoform-level changed miRNAs and AD related miRNAs extracted from HMDD2 supports that these miRNA isoforms are not degradation products. Based on the most common isomiR seed analysis of isoform-level changed AD related miRNAs, the predicted targets are also found to be enriched for genes involved in transcriptional regulation and the nervous system. After comparing with the expression level based method, we detected that changes of 5' isoform levels are more stable than those of expression levels for AD related miRNA detecting.
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Affiliation(s)
- Shengqin Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuming Xu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Musheng Li
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jing Tu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100781, China.
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Ahmed F, Senthil-Kumar M, Lee S, Dai X, Mysore KS, Zhao PX. Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in Arabidopsis thaliana. RNA Biol 2015; 11:1414-29. [PMID: 25629686 PMCID: PMC4615835 DOI: 10.1080/15476286.2014.996474] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Along with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from Arabidopsis to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in Arabidopsis. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.
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Affiliation(s)
- Firoz Ahmed
- a Plant Biology Division; Samuel Roberts Noble Foundation ; Ardmore , OK USA
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32
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Mennigen JA. Micromanaging metabolism-a role for miRNAs in teleost energy metabolism. Comp Biochem Physiol B Biochem Mol Biol 2015; 199:115-125. [PMID: 26384523 DOI: 10.1016/j.cbpb.2015.09.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/08/2015] [Accepted: 09/08/2015] [Indexed: 10/23/2022]
Abstract
MicroRNAs (miRNAs) are small, non-protein coding RNA sequences, which are found in most eukaryotes. Since their initial discovery, miRNAs have emerged as important regulators of many biological processes. One of the most important processes profoundly regulated by miRNAs is energy metabolism. Traditionally, metabolic functions of miRNAs have been studied in genome-sequenced mammalian organisms, especially the mouse model. However, partially driven by commercial interest in aquaculture, increasingly feasible large-scale molecular techniques have resulted in the characterization of miRNA repertoires, and importantly, several genome sequences of several (commercially important) teleost species, which also hold important roles as research models in the comparative physiology of energy metabolism. This review aims to introduce the recent advances in miRNA research in teleost fish and to describe the current knowledge of miRNA function in teleost energy metabolism. The most pressing research needs and questions to determine metabolic roles of miRNAs in teleost models are presented, as well as applicable technical approaches and current bottlenecks. Rainbow trout, which possess the advantages of newly available molecular tools and a long history as comparative research model in teleost energy metabolism, are discussed as a promising research model to address these questions.
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Affiliation(s)
- Jan A Mennigen
- College of Pharmacy, Department of Toxicology and Pharmacology, University of Austin at Texas, 107 W Dean Keeton, Austin, TX 78712, USA
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33
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Ibarra-Laclette E, Zamudio-Hernández F, Pérez-Torres CA, Albert VA, Ramírez-Chávez E, Molina-Torres J, Fernández-Cortes A, Calderón-Vázquez C, Olivares-Romero JL, Herrera-Estrella A, Herrera-Estrella L. De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis. BMC Genomics 2015; 16:657. [PMID: 26330142 PMCID: PMC4557841 DOI: 10.1186/s12864-015-1821-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 08/07/2015] [Indexed: 12/04/2022] Open
Abstract
Background Lophophora williamsii (commonly named peyote) is a small, spineless cactus with psychoactive alkaloids, particularly mescaline. Peyote utilizes crassulacean acid metabolism (CAM), an alternative form of photosynthesis that exists in succulents such as cacti and other desert plants. Therefore, its transcriptome can be considered an important resource for future research focused on understanding how these plants make more efficient use of water in marginal environments and also for research focused on better understanding of the overall mechanisms leading to production of plant natural products and secondary metabolites. Results In this study, two cDNA libraries were generated from L. williamsii. These libraries, representing buttons (tops of stems) and roots were sequenced using different sequencing platforms (GS-FLX, GS-Junior and PGM, respectively). A total of 5,541,550 raw reads were generated, which were assembled into 63,704 unigenes with an average length of 564.04 bp. A total of 25,149 unigenes (62.19 %) was annotated using public databases. 681 unigenes were found to be differentially expressed when comparing the two libraries, where 400 were preferentially expressed in buttons and 281 in roots. Some of the major alkaloids, including mescaline, were identified by GC-MS and relevant metabolic pathways were reconstructed using the Kyoto encyclopedia of genes and genomes database (KEGG). Subsequently, the expression patterns of preferentially expressed genes putatively involved in mescaline production were examined and validated by qRT-PCR. Conclusions High throughput transcriptome sequencing (RNA-seq) analysis allowed us to efficiently identify candidate genes involved in mescaline biosynthetic pathway in L. williamsii; these included tyrosine/DOPA decarboxylase, hydroxylases, and O-methyltransferases. This study sets the theoretical foundation for bioassay design directed at confirming the participation of these genes in mescaline production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1821-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Enrique Ibarra-Laclette
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México. .,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México.
| | - Flor Zamudio-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Claudia Anahí Pérez-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México. .,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México. .,Investigador Cátedra CONACyT, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México.
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, 14260, USA.
| | - Enrique Ramírez-Chávez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36821, Irapuato, Guanajuato, México.
| | - Jorge Molina-Torres
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36821, Irapuato, Guanajuato, México.
| | - Araceli Fernández-Cortes
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Carlos Calderón-Vázquez
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Instituto Politécnico Nacional, 81000, Guasave, Sinaloa, México.
| | | | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
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Yuan Z, Ding S, Yan M, Zhu X, Liu L, Tan S, Jin Y, Sun Y, Li Y, Huang T. Variability of miRNA expression during the differentiation of human embryonic stem cells into retinal pigment epithelial cells. Gene 2015; 569:239-49. [PMID: 26028588 DOI: 10.1016/j.gene.2015.05.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 05/23/2015] [Accepted: 05/25/2015] [Indexed: 01/08/2023]
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells can be induced to differentiate into retinal pigment epithelium (RPE). MiRNAs have been characterized and found playing important roles in the differentiation process of ESCs, but their length and sequence heterogeneity (isomiRs), and their non-canonical forms of miRNAs are underestimated or ignored. In this report, we found some non-canonical miRNAs (dominant isomiRs) in all differentiation stages, and 27 statistically significant editing sites were identified in 24 different miRNAs. Moreover, we found marked major-to-minor arm-switching events in 14 pre-miRNAs during the hESC to RPE cell differentiation phases. Our study for the first time reports exploring the variability of miRNA expression during the differentiation of hESCs into RPE cells and the results show that miRNA variability is a ubiquitous phenomenon in the ESC differentiation.
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Affiliation(s)
- Zhidong Yuan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China.
| | - Suping Ding
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Mingli Yan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Xiao Zhu
- Guangdong Province Key Laboratory of Medical Molecular Diagnosis, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan 523808, China
| | - Lili Liu
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Shuhua Tan
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Yuanchang Jin
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yuandong Sun
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
| | - Yufeng Li
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Ting Huang
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
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Kaitetzidou E, Xiang J, Antonopoulou E, Tsigenopoulos CS, Sarropoulou E. Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax). Physiol Genomics 2015; 47:158-69. [DOI: 10.1152/physiolgenomics.00001.2015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/23/2015] [Indexed: 01/06/2023] Open
Abstract
Larval and embryonic stages are the most critical period in the life cycle of marine fish. Key developmental events occur early in development and are influenced by external parameters like stress, temperature, salinity, and photoperiodism. Any failure may cause malformations, developmental delays, poor growth, and massive mortalities. Advanced understanding of molecular processes underlying marine larval development may lead to superior larval rearing conditions. Today, the new sequencing and bioinformatic methods allow transcriptome screens comprising messenger (mRNA) and microRNA (miRNA) with the scope of detecting differential expression for any species of interest. In the present study, we applied Illumina technology to investigate the transcriptome of early developmental stages of the European seabass ( Dicentrarchus labrax). The European seabass, in its natural environment, is a euryhaline species and has shown high adaptation processes in early life phases. During its embryonic and larval phases the European seabass lives in a marine environment and as a juvenile it migrates to coastal zones, estuaries, and lagoons. Investigating the dynamics of gene expression in its early development may shed light on factors promoting phenotypic plasticity and may also contribute to the improvement and advancement of rearing methods of the European seabass, a species of high economic importance in European and Mediterranean aquaculture. We present the identification, characterization, and expression of mRNA and miRNA, comprising paralogous genes and differentially spliced transcripts from early developmental stages of the European seabass. We further investigated the detection of possible interactions of miRNA with mRNA.
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Affiliation(s)
- E. Kaitetzidou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Greece
- School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Greece; and
| | - J. Xiang
- Genomics Resources Core Facility, Weill Cornell Medical College, New York, New York
| | - E. Antonopoulou
- School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Greece; and
| | - C. S. Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Greece
| | - E. Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Greece
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Bizuayehu TT, Johansen SD, Puvanendran V, Toften H, Babiak I. Temperature during early development has long-term effects on microRNA expression in Atlantic cod. BMC Genomics 2015; 16:305. [PMID: 25881242 PMCID: PMC4403832 DOI: 10.1186/s12864-015-1503-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 03/27/2015] [Indexed: 12/22/2022] Open
Abstract
Background Environmental temperature has serious implications in life cycle of aquatic ectotherms. Understanding the molecular mechanisms of temperature acclimation and adaptation of marine organisms is of the uttermost importance for ecology, fisheries, and aquaculture, as it allows modeling the effects of global warming on population dynamics. Regulatory molecules are major modulators of acclimation and adaptation; among them, microRNAs (miRNAs) are versatile and substantial contributors to regulatory networks of development and adaptive plasticity. However, their role in thermal plasticity is poorly known. We have asked whether the temperature and its shift during the early ontogeny (embryonic and larval development) affect the miRNA repertoire of Atlantic cod (Gadus morhua), and if thermal experience has long-term consequences in the miRNA profile. Results We characterized miRNA during different developmental stages and in juvenile tissues using next generation sequencing. We identified 389 putative miRNA precursor loci, 120 novel precursor miRNAs, and 281 mature miRNAs. Some miRNAs showed stage- or tissue-enriched expression and miRNAs, such as the miR-17 ~ 92 cluster, myomiRs (miR-206), neuromiRs (miR-9, miR-124), miR-130b, and miR-430 showed differential expression in different temperature regimes. Long-term effect of embryonic incubation temperature was revealed on expression of some miRNAs in juvenile pituitary (miR-449), gonad (miR-27c, miR-30c, and miR-200a), and liver (let-7 h, miR-7a, miR-22, miR-34c, miR-132a, miR-192, miR-221, miR-451, miR-2188, and miR-7550), but not in brain. Some of differentially expressed miRNAs in the liver were confirmed using LNA-based rt-qPCR. The effect of temperature on methylation status of selected miRNA promoter regions was mostly inconclusive. Conclusions Temperature elevation by several degrees during embryonic and larval developmental stages significantly alters the miRNA profile, both short-term and long-term. Our results suggest that a further rise in seas temperature might affect life history of Atlantic cod. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1503-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Steinar D Johansen
- University of Nordland, Faculty of Biosciences and Aquaculture, Post Box 1490, 8049, Bodø, Norway. .,Arctic University of Norway, FHS, RNA Lab, Dept Med Biol, N-9037, Tromsø, Norway.
| | | | - Hilde Toften
- Nofima AS, Muninbakken 9-13, P.O. box 6122, NO, 9291, Tromsø, Norway.
| | - Igor Babiak
- University of Nordland, Faculty of Biosciences and Aquaculture, Post Box 1490, 8049, Bodø, Norway.
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37
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Wang S, Tu J, Wang L, Lu Z. Entropy-based model for miRNA isoform analysis. PLoS One 2015; 10:e0118856. [PMID: 25785816 PMCID: PMC4364746 DOI: 10.1371/journal.pone.0118856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 01/18/2015] [Indexed: 11/19/2022] Open
Abstract
MiRNAs have been widely studied due to their important post-transcriptional regulatory roles in gene expression. Many reports have demonstrated the evidence of miRNA isoform products (isomiRs) in high-throughput small RNA sequencing data. However, the biological function involved in these molecules is still not well investigated. Here, we developed a Shannon entropy-based model to estimate isomiR expression profiles of high-throughput small RNA sequencing data extracted from miRBase webserver. By using the Kolmogorov-Smirnov statistical test (KS test), we demonstrated that the 5p and 3p miRNAs present more variants than the single arm miRNAs. We also found that the isomiR variant, except the 3’ isomiR variant, is strongly correlated with Minimum Free Energy (MFE) of pre-miRNA, suggesting the intrinsic feature of pre-miRNA should be one of the important factors for the miRNA regulation. The functional enrichment analysis showed that the miRNAs with high variation, particularly the 5’ end variation, are enriched in a set of critical functions, supporting these molecules should not be randomly produced. Our results provide a probabilistic framework for miRNA isoforms analysis, and give functional insights into pre-miRNA processing.
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Affiliation(s)
- Shengqin Wang
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Jing Tu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Lei Wang
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zuhong Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100781, China
- * E-mail:
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Honda S, Kirino Y. Dumbbell-PCR: a method to quantify specific small RNA variants with a single nucleotide resolution at terminal sequences. Nucleic Acids Res 2015; 43:e77. [PMID: 25779041 PMCID: PMC4499115 DOI: 10.1093/nar/gkv218] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/04/2015] [Indexed: 12/15/2022] Open
Abstract
Recent advances in next-generation sequencing technologies have revealed that cellular functional RNAs are not always expressed as single entities with fixed terminal sequences but as multiple isoforms bearing complex heterogeneity in both length and terminal sequences, such as isomiRs, the isoforms of microRNAs. Unraveling the biogenesis and biological significance of heterogenetic RNA expression requires distinctive analysis of each RNA variant. Here, we report the development of dumbbell PCR (Db-PCR), an efficient and convenient method to distinctively quantify a specific individual small RNA variant. In Db-PCR, 5′- and 3′-stem–loop adapters are specifically hybridized and ligated to the 5′- and 3′-ends of target RNAs, respectively, by T4 RNA ligase 2 (Rnl2). The resultant ligation products with ‘dumbbell-like’ structures are subsequently quantified by TaqMan RT-PCR. We confirmed that high specificity of Rnl2 ligation and TaqMan RT-PCR toward target RNAs assured both 5′- and 3′-terminal sequences of target RNAs with single nucleotide resolution so that Db-PCR specifically detected target RNAs but not their corresponding terminal variants. Db-PCR had broad applicability for the quantification of various small RNAs in different cell types, and the results were consistent with those from other quantification method. Therefore, Db-PCR provides a much-needed simple method for analyzing RNA terminal heterogeneity.
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Affiliation(s)
- Shozo Honda
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
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39
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Mione M, Bosserhoff A. MicroRNAs in melanocyte and melanoma biology. Pigment Cell Melanoma Res 2015; 28:340-54. [PMID: 25515738 DOI: 10.1111/pcmr.12346] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/15/2014] [Indexed: 12/18/2022]
Abstract
The importance of microRNAs as key molecular components of cellular processes is now being recognized. Recent reports have shown that microRNAs regulate processes as diverse as protein expression and nuclear functions inside cells and are able to signal extracellularly, delivered via exosomes, to influence cell fate at a distance. The versatility of microRNAs as molecular tools inspires the design of novel strategies to control gene expression, protein stability, DNA repair and chromatin accessibility that may prove very useful for therapeutic approaches due to the extensive manageability of these small molecules. However, we still lack a comprehensive understanding of the microRNA network and its interactions with the other layers of regulatory elements in cellular and extracellular functions. This knowledge may be necessary before we exploit microRNA versatility in therapeutic settings. To identify rules of interactions between microRNAs and other regulatory systems, we begin by reviewing microRNA activities in a single cell type: the melanocyte, from development to disease.
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Affiliation(s)
- Marina Mione
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggestein-Leopoldshafen, Germany
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40
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Wang H, Liu S, Cui J, Li C, Qiu X, Chang Y, Liu Z, Wang X. Characterization and expression analysis of microRNAs in the tube foot of sea cucumber Apostichopus japonicus. PLoS One 2014; 9:e111820. [PMID: 25372871 PMCID: PMC4221132 DOI: 10.1371/journal.pone.0111820] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/30/2014] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous non-coding small RNA with average length of 22 nucleotides, participating in the post-transcriptional regulation of gene expression. In this study, we report the identification and characterization of miRNAs in the tube foot of sea cucumber (Apostichopus japonicus) by next generation sequencing with Illumina HiSeq 2000 platform. Through the bioinformatic analysis, we identified 260 conserved miRNAs and six novel miRNAs from the tube foot small RNA transcriptome. Quantitative realtime PCR (qRT-PCR) was performed to characterize the specific expression in the tube foot. The results indicated that four miRNAs, including miR-29a, miR-29b, miR-2005 and miR-278-3p, were significantly up-regulated in the tube foot. The target genes of the four specifically expressed miRNAs were predicted in silico and validated by performing qRT-PCR. Gene ontology (GO) and KEGG pathway analyses with the target genes of these four miRNAs were conducted to further understand the regulatory function in the tube foot. This is the first study to profile the miRNA transcriptome of the tube foot in sea cucumber. This work will provide valuable genomic resources to understand the mechanisms of gene regulation in the tube foot, and will be useful to assist the molecular breeding in sea cucumber.
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Affiliation(s)
- Hongdi Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, Alabama, United States of America
| | - Jun Cui
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Chengze Li
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Xuemei Qiu
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, Alabama, United States of America
| | - Xiuli Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
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Abstract
MicroRNAs (miRNAs) are transcriptional and posttranscriptional regulators involved in nearly all known biological processes in distant eukaryotic clades. Their discovery and functional characterization have broadened our understanding of biological regulatory mechanisms in animals and plants. They show both evolutionary conserved and unique features across Metazoa. Here, we present the current status of the knowledge about the role of miRNA in development, growth, and physiology of teleost fishes, in comparison to other vertebrates. Infraclass Teleostei is the most abundant group among vertebrate lineage. Fish are an important component of aquatic ecosystems and human life, being the prolific source of animal proteins worldwide and a vertebrate model for biomedical research. We review miRNA biogenesis, regulation, modifications, and mechanisms of action. Specific sections are devoted to the role of miRNA in teleost development, organogenesis, tissue differentiation, growth, regeneration, reproduction, endocrine system, and responses to environmental stimuli. Each section discusses gaps in the current knowledge and pinpoints the future directions of research on miRNA in teleosts.
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Affiliation(s)
| | - Igor Babiak
- Faculty of Aquaculture and Biosciences, University of Nordland, Bodø, Norway
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42
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Xu WN, Liu WB, Yang WW, Zhang DD, Jiang GZ. Identification and differential expression of hepatopancreas microRNAs in red swamp crayfish fed with emodin diet. FISH & SHELLFISH IMMUNOLOGY 2014; 39:1-7. [PMID: 24780639 DOI: 10.1016/j.fsi.2014.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/20/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
Using high-throughput Illumina Solexa system, the differential miRNA expressions from hepatopancreas in red swamp crayfish (Procambarus clarkii) fed with diets containing 0 (control) and 75 mg emodin kg(-1) (trial) were identified, respectively. As a result, 13,335,928 raw reads from the control sample and 14,938,951 raw reads from the trial sample were obtained while 13,053,344 (98.77%) and 14,517,522 (98.34%) small RNA were identified, respectively. 106 mature miRNAs (belonging to 68 miRNA gene families) were identified. 35 miRNAs displayed significantly differential expressions between two libraries. Of these, comparing to the control library, 6 miRNAs were significantly up-regulated and 29 miRNAs were significantly down-regulated. Moreover, 5 novel miRNAs (2 from control sample, 3 from trial sample) and target genes were predicted. GO analysis suggested that these miRNAs might be involved in innate immune response, growth, metabolism, cellular process, biological regulation and stimulus response. Our knowledge from this study could contribute to a better understanding of the miRNAs roles in regulating innate immune response and the study of miRNA function in crayfish.
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Affiliation(s)
- Wei-Na Xu
- Key Lab of Aquatic Animal Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen-Bin Liu
- Key Lab of Aquatic Animal Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wei-Wei Yang
- Key Lab of Aquatic Animal Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ding-Dong Zhang
- Key Lab of Aquatic Animal Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guang-Zhen Jiang
- Key Lab of Aquatic Animal Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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43
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Campos C, Sundaram AYM, Valente LMP, Conceição LEC, Engrola S, Fernandes JMO. Thermal plasticity of the miRNA transcriptome during Senegalese sole development. BMC Genomics 2014; 15:525. [PMID: 24966054 PMCID: PMC4097167 DOI: 10.1186/1471-2164-15-525] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 06/17/2014] [Indexed: 12/17/2022] Open
Abstract
Background Several miRNAs are known to control myogenesis in vertebrates. Some of them are specifically expressed in muscle while others have a broader tissue expression but are still involved in establishing the muscle phenotype. In teleosts, water temperature markedly affects embryonic development and larval growth. It has been previously shown that higher embryonic temperatures promoted faster development and increased size of Senegalese sole (Solea senegalensis) larvae relatively to a lower temperature. The role of miRNAs in thermal-plasticity of growth is hitherto unknown. Hence, we have used high-throughput SOLiD sequencing to determine potential changes in the miRNA transcriptome in Senegalese sole embryos that were incubated at 15°C or 21°C until hatching and then reared at a common temperature of 21°C. Results We have identified 320 conserved miRNAs in Senegalese sole, of which 48 had not been previously described in teleosts. mir-17a-5p, mir-26a, mir-130c, mir-206-3p, mir-181a-5p, mir-181a-3p and mir-199a-5p expression levels were further validated by RT- qPCR. The majority of miRNAs were dynamically expressed during early development, with peaks of expression at pre-metamorphosis or metamorphosis. Also, a higher incubation temperature (21°C) was associated with expression of some miRNAs positively related with growth (e.g., miR-17a, miR-181-5p and miR-206) during segmentation and at hatching. Target prediction revealed that these miRNAs may regulate myogenesis through MAPK and mTOR pathways. Expression of miRNAs involved in lipid metabolism and energy production (e.g., miR-122) also differed between temperatures. A miRNA that can potentially target calpain (miR-181-3p), and therefore negatively regulate myogenesis, was preferentially expressed during segmentation at 15°C compared to 21°C. Conclusions Temperature has a strong influence on expression of miRNAs during embryonic and larval development in fish. Higher expression levels of miR-17a, miR-181-5p and miR-206-3p and down-regulation of miR-181a-3p at 21°C may promote myogenesis and are in agreement with previous studies in Senegalese sole, which reported enhanced growth at higher embryonic temperatures compared to 15°C. Moreover, miRNAs involved in lipid metabolism and energy production may also contribute to increased larval growth at 21°C compared to 15°C. Taken together, our data indicate that miRNAs may play a role in temperature-induced phenotypic plasticity of growth in teleosts. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-525) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Jorge M O Fernandes
- Faculty of Biosciences and Aquaculture, University of Nordland, Bodø 8049, Norway.
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44
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Yi S, Lu D, Peng W, Wang T, Zhang Y, Lin H. Differential expression profiling of spleen microRNAs in response to two distinct type II interferons in Tetraodon nigroviridis. PLoS One 2014; 9:e96336. [PMID: 24800866 PMCID: PMC4011704 DOI: 10.1371/journal.pone.0096336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 04/04/2014] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs are endogenous, small non-coding RNAs approximately 18-26 nucleotides in length that regulate target gene expression at the post-transcription level. Interferon-γ (IFN-γ) is a Th1 cytokine that is involved in both the innate and adaptive immune responses. We previously identified two IFN-γ genes in green-spotted puffer fish (Tetraodon nigroviridis). To determine whether miRNAs participate in IFN-γ-related immune responses, T. nigroviridis spleen cells were treated with recombinant IFN-γ isoforms, and a Solexa high-throughput sequencing method was used to identify miRNAs. In total, 1,556, 1,538 and 1,573 miRNAs were found in the three samples, and differentially expressed miRNAs were determined. In total, 398 miRNAs were differentially expressed after rIFN-γ1 treatment, and 438 miRNAs were differentially expressed after rIFN-γ2 treatment; additionally, 403 miRNAs were differentially expressed between the treatment groups. Ten differentially expressed miRNAs were chosen for validation using qRT-PCR. Target genes for the differentially expressed miRNAs were predicted, and GO and KEGG analyses were performed. This study provides basic knowledge regarding fish IFN-γ-induced miRNAs and offers clues for further studies into the mechanisms underlying fish IFN-γ-mediated immune responses.
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Affiliation(s)
- Shibai Yi
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Danqi Lu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
- * E-mail: (DL); (HL)
| | - Wan Peng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Ting Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
- * E-mail: (DL); (HL)
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45
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Mennigen JA, Plagnes-Juan E, Figueredo-Silva CA, Seiliez I, Panserat S, Skiba-Cassy S. Acute endocrine and nutritional co-regulation of the hepatic omy-miRNA-122b and the lipogenic gene fas in rainbow trout, Oncorhynchus mykiss. Comp Biochem Physiol B Biochem Mol Biol 2014; 169:16-24. [DOI: 10.1016/j.cbpb.2013.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/23/2013] [Accepted: 12/04/2013] [Indexed: 12/25/2022]
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Trattner S, Vestergren AS. Tissue distribution of selected micro
RNA
in Atlantic salmon. EUR J LIPID SCI TECH 2013. [DOI: 10.1002/ejlt.201200428] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sofia Trattner
- Department of Wildlife, Fish, and Environmental StudiesSwedish University of Agricultural Sciences (SLU)SLUUmeåSweden
- Department of Food ScienceSwedish University of Agricultural Sciences (SLU), Uppsala BioCenterUppsalaSweden
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Knutsen E, Fiskaa T, Ursvik A, Jørgensen TE, Perander M, Lund E, Seternes OM, Johansen SD, Andreassen M. Performance comparison of digital microRNA profiling technologies applied on human breast cancer cell lines. PLoS One 2013; 8:e75813. [PMID: 24116077 PMCID: PMC3793004 DOI: 10.1371/journal.pone.0075813] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 08/20/2013] [Indexed: 12/21/2022] Open
Abstract
MicroRNA profiling represents an important first-step in deducting individual RNA-based regulatory function in a cell, tissue, or at a specific developmental stage. Currently there are several different platforms to choose from in order to make the initial miRNA profiles. In this study we investigate recently developed digital microRNA high-throughput technologies. Four different platforms were compared including next generation SOLiD ligation sequencing and Illumina HiSeq sequencing, hybridization-based NanoString nCounter, and miRCURY locked nucleic acid RT-qPCR. For all four technologies, full microRNA profiles were generated from human cell lines that represent noninvasive and invasive tumorigenic breast cancer. This study reports the correlation between platforms, as well as a more extensive analysis of the accuracy and sensitivity of data generated when using different platforms and important consideration when verifying results by the use of additional technologies. We found all the platforms to be highly capable for microRNA analysis. Furthermore, the two NGS platforms and RT-qPCR all have equally high sensitivity, and the fold change accuracy is independent of individual miRNA concentration for NGS and RT-qPCR. Based on these findings we propose new guidelines and considerations when performing microRNA profiling.
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Affiliation(s)
- Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Tonje Fiskaa
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Anita Ursvik
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Tor Erik Jørgensen
- Marine Genomics group, Faculty of Biosciences and Aquaculture, University of Nordland, Bodø, Norway
| | - Maria Perander
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Eiliv Lund
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Ole Morten Seternes
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Steinar D. Johansen
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- Marine Genomics group, Faculty of Biosciences and Aquaculture, University of Nordland, Bodø, Norway
- * E-mail: (SJ); (MA)
| | - Morten Andreassen
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- * E-mail: (SJ); (MA)
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de Oliveira LFV, Christoff AP, Margis R. isomiRID: a framework to identify microRNA isoforms. Bioinformatics 2013; 29:2521-3. [DOI: 10.1093/bioinformatics/btt424] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bizuayehu TT, Fernandes JMO, Johansen SD, Babiak I. Characterization of novel precursor miRNAs using next generation sequencing and prediction of miRNA targets in Atlantic halibut. PLoS One 2013; 8:e61378. [PMID: 23626677 PMCID: PMC3634072 DOI: 10.1371/journal.pone.0061378] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 03/07/2013] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND microRNAs (miRNAs) are implicated in regulation of many cellular processes. miRNAs are processed to their mature functional form in a step-wise manner by multiple proteins and cofactors in the nucleus and cytoplasm. Many miRNAs are conserved across vertebrates. Mature miRNAs have recently been characterized in Atlantic halibut (Hippoglossus hippoglossus L.). The aim of this study was to identify and characterize precursor miRNA (pre-miRNAs) and miRNA targets in this non-model flatfish. Discovery of miRNA precursor forms and targets in non-model organisms is difficult because of limited source information available. Therefore, we have developed a methodology to overcome this limitation. METHODS Genomic DNA and small transcriptome of Atlantic halibut were sequenced using Roche 454 pyrosequencing and SOLiD next generation sequencing (NGS), respectively. Identified pre- miRNAs were further validated with reverse-transcription PCR. miRNA targets were identified using miRanda and RNAhybrid target prediction tools using sequences from public databases. Some of miRNA targets were also identified using RACE-PCR. miRNA binding sites were validated with luciferase assay using the RTS34st cell line. RESULTS We obtained more than 1.3 M and 92 M sequence reads from 454 genomic DNA sequencing and SOLiD small RNA sequencing, respectively. We identified 34 known and 9 novel pre-miRNAs. We predicted a number of miRNA target genes involved in various biological pathways. miR-24 binding to kisspeptin 1 receptor-2 (kiss1-r2) was confirmed using luciferase assay. CONCLUSION This study demonstrates that identification of conserved and novel pre-miRNAs in a non-model vertebrate lacking substantial genomic resources can be performed by combining different next generation sequencing technologies. Our results indicate a wide conservation of miRNA precursors and involvement of miRNA in multiple regulatory pathways, and provide resources for further research on miRNA in non-model animals.
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Affiliation(s)
| | | | - Steinar D. Johansen
- Faculty of Biosciences and Aquaculture, University of Nordland, Bodø, Norway
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Igor Babiak
- Faculty of Biosciences and Aquaculture, University of Nordland, Bodø, Norway
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Ribas L, Pardo BG, Fernández C, Alvarez-Diós JA, Gómez-Tato A, Quiroga MI, Planas JV, Sitjà-Bobadilla A, Martínez P, Piferrer F. A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus). BMC Genomics 2013; 14:180. [PMID: 23497389 PMCID: PMC3700835 DOI: 10.1186/1471-2164-14-180] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 02/27/2013] [Indexed: 02/02/2023] Open
Abstract
Background Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry. Results Expressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immune-related tissues after several parasitic challenges. The resulting database (“Turbot 2 database”) was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences (“Turbot 3 database”), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot (AR, AMH, SRY-related genes, CYP19A, ZPGs, STAR FSHR, etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified (BCL, TRAF, NCK, CD28 and TOLLIP, among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50–90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single nucleotide polymorphisms (SNPs) were also compiled. Further, 2,976 putative natural antisense transcripts (NATs) including microRNAs were also identified. Conclusions The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs.
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Affiliation(s)
- Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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