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Castro Colabianchi AM, González Pérez NG, Franchini LF, López SL. A maternal dorsoventral prepattern revealed by an asymmetric distribution of ventralizing molecules before fertilization in Xenopus laevis. Front Cell Dev Biol 2024; 12:1365705. [PMID: 38572484 PMCID: PMC10987785 DOI: 10.3389/fcell.2024.1365705] [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: 01/04/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
The establishment of the embryonic dorsoventral axis in Xenopus occurs when the radial symmetry around the egg's animal-vegetal axis is broken to give rise to the typical symmetry of Bilaterians. We have previously shown that the Notch1 protein is ventrally enriched during early embryogenesis in Xenopus laevis and zebrafish and exerts ventralizing activity through β-Catenin destabilization and the positive regulation of ventral center genes in X. laevis. These findings led us to further investigate when these asymmetries arise. In this work, we show that the asymmetrical distribution of Notch1 protein and mRNA precedes cortical rotation and even fertilization in X. laevis. Moreover, we found that in unfertilized eggs transcripts encoded by the ventralizing gene bmp4 are also asymmetrically distributed in the animal hemisphere and notch1 transcripts accumulate consistently on the same side of the eccentric maturation point. Strikingly, a Notch1 asymmetry orthogonal to the animal-vegetal axis appears during X. laevis oogenesis. Thus, we show for the first time a maternal bias in the distribution of molecules that are later involved in ventral patterning during embryonic axialization, strongly supporting the hypothesis of a dorsoventral prepattern or intrinsic bilaterality of Xenopus eggs before fertilization.
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Affiliation(s)
- Aitana M. Castro Colabianchi
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Biología Celular e Histología / 1° U.A. Departamento de Histología, Embriología, Biología Celular y Genética, Laboratorio de Embriología Molecular “Prof. Dr. Andrés E. Carrasco”, Buenos Aires, Argentina
- CONICET–Universidad de Buenos Aires, Instituto de Biología Celular y Neurociencias “Prof. E. De Robertis” (IBCN), Buenos Aires, Argentina
| | - Nicolás G. González Pérez
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Biología Celular e Histología / 1° U.A. Departamento de Histología, Embriología, Biología Celular y Genética, Laboratorio de Embriología Molecular “Prof. Dr. Andrés E. Carrasco”, Buenos Aires, Argentina
- CONICET–Universidad de Buenos Aires, Instituto de Biología Celular y Neurociencias “Prof. E. De Robertis” (IBCN), Buenos Aires, Argentina
| | - Lucía F. Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Silvia L. López
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Biología Celular e Histología / 1° U.A. Departamento de Histología, Embriología, Biología Celular y Genética, Laboratorio de Embriología Molecular “Prof. Dr. Andrés E. Carrasco”, Buenos Aires, Argentina
- CONICET–Universidad de Buenos Aires, Instituto de Biología Celular y Neurociencias “Prof. E. De Robertis” (IBCN), Buenos Aires, Argentina
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2
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Gong S, McLamb F, Shea D, Vu JP, Vasquez MF, Feng Z, Bozinovic K, Hirata KK, Gersberg RM, Bozinovic G. Toxicity assessment of hexafluoropropylene oxide-dimer acid on morphology, heart physiology, and gene expression during zebrafish (Danio rerio) development. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:32320-32336. [PMID: 36462083 PMCID: PMC10017623 DOI: 10.1007/s11356-022-24542-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/25/2022] [Indexed: 05/25/2023]
Abstract
Hexafluoropropylene oxide-dimer acid (HFPO-DA) is one of the emerging replacements for the "forever" carcinogenic and toxic long-chain PFAS. HFPO-DA is a polymerization aid used for manufacturing fluoropolymers, whose global distribution and undetermined toxic properties are a concern regarding human and ecological health. To assess embryotoxic potential, zebrafish embryos were exposed to HFPO-DA at concentrations of 0.5-20,000 mg/L at 24-, 48-, and 72-h post-fertilization (hpf). Heart rate increased significantly in embryos exposed to 2 mg/L and 10 mg/L HFPO-DA across all time points. Spinal deformities and edema phenotypes were evident among embryos exposed to 1000-16,000 mg/L HFPO-DA at 72 hpf. A median lethal concentration (LC50) was derived as 7651 mg/L at 72 hpf. Shallow RNA sequencing analysis of 9465 transcripts identified 38 consistently differentially expressed genes at 0.5 mg/L, 1 mg/L, 2 mg/L, and 10 mg/L HFPO-DA exposures. Notably, seven downregulated genes were associated with visual response, and seven upregulated genes were expressed in or regulated the cardiovascular system. This study identifies biological targets and molecular pathways affected during animal development by an emerging, potentially problematic, and ubiquitous industrial chemical.
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Affiliation(s)
- Sylvia Gong
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
- Division of Extended Studies, University of California San Diego, La Jolla, CA, 92093-0355, USA
- School of Public Health, San Diego State University, San Diego, CA, USA
| | - Flannery McLamb
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
- Division of Extended Studies, University of California San Diego, La Jolla, CA, 92093-0355, USA
| | | | - Jeanne P Vu
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
- Division of Extended Studies, University of California San Diego, La Jolla, CA, 92093-0355, USA
- School of Public Health, San Diego State University, San Diego, CA, USA
| | - Miguel F Vasquez
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
- Division of Extended Studies, University of California San Diego, La Jolla, CA, 92093-0355, USA
| | - Zuying Feng
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
- School of Public Health, San Diego State University, San Diego, CA, USA
| | - Kesten Bozinovic
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
- Division of Extended Studies, University of California San Diego, La Jolla, CA, 92093-0355, USA
- Graduate School of Arts and Sciences, Georgetown University, Washington, DC, USA
| | - Ken K Hirata
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA
- Division of Extended Studies, University of California San Diego, La Jolla, CA, 92093-0355, USA
| | | | - Goran Bozinovic
- Boz Life Science Research and Teaching Institute, San Diego, CA, USA.
- School of Public Health, San Diego State University, San Diego, CA, USA.
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093-0355, USA.
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3
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Zhou C, Zhao W, Zhang S, Ma J, Sultan Y, Li X. High-throughput transcriptome sequencing reveals the key stages of cardiovascular development in zebrafish embryos. BMC Genomics 2022; 23:587. [PMID: 35964013 PMCID: PMC9375324 DOI: 10.1186/s12864-022-08808-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/25/2022] [Indexed: 11/15/2022] Open
Abstract
Background The cardiovascular developmental process is a tightly regulated network involving multiple genes. The current understanding of the molecular mechanism behind cardiovascular development is insufficient and requires further research. Results Transcriptome sequencing of three developmental stages in zebrafish embryos was performed and revealed three key cardiovascular developmental stages. Then, the differentially expressed genes (DEGs) involved in cardiovascular development were screened out. The three developmental stages were 18 (T1), 24 (T2), and 42 h post fertilization (hpf) (T3), and the three stages were confirmed by detecting differences in expression between cardiomyocyte and endothelial marker genes (cmlc2, fli1) using in situ hybridization, which represents the characteristics of cardiovascular development. Thousands of DEGs were identified using transcriptome analysis. Of them, 2605 DEGs were in T1-vs-T2, including 2003 up-regulated and 602 down-regulated genes, 6446 DEGs were in T1-vs-T3, consisting of 4608 up-regulated and 1838 down-regulated genes, and 3275 DEGs were in T2-vs-T3, including 2420 up-regulated and 855 down-regulated genes. There were 644 common DEGs and 167 common five-fold higher differentially expressed genes (HDEGs) identified, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). Significant differences was observed in the levels of gene expression among different developmental stages in multiple GO terms and KEGG pathways, such as cell migration to the midline involved in heart development, cardiovascular system development, circulatory system process for biological processes of GO terms; and cardiac muscle contraction, adrenergic signaling in cardiomyocytes for KEGG pathways. These results demonstrated that these three stages were important period for the development of the cardiovascular system. Lastly, we used quantitative real-time PCR (qPCR) to validate the reliability of RNA-sequencing by selecting 21 DEGs. Conclusions These results demonstrated that these three stages represented the important periods for cardiovascular system development of zebrafish and some candidate genes was obtained and provided a solid foundation for additional functional studies of the DEGs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08808-x.
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Affiliation(s)
- Chune Zhou
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Wei Zhao
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Shuqiang Zhang
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Junguo Ma
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yousef Sultan
- Department of Food Toxicology and Contaminants, National Research Centre, Dokki, Cairo, 12622, Egypt
| | - Xiaoyu Li
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China.
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4
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Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis. FISHES 2022. [DOI: 10.3390/fishes7030115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Early development, when many important developmental events occur, is a critical period for fish. However, research on the early development of clearhead icefish is very limited, especially in molecular research. In this study, we aimed to explore the dynamic changes in the biological functions of five key periods in clearhead icefish early development, namely the YL (embryonic), PM (first day after hatching), KK (fourth day after hatching), LC (seventh day after hatching), and SL (tenth day after hatching) stages, through transcriptome sequencing and different analysis strategies. A trend expression analysis and an enrichment analysis revealed that the expression ofgenes encoding G protein-coupled receptors and their ligands, i.e., prss1_2_3, pomc, npy, npb, sst, rln3, crh, gh, and prl that are associated with digestion and feeding regulation gradually increased during early development. In addition, a weighted gene co-expression network analysis (WGCNA) showed that eleven modules were significantly associated with early development, among which nine modules were significantly positively correlated. Through the enrichment analysis and hub gene identification results of these nine modules, it was found that the pathways related to eye, bone, and heart development were significantly enriched in the YL stage, and the ccnd2, seh1l, kdm6a, arf4, and ankrd28 genes that are associated with cell proliferation and differentiation played important roles in these developmental processes; the pak3, dlx3, dgat2, and tas1r1 genes that are associated with jaw and tooth development, TG (triacylglycerol) synthesis, and umami amino acid receptors were identified as hub genes for the PM stage; the pathways associated with aerobic metabolism and unsaturated fatty acid synthesis were significantly enriched in the KK stage, with the foxk, slc13a2_3_5, ndufa5, and lsc2 genes playing important roles; the pathways related to visual perception were significantly enriched in the LC stage; and the bile acid biosynthetic and serine-type peptidase activity pathways were significantly enriched in the SL stage. These results provide a more detailed understanding of the processes of early development of clearhead icefish.
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5
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Huang T, Gu W, Liu E, Zhang L, Dong F, He X, Jiao W, Li C, Wang B, Xu G. Screening and Validation of p38 MAPK Involved in Ovarian Development of Brachymystax lenok. Front Vet Sci 2022; 9:752521. [PMID: 35252414 PMCID: PMC8889577 DOI: 10.3389/fvets.2022.752521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Brachymystax lenok (lenok) is a rare cold-water fish native to China that is of high meat quality. Its wild population has declined sharply in recent years, and therefore, exploring the molecular mechanisms underlying the development and reproduction of lenoks for the purposes of artificial breeding and genetic improvement is necessary. The lenok comparative transcriptome was analyzed by combining single molecule, real-time, and next generation sequencing (NGS) technology. Differentially expressed genes (DEGs) were identified in five tissues (head kidney, spleen, liver, muscle, and gonad) between immature [300 days post-hatching (dph)] and mature [three years post-hatching (ph)] lenoks. In total, 234,124 and 229,008 full-length non-chimeric reads were obtained from the immature and mature sequencing data, respectively. After NGS correction, 61,405 and 59,372 non-redundant transcripts were obtained for the expression level and pathway enrichment analyses, respectively. Compared with the mature group, 719 genes with significantly increased expression and 1,727 genes with significantly decreased expression in all five tissues were found in the immature group. Furthermore, DEGs and pathways involved in the endocrine system and gonadal development were identified, and p38 mitogen-activated protein kinases (MAPKs) were identified as potentially regulating gonadal development in lenok. Inhibiting the activity of p38 MAPKs resulted in abnormal levels of gonadotropin-releasing hormone, follicle-stimulating hormone, and estradiol, and affected follicular development. The full-length transcriptome data obtained in this study may provide a valuable reference for the study of gene function, gene expression, and evolutionary relationships in B. lenok and may illustrate the basic regulatory mechanism of ovarian development in teleosts.
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Affiliation(s)
- Tianqing Huang
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Wei Gu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Enhui Liu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Lanlan Zhang
- Heilongjiang Province General Station of Aquatic Technology Promotion, Harbin, China
| | - Fulin Dong
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Xianchen He
- Heilongjiang Aquatic Animal Resource Conservation Center, Harbin, China
| | - Wenlong Jiao
- Gansu Fisheries Research Institute, Lanzhou, China
| | - Chunyu Li
- Xinjiang Tianyun Organic Agriculture Co., Yili Group, Hohhot, China
| | - Bingqian Wang
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- *Correspondence: Bingqian Wang
| | - Gefeng Xu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Gefeng Xu
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6
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Chan ME, Bhamidipati PS, Goldsby HJ, Hintze A, Hofmann HA, Young RL. Comparative Transcriptomics Reveals Distinct Patterns of Gene Expression Conservation through Vertebrate Embryogenesis. Genome Biol Evol 2021; 13:6319027. [PMID: 34247223 PMCID: PMC8358226 DOI: 10.1093/gbe/evab160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/12/2022] Open
Abstract
Despite life's diversity, studies of variation often remind us of our shared evolutionary past. Abundant genome sequencing and analyses of gene regulatory networks illustrate that genes and entire pathways are conserved, reused, and elaborated in the evolution of diversity. Predating these discoveries, 19th-century embryologists observed that though morphology at birth varies tremendously, certain stages of vertebrate embryogenesis appear remarkably similar across vertebrates. In the mid to late 20th century, anatomical variability of early and late-stage embryos and conservation of mid-stages embryos (the "phylotypic" stage) was named the hourglass model of diversification. This model has found mixed support in recent analyses comparing gene expression across species possibly owing to differences in species, embryonic stages, and gene sets compared. We compare 186 microarray and RNA-seq data sets covering embryogenesis in six vertebrate species. We use an unbiased clustering approach to group stages of embryogenesis by transcriptomic similarity and ask whether gene expression similarity of clustered embryonic stages deviates from a null expectation. We characterize expression conservation patterns of each gene at each evolutionary node after correcting for phylogenetic nonindependence. We find significant enrichment of genes exhibiting early conservation, hourglass, late conservation patterns in both microarray and RNA-seq data sets. Enrichment of genes showing patterned conservation through embryogenesis indicates diversification of embryogenesis may be temporally constrained. However, the circumstances under which each pattern emerges remain unknown and require both broad evolutionary sampling and systematic examination of embryogenesis across species.
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Affiliation(s)
- Megan E Chan
- Department of Integrative Biology, The University of Texas at Austin, Texas, USA.,Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Texas, USA
| | - Pranav S Bhamidipati
- Department of Integrative Biology, The University of Texas at Austin, Texas, USA.,Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Texas, USA
| | - Heather J Goldsby
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Arend Hintze
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Hans A Hofmann
- Department of Integrative Biology, The University of Texas at Austin, Texas, USA.,Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Texas, USA.,Institute for Cellular and Molecular Biology, Institute for Neuroscience, The University of Texas at Austin, Texas, USA
| | - Rebecca L Young
- Department of Integrative Biology, The University of Texas at Austin, Texas, USA.,Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Texas, USA
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7
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Zhang W, Li S, Li K, Li LI, Yin P, Tong G. The role of protein arginine methyltransferase 7 in human developmentally arrested embryos cultured in vitro. Acta Biochim Biophys Sin (Shanghai) 2021; 53:925-932. [PMID: 34041522 DOI: 10.1093/abbs/gmab068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
Human embryos of in vitro fertilization (IVF) are often susceptible to developmental arrest, which greatly reduces the efficiency of IVF treatment. In recent years, it has been found that protein arginine methyltransferase 7 (PRMT7) plays an important role in the process of early embryonic development. However, not much is known about the relationship between PRMT7 and developmentally arrested embryos. The role of PRMT7 in developmentally arrested embryos was thus investigated in this study. Discarded human embryos from IVF were collected for experimental materials. Quantitative real-time polymerase chain reaction (qRT-PCR) and confocal analyses were used to identify PRMT7 mRNA and protein levels in early embryos at different developmental stages, as well as changes in the methylation levels of H4R3me2s. Additionally, PRMT7 was knocked down in the developmentally arrested embryos to observe the further development of these embryos. Our results demonstrated that PRMT7 mRNA and protein levels in arrested embryos were significantly increased compared with those in control embryos; meanwhile, the methylation levels of H4R3me2s in arrested embryos were also increased significantly. Knockdown of PRMT7 could rescue partially developmentally arrested embryos, and even individual developmentally arrested embryos could develop into blastocysts. In conclusion, over-expression of PRMT7 disrupts the early embryo development process, leading to early embryos developmental arrest, but these developmentally arrested defects could be partially rescued by knockdown of the PRMT7 protein.
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Affiliation(s)
- Wuwen Zhang
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shifeng Li
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Li
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - L i Li
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ping Yin
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guoqing Tong
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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8
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Mignani L, Zizioli D, Borsani G, Monti E, Finazzi D. The Downregulation of c19orf12 Negatively Affects Neuronal and Musculature Development in Zebrafish Embryos. Front Cell Dev Biol 2021; 8:596069. [PMID: 33425903 PMCID: PMC7785858 DOI: 10.3389/fcell.2020.596069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial membrane Protein Associated Neurodegeneration (MPAN) is a rare genetic disorder due to mutations in C19orf12 gene. In most cases, the disorder is transmitted as an autosomal recessive trait and the main clinical features are progressive spastic para/tetraparesis, dystonia, motor axonal neuropathy, parkinsonisms, psychiatric symptoms, and optic atrophy. Besides iron accumulation in the globus pallidus and substantia nigra, the neuropathology shows features also observed in Parkinson’s Disease brains, such as α-synuclein-positive Lewy bodies and hyperphosphorylated tau. Mutations in the gene have been found in other neurodegenerative disorders, including PD, hereditary spastic paraplegia, pallido-pyramidal syndrome, and amyotrophic lateral sclerosis. The biological function of C19orf12 gene is poorly defined. In humans, it codes for two protein isoforms: the longer one is present in mitochondria, endoplasmic reticulum, and contact regions between mitochondria and ER. Mutations in the gene appear to be linked to defects in mitochondrial activity, lipid metabolism and autophagy/mitophagy. To increase the available tools for the investigation of MPAN pathogenesis, we generated a new animal model in zebrafish embryos. The zebrafish genome contains four co-orthologs of human C19orf12. One of them, located on chromosome 18, is expressed at higher levels at early stages of development. We downregulated its expression by microinjecting embryos with a specific ATG-blocking morpholino, and we analyzed embryonal development. Most embryos showed morphological defects such as unsettled brain morphology, with smaller head and eyes, reduced yolk extension, tilted and thinner tail. The severity of the defects progressively increased and all injected embryos died within 7 days post fertilization. Appropriate controls confirmed the specificity of the observed phenotype. Changes in the expression and distribution of neural markers documented a defective neuronal development, particularly evident in the eyes, the optic tectum, the midbrain-hindbrain boundary; Rohon Beard and dorsal root ganglia neurons were also affected. Phalloidin staining evidenced a significant perturbation of musculature formation that was associated with defective locomotor behavior. These data are consistent with the clinical features of MPAN and support the validity of the model to investigate the pathogenesis of the disease and evaluate molecules with potential therapeutic effect.
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Affiliation(s)
- Luca Mignani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Daniela Zizioli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giuseppe Borsani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Eugenio Monti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Dario Finazzi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.,Laboratory of Clinical Chemistry, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili di Brescia, Brescia, Italy
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9
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Boezio GL, Bensimon-Brito A, Piesker J, Guenther S, Helker CS, Stainier DY. Endothelial TGF-β signaling instructs smooth muscle cell development in the cardiac outflow tract. eLife 2020; 9:57603. [PMID: 32990594 PMCID: PMC7524555 DOI: 10.7554/elife.57603] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/09/2020] [Indexed: 12/14/2022] Open
Abstract
The development of the cardiac outflow tract (OFT), which connects the heart to the great arteries, relies on a complex crosstalk between endothelial (ECs) and smooth muscle (SMCs) cells. Defects in OFT development can lead to severe malformations, including aortic aneurysms, which are frequently associated with impaired TGF-β signaling. To better understand the role of TGF-β signaling in OFT formation, we generated zebrafish lacking the TGF-β receptor Alk5 and found a strikingly specific dilation of the OFT: alk5-/- OFTs exhibit increased EC numbers as well as extracellular matrix (ECM) and SMC disorganization. Surprisingly, endothelial-specific alk5 overexpression in alk5-/- rescues the EC, ECM, and SMC defects. Transcriptomic analyses reveal downregulation of the ECM gene fibulin-5, which when overexpressed in ECs ameliorates OFT morphology and function. These findings reveal a new requirement for endothelial TGF-β signaling in OFT morphogenesis and suggest an important role for the endothelium in the etiology of aortic malformations.
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Affiliation(s)
- Giulia Lm Boezio
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Anabela Bensimon-Brito
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Janett Piesker
- Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Guenther
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Christian Sm Helker
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Didier Yr Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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10
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Liu Y, Zhu Z, Ho IHT, Shi Y, Li J, Wang X, Chan MTV, Cheng CHK. Genetic Deletion of miR-430 Disrupts Maternal-Zygotic Transition and Embryonic Body Plan. Front Genet 2020; 11:853. [PMID: 32849832 PMCID: PMC7417628 DOI: 10.3389/fgene.2020.00853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/13/2020] [Indexed: 11/13/2022] Open
Abstract
MiR-430 is considered an important regulator during embryonic development, but genetic loss-of-function study is still lacking. Here we demonstrated that genetic deletion of the miR-430 cluster resulted in developmental defects in cell movement, germ layer specification, axis patterning and organ progenitor formation in zebrafish. Transcriptome analysis indicated that the maternally provided transcripts were not properly degraded whereas the zygotic genome expressed genes were not fully activated in the miR-430 mutants. We further found that a reciprocal regulatory loop exists between miR-430 and maternally provided transcripts: the maternally provided transcripts (Nanog, Dicer1, Dgcr8, and AGOs) are required for miR-430 biogenesis and function, whereas miR-430 is required for the clearance of these maternally provided transcripts. These data provide the first genetic evidence that miR-430 is required for maternal-zygotic transition and subsequent establishment of embryonic body plan.
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Affiliation(s)
- Yun Liu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Zelong Biological Technology Limited Cooperation, Shenzhen, China
| | - Zeyao Zhu
- Department of Anatomy, Histology and Developmental Biology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China
| | - Idy H T Ho
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Anesthesia and Intensive Care, Prince of Wales Hospital, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yujian Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jianzhen Li
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Xia Wang
- Department of Anatomy, Histology and Developmental Biology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China
| | - Matthew T V Chan
- Department of Anesthesia and Intensive Care, Prince of Wales Hospital, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Christopher H K Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
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11
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Varga M, Csályi K, Bertyák I, Menyhárd DK, Poole RJ, Cerveny KL, Kövesdi D, Barátki B, Rouse H, Vad Z, Hawkins TA, Stickney HL, Cavodeassi F, Schwarz Q, Young RM, Wilson SW. Tissue-Specific Requirement for the GINS Complex During Zebrafish Development. Front Cell Dev Biol 2020; 8:373. [PMID: 32548116 PMCID: PMC7270345 DOI: 10.3389/fcell.2020.00373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022] Open
Abstract
Efficient and accurate DNA replication is particularly critical in stem and progenitor cells for successful proliferation and survival. The replisome, an amalgam of protein complexes, is responsible for binding potential origins of replication, unwinding the double helix, and then synthesizing complimentary strands of DNA. According to current models, the initial steps of DNA unwinding and opening are facilitated by the CMG complex, which is composed of a GINS heterotetramer that connects Cdc45 with the mini-chromosome maintenance (Mcm) helicase. In this work, we provide evidence that in the absence of GINS function DNA replication is cell autonomously impaired, and we also show that gins1 and gins2 mutants exhibit elevated levels of apoptosis restricted to actively proliferating regions of the central nervous system (CNS). Intriguingly, our results also suggest that the rapid cell cycles during early embryonic development in zebrafish may not require the function of the canonical GINS complex as neither zygotic Gins1 nor Gins2 isoforms seem to be present during these stages.
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Affiliation(s)
- Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary.,Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Kitti Csályi
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - István Bertyák
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dóra K Menyhárd
- HAS-ELTE Protein Modeling Research Group and Laboratory of Structural Chemistry and Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Richard J Poole
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Kara L Cerveny
- Biology Department, Reed College, Portland, OR, United States
| | - Dorottya Kövesdi
- Office of Supported Research Groups of the Hungarian Academy of Sciences, Budapest, Hungary.,Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Balázs Barátki
- Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Hannah Rouse
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Zsuzsa Vad
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Thomas A Hawkins
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Heather L Stickney
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Florencia Cavodeassi
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom.,Institute of Medical and Biomedical Education, St. George's University of London, London, United Kingdom
| | - Quenten Schwarz
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Rodrigo M Young
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
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12
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Fu J, Zhu W, Wang L, Luo M, Song F, Dong Z. Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis). BMC Genomics 2019; 20:781. [PMID: 31660854 PMCID: PMC6819325 DOI: 10.1186/s12864-019-6181-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/11/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Early development is a key process of the life history of fish. However, the relationship between the transcriptome and the dynamic regulation of early development is still uncharacterized in the bighead carp (Hypophthalmichthys nobilis). In the present study, we performed transcriptome analysis of six development stages in H. nobilis, aiming to understand the dynamic molecular regulation of early development in this fish. RESULTS A total of 76,573 unigenes were assembled from clean sequence reads, with an average length of 1768 base. Among which, 41,742 (54.54%) unigenes were annotated to public protein databases, and an additional 59,014 simple sequence repeat (SSR) loci were identified among the unigenes. Furthermore, 30,199 differentially expressed transcripts (DETs) (fold change > 4 or < 0.25, and the false discovery rate FDR < 0.01) were observed in comparisons between the adjacent developmental stages, and nine expression patterns (profiles) were simulated using series-cluster analysis across six developmental stages. The unigenes expression level markedly increased after the DS1 stage (early blastula), and the numbers of DETs gradually decreased during subsequent development. The largest transcriptomic change (up- or down-regulated) was detected during the period from DS1 to DS2 (6-somite stage), which was enriched for many biological processes and metabolic pathways related to maternal to zygotic transition (MZT). Distinctly protein-protein interaction (PPI) networks were plotted for DETs during the period from DS1 to DS2. The genes (or proteins) from the same pathways were integrated together, and showed with obvious co-regulation patterns. In the series-cluster analysis, a remarkable profile of gene expression (profile_48) was identified that is probably related to the hatching during H. nobilis development, and the strict co-expression of a hatching enzyme gene (hce1) with 33 other annotated genes was identified from this profile. CONCLUSIONS The results indicated that strict dynamic regulation occurs during the early development in H. nobilis, especially in embryogenesis before hatching. This study provides valuable new information and transcriptomic resources related to H. nobilis early development, and for certain events such as MZT and hatching.
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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, 214081, 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, 214081, 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, 214081, China
| | - Mingkun Luo
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Feibiao Song
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, 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, 214081, China.
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13
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Zhang X, Li X, Li R, Zhang Y, Li Y, Li S. Transcriptomic profile of early zebrafish PGCs by single cell sequencing. PLoS One 2019; 14:e0220364. [PMID: 31412047 PMCID: PMC6693734 DOI: 10.1371/journal.pone.0220364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/15/2019] [Indexed: 12/30/2022] Open
Abstract
Single cell RNA-seq is a powerful and sensitive way to capture the genome-wide gene expression. Here, single cell RNA-seq was utilized to study the transcriptomic profile of early zebrafish PGCs (primordial germ cells) at three different developmental stages. The three stages were 6, 11 and 24 hpf (hours post fertilization). For each developmental stage, three zebrafish PGCs from one embryo were collected, and 9 samples in total were used in this experiment. Single cell RNA-seq results showed that 5099–7376 genes were detected among the 9 samples, and the number of expressed genes decreased as development progressed. Based on the gene expression pattern, samples from 6 and 11 hpf clustered closely, while samples from 24 hpf were more dispersed. By WGCNA (weighted gene co-expression network analysis), the two biggest modules that had inverse gene expression patterns were found to be related to PGC formation or migration. Functional enrichment analysis for these two modules showed that PGCs mainly conducted migration and cell division in early development (6/11 hpf) and translation activity became active in late development (24 hpf). Differentially expressed gene analyses showed that more genes were downregulated than upregulated between two adjacent stages, and genes related to PGC formation or migration reported by previous studies decreased significantly from 11 to 24 hpf. Our results provide base knowledge about zebrafish PGC development at the single cell level and can be further studied by other researchers interested in biological development.
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Affiliation(s)
- Xiaoyuan Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xintian Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ronghong Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yunbin Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yiping Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Shifeng Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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14
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Tobia C, Chiodelli P, Barbieri A, Buraschi S, Ferrari E, Mitola S, Borsani G, Guerra J, Presta M. Atypical Chemokine Receptor 3 Generates Guidance Cues for CXCL12-Mediated Endothelial Cell Migration. Front Immunol 2019; 10:1092. [PMID: 31156639 PMCID: PMC6529557 DOI: 10.3389/fimmu.2019.01092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/29/2019] [Indexed: 11/23/2022] Open
Abstract
Chemokine receptor CXCR4, its ligand stromal cell-derived factor-1 (CXCL12) and the decoy receptor atypical chemokine receptor 3 (ACKR3, also named CXCR7), are involved in the guidance of migrating cells in different anatomical districts. Here, we investigated the role of the ACKR3 zebrafish ortholog ackr3b in the vascularization process during embryonic development. Bioinformatics and functional analyses confirmed that ackr3b is a CXCL12-binding ortholog of human ACKR3. ackr3b is transcribed in the endoderm of zebrafish embryos during epiboly and is expressed in a wide range of tissues during somitogenesis, including central nervous system and somites. Between 18 somite and 26 h-post fertilization stages, the broad somitic expression of ackr3b becomes restricted to the basal part of the somites. After ackr3b knockdown, intersomitic vessels (ISVs) lose the correct direction of migration and are characterized by the presence of aberrant sprouts and ectopic filopodia protrusions, showing downregulation of the tip/stalk cell marker hlx1. In addition, ackr3b morphants show significant alterations of lateral dorsal aortae formation. In keeping with a role for ackr3b in endothelial cell guidance, CXCL12 gradient generated by ACKR3 expression in CHO cell transfectants guides human endothelial cell migration in an in vitro cell co-culture chemotaxis assay. Our results demonstrate that ackr3b plays a non-redundant role in the guidance of sprouting endothelial cells during vascular development in zebrafish. Moreover, ACKR3 scavenging activity generates guidance cues for the directional migration of CXCR4-expressing human endothelial cells in response to CXCL12.
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Affiliation(s)
- Chiara Tobia
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Paola Chiodelli
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Andrea Barbieri
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Simone Buraschi
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Elena Ferrari
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Stefania Mitola
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Giuseppe Borsani
- Unit of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Jessica Guerra
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
| | - Marco Presta
- Unit of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy
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15
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Ugwuagbo KC, Maiti S, Omar A, Hunter S, Nault B, Northam C, Majumder M. Prostaglandin E2 promotes embryonic vascular development and maturation in zebrafish. Biol Open 2019; 8:bio.039768. [PMID: 30890523 PMCID: PMC6504002 DOI: 10.1242/bio.039768] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Prostaglandin (PG)-E2 is essential for growth and development of vertebrates. PGE2 binds to G-coupled receptors to regulate embryonic stem cell differentiation and maintains tissue homeostasis. Overproduction of PGE2 by breast tumor cells promotes aggressive breast cancer phenotypes and tumor-associated lymphangiogenesis. In this study, we investigated novel roles of PGE2 in early embryonic vascular development and maturation with the microinjection of PGE2 in fertilized zebrafish (Danio rerio) eggs. We injected Texas Red dextran to trace vascular development. Embryos injected with the solvent of PGE2 served as vehicle. Distinct developmental changes were noted from 28-96 h post fertilization (hpf), showing an increase in embryonic tail flicks, pigmentation, growth, hatching and larval movement post-hatching in the PGE2-injected group compared to the vehicle. We recorded a significant increase in trunk vascular fluorescence and maturation of vascular anatomy, embryo heartbeat and blood vessel formation in the PGE2 injected group. At 96 hpf, all larvae were euthanized to measure vascular marker mRNA expression. We observed a significant increase in the expression of stem cell markers efnb2a, ephb4a, angiogenesis markers vegfa, kdrl, etv2 and lymphangiogenesis marker prox1 in the PGE2-group compared to the vehicle. This study shows the novel roles of PGE2 in promoting embryonic vascular maturation and angiogenesis in zebrafish.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | - Sujit Maiti
- Department of Biology, Brandon University, Brandon, Manitoba R7A 6A9, Canada
| | - Ahmed Omar
- Department of Biology, Brandon University, Brandon, Manitoba R7A 6A9, Canada
| | - Stephanie Hunter
- Department of Biology, Brandon University, Brandon, Manitoba R7A 6A9, Canada
| | - Braydon Nault
- Department of Biology, Brandon University, Brandon, Manitoba R7A 6A9, Canada
| | - Caleb Northam
- Department of Biology, Brandon University, Brandon, Manitoba R7A 6A9, Canada
| | - Mousumi Majumder
- Department of Biology, Brandon University, Brandon, Manitoba R7A 6A9, Canada
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16
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Fernandez-Valverde SL, Aguilera F, Ramos-Díaz RA. Inference of Developmental Gene Regulatory Networks Beyond Classical Model Systems: New Approaches in the Post-genomic Era. Integr Comp Biol 2019; 58:640-653. [PMID: 29917089 DOI: 10.1093/icb/icy061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The advent of high-throughput sequencing (HTS) technologies has revolutionized the way we understand the transformation of genetic information into morphological traits. Elucidating the network of interactions between genes that govern cell differentiation through development is one of the core challenges in genome research. These networks are known as developmental gene regulatory networks (dGRNs) and consist largely of the functional linkage between developmental control genes, cis-regulatory modules, and differentiation genes, which generate spatially and temporally refined patterns of gene expression. Over the last 20 years, great advances have been made in determining these gene interactions mainly in classical model systems, including human, mouse, sea urchin, fruit fly, and worm. This has brought about a radical transformation in the fields of developmental biology and evolutionary biology, allowing the generation of high-resolution gene regulatory maps to analyze cell differentiation during animal development. Such maps have enabled the identification of gene regulatory circuits and have led to the development of network inference methods that can recapitulate the differentiation of specific cell-types or developmental stages. In contrast, dGRN research in non-classical model systems has been limited to the identification of developmental control genes via the candidate gene approach and the characterization of their spatiotemporal expression patterns, as well as to the discovery of cis-regulatory modules via patterns of sequence conservation and/or predicted transcription-factor binding sites. However, thanks to the continuous advances in HTS technologies, this scenario is rapidly changing. Here, we give a historical overview on the architecture and elucidation of the dGRNs. Subsequently, we summarize the approaches available to unravel these regulatory networks, highlighting the vast range of possibilities of integrating multiple technical advances and theoretical approaches to expand our understanding on the global gene regulation during animal development in non-classical model systems. Such new knowledge will not only lead to greater insights into the evolution of molecular mechanisms underlying cell identity and animal body plans, but also into the evolution of morphological key innovations in animals.
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Affiliation(s)
- Selene L Fernandez-Valverde
- CONACYT, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - René Alexander Ramos-Díaz
- CONACYT, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
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17
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Uusi-Mäkelä MIE, Barker HR, Bäuerlein CA, Häkkinen T, Nykter M, Rämet M. Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio). PLoS One 2018; 13:e0196238. [PMID: 29684067 PMCID: PMC5912780 DOI: 10.1371/journal.pone.0196238] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/09/2018] [Indexed: 12/03/2022] Open
Abstract
CRISPR-Cas9 technology is routinely applied for targeted mutagenesis in model organisms and cell lines. Recent studies indicate that the prokaryotic CRISPR-Cas9 system is affected by eukaryotic chromatin structures. Here, we show that the likelihood of successful mutagenesis correlates with transcript levels during early development in zebrafish (Danio rerio) embryos. In an experimental setting, we found that guide RNAs differ in their onset of mutagenesis activity in vivo. Furthermore, some guide RNAs with high in vitro activity possessed poor mutagenesis activity in vivo, suggesting the presence of factors that limit the mutagenesis in vivo. Using open access datasets generated from early developmental stages of the zebrafish, and guide RNAs selected from the CRISPRz database, we provide further evidence for an association between gene expression during early development and the success of CRISPR-Cas9 mutagenesis in zebrafish embryos. In order to further inspect the effect of chromatin on CRISPR-Cas9 mutagenesis, we analysed the relationship of selected chromatin features on CRISPR-Cas9 mutagenesis efficiency using publicly available data from zebrafish embryos. We found a correlation between chromatin openness and the efficiency of CRISPR-Cas9 mutagenesis. These results indicate that CRISPR-Cas9 mutagenesis is influenced by chromatin accessibility in zebrafish embryos.
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Affiliation(s)
- Meri I. E. Uusi-Mäkelä
- Laboratory of Experimental Immunology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Harlan R. Barker
- Laboratory of Anatomy, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Carina A. Bäuerlein
- Laboratory of Experimental Immunology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Tomi Häkkinen
- Laboratory of Computational Biology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Matti Nykter
- Laboratory of Computational Biology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Mika Rämet
- Laboratory of Experimental Immunology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- PEDEGO Research Unit, Medical Research Center Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
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18
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Wang P, Xia P, Yang J, Wang Z, Peng Y, Shi W, Villeneuve DL, Yu H, Zhang X. A Reduced Transcriptome Approach to Assess Environmental Toxicants Using Zebrafish Embryo Test. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:821-830. [PMID: 29224359 PMCID: PMC5839301 DOI: 10.1021/acs.est.7b04073] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Omics approaches can monitor responses and alterations of biological pathways at genome-scale, which are useful to predict potential adverse effects by environmental toxicants. However, high throughput application of transcriptomics in chemical assessment is limited due to the high cost and lack of "standardized" toxicogenomic methods. Here, a reduced zebrafish transcriptome (RZT) approach was developed to represent the whole transcriptome and to profile bioactivity of chemical and environmental mixtures in zebrafish embryo. RZT gene set of 1637 zebrafish Entrez genes was designed to cover a wide range of biological processes, and to faithfully capture gene-level and pathway-level changes by toxicants compared with the whole transcriptome. Concentration-response modeling was used to calculate the effect concentrations (ECs) of DEGs and corresponding molecular pathways. To validate the RZT approach, quantitative analysis of gene expression by RNA-ampliseq technology was used to identify differentially expressed genes (DEGs) at 32 hpf following exposure to seven serial dilutions of reference chemical BPA (10-10E-5μM) or each of four water samples ranging from wastewater to drinking water (relative enrichment factors 10-6.4 × 10-4). The RZT-ampliseq-embryo approach was both sensitive and able to identify a wide spectrum of biological activities associated with BPA exposure. Water quality was benchmarked based on the sensitivity distribution curve of biological pathways detected using RZT-ampliseq-embryo. Finally, the most sensitive biological pathways were identified, including those linked with adverse reproductive outcomes, genotoxicity and development outcomes. RZT-ampliseq-embryo approach provides an efficient and cost-effective tool to prioritize toxicants based on responsiveness of biological pathways.
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Affiliation(s)
- Pingping Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Zhihao Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Ying Peng
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Wei Shi
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Daniel L. Villeneuve
- United States Environmental Protection Agency, Mid-Continent Ecology Division, Duluth, MN, USA
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
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19
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Concentration dependent transcriptome responses of zebrafish embryos after exposure to cadmium, cobalt and copper. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 24:29-40. [DOI: 10.1016/j.cbd.2017.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/14/2017] [Accepted: 07/28/2017] [Indexed: 12/11/2022]
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20
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White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. A high-resolution mRNA expression time course of embryonic development in zebrafish. eLife 2017; 6. [PMID: 29144233 PMCID: PMC5690287 DOI: 10.7554/elife.30860] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/04/2017] [Indexed: 12/18/2022] Open
Abstract
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.
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Affiliation(s)
| | - John E Collins
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Ian M Sealy
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Neha Wali
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Zsofia Digby
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Matthew P Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anton J Enright
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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21
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Germline mutations affecting the histone H4 core cause a developmental syndrome by altering DNA damage response and cell cycle control. Nat Genet 2017; 49:1642-1646. [PMID: 28920961 DOI: 10.1038/ng.3956] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/23/2017] [Indexed: 12/13/2022]
Abstract
Covalent modifications of histones have an established role as chromatin effectors, as they control processes such as DNA replication and transcription, and repair or regulate nucleosomal structure. Loss of modifications on histone N tails, whether due to mutations in genes belonging to histone-modifying complexes or mutations directly affecting the histone tails, causes developmental disorders or has a role in tumorigenesis. More recently, modifications affecting the globular histone core have been uncovered as being crucial for DNA repair, pluripotency and oncogenesis. Here we report monoallelic missense mutations affecting lysine 91 in the histone H4 core (H4K91) in three individuals with a syndrome of growth delay, microcephaly and intellectual disability. Expression of the histone H4 mutants in zebrafish embryos recapitulates the developmental anomalies seen in the patients. We show that the histone H4 alterations cause genomic instability, resulting in increased apoptosis and cell cycle progression anomalies during early development. Mechanistically, our findings indicate an important role for the ubiquitination of H4K91 in genomic stability during embryonic development.
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22
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Jukam D, Shariati SAM, Skotheim JM. Zygotic Genome Activation in Vertebrates. Dev Cell 2017; 42:316-332. [PMID: 28829942 PMCID: PMC5714289 DOI: 10.1016/j.devcel.2017.07.026] [Citation(s) in RCA: 259] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/25/2017] [Accepted: 07/28/2017] [Indexed: 12/12/2022]
Abstract
The first major developmental transition in vertebrate embryos is the maternal-to-zygotic transition (MZT) when maternal mRNAs are degraded and zygotic transcription begins. During the MZT, the embryo takes charge of gene expression to control cell differentiation and further development. This spectacular organismal transition requires nuclear reprogramming and the initiation of RNAPII at thousands of promoters. Zygotic genome activation (ZGA) is mechanistically coordinated with other embryonic events, including changes in the cell cycle, chromatin state, and nuclear-to-cytoplasmic component ratios. Here, we review progress in understanding vertebrate ZGA dynamics in frogs, fish, mice, and humans to explore differences and emphasize common features.
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Affiliation(s)
- David Jukam
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - S Ali M Shariati
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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23
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Liu Y, Zhu Z, Ho IHT, Shi Y, Xie Y, Li J, Zhang Y, Chan MTV, Cheng CHK. Germline-specific dgcr8 knockout in zebrafish using a BACK approach. Cell Mol Life Sci 2017; 74:2503-2511. [PMID: 28224202 PMCID: PMC11107783 DOI: 10.1007/s00018-017-2471-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 12/21/2016] [Accepted: 01/19/2017] [Indexed: 11/30/2022]
Abstract
Zebrafish is an important model to study developmental biology and human diseases. However, an effective approach to achieve spatial and temporal gene knockout in zebrafish has not been well established. In this study, we have developed a new approach, namely bacterial artificial chromosome-rescue-based knockout (BACK), to achieve conditional gene knockout in zebrafish using the Cre/loxP system. We have successfully deleted the DiGeorge syndrome critical region gene 8 (dgcr8) in zebrafish germ line and demonstrated that the maternal-zygotic dgcr8 (MZdgcr8) embryos exhibit MZdicer-like phenotypes with morphological defects which could be rescued by miR-430, indicating that canonical microRNAs play critical role in early development. Our findings establish that Cre/loxP-mediated tissue-specific gene knockout could be achieved using this BACK strategy and that canonical microRNAs play important roles in early embryonic development in zebrafish.
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Affiliation(s)
- Yun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Zeyao Zhu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Idy H T Ho
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Department of Anaesthesia and Intensive Care, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Yujian Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Yuxin Xie
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Jianzhen Li
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Christopher H K Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
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24
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Mao H, Chen K, Zhu X, Luo Q, Zhao J, Li W, Wu X, Xu H. Identification of suitable reference genes for quantitative real-time PCR normalization in blotched snakehead Channa maculata. JOURNAL OF FISH BIOLOGY 2017; 90:2312-2322. [PMID: 28386932 DOI: 10.1111/jfb.13308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/06/2017] [Indexed: 06/07/2023]
Abstract
A systematic study was conducted to identify reliable reference genes for normalization of gene expression analysis in the blotched snakehead Channa maculata under normal physiological conditions. Firstly, the partial complementary (c)DNA of nine candidate reference genes (actb, tmem104, ube2l3, ef1α, churc1, tmem256, rpl13a, sep15 and g6pd) were cloned from C. maculata. The expression levels of these genes were then assessed in embryos of different developmental stages and various tissue types of adult fish using quantitative real-time (qrt-)PCR. RefFinder algorithm was used to evaluate the expression stability of these genes based on their cycle-threshold (Ct ) values in the qrt-PCR analysis. Results showed that there was no single best reference gene for all stages of embryos and adult tissues tested. Furthermore, it was found that, among the nine candidate genes tested, actb and tmem104 were the most stable reference genes across adult tissue types, while sep15 and tmem256 were the most stable ones across developmental stages of embryos. These stable reference genes are recommended for normalization of gene expression analysis in C. maculata.
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Affiliation(s)
- H Mao
- Pearl River Fisheries Research Institute, Chinese Academic of Fisheries Sciences, Guangzhou, 510380, China
- College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
| | - K Chen
- Pearl River Fisheries Research Institute, Chinese Academic of Fisheries Sciences, Guangzhou, 510380, China
- College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
| | - X Zhu
- Pearl River Fisheries Research Institute, Chinese Academic of Fisheries Sciences, Guangzhou, 510380, China
| | - Q Luo
- Pearl River Fisheries Research Institute, Chinese Academic of Fisheries Sciences, Guangzhou, 510380, China
| | - J Zhao
- Pearl River Fisheries Research Institute, Chinese Academic of Fisheries Sciences, Guangzhou, 510380, China
| | - W Li
- Pearl River Fisheries Research Institute, Chinese Academic of Fisheries Sciences, Guangzhou, 510380, China
| | - X Wu
- Pearl River Fisheries Research Institute, Chinese Academic of Fisheries Sciences, Guangzhou, 510380, China
- College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
| | - H Xu
- Pearl River Fisheries Research Institute, Chinese Academic of Fisheries Sciences, Guangzhou, 510380, China
- College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
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25
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γ2 and γ1AP-1 complexes: Different essential functions and regulatory mechanisms in clathrin-dependent protein sorting. Eur J Cell Biol 2017; 96:356-368. [PMID: 28372831 DOI: 10.1016/j.ejcb.2017.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/24/2017] [Accepted: 03/24/2017] [Indexed: 11/20/2022] Open
Abstract
γ2 adaptin is homologous to γ1, but is only expressed in vertebrates while γ1 is found in all eukaryotes. We know little about γ2 functions and their relation to γ1. γ1 is an adaptin of the heterotetrameric AP-1 complexes, which sort proteins in and do form clathrin-coated transport vesicles and they also regulate maturation of early endosomes. γ1 knockout mice develop only to blastocysts and thus γ2 does not compensate γ1-deficiency in development. γ2 has not been classified as a clathrin-coated vesicle adaptor protein in proteome analyses and functions for monomeric γ2 in endosomal protein sorting have been proposed, but adaptin interaction studies suggested formation of heterotetrameric AP-1/γ2 complexes. We detected γ2 at the trans-Golgi network, on peripheral vesicles and identified γ2 clathrin-coated vesicles in mice. Ubiquitous σ1A and tissue-specific σ1B adaptins bind γ2 and γ1. σ1B knockout in mice does not effect γ1/σ1A AP-1 levels, but γ2/σ1A AP-1 levels are increased in brain and adipocytes. Also γ2 is essential in development. In zebrafish AP-1/γ2 and AP-1/γ1 fulfill different, essential functions in brain and the vascular system.
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26
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Noyes PD, Garcia GR, Tanguay RL. ZEBRAFISH AS AN IN VIVO MODEL FOR SUSTAINABLE CHEMICAL DESIGN. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2016; 18:6410-6430. [PMID: 28461781 PMCID: PMC5408959 DOI: 10.1039/c6gc02061e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Heightened public awareness about the many thousands of chemicals in use and present as persistent contaminants in the environment has increased the demand for safer chemicals and more rigorous toxicity testing. There is a growing recognition that the use of traditional test models and empirical approaches is impractical for screening for toxicity the many thousands of chemicals in the environment and the hundreds of new chemistries introduced each year. These realities coupled with the green chemistry movement have prompted efforts to implement more predictive-based approaches to evaluate chemical toxicity early in product development. While used for many years in environmental toxicology and biomedicine, zebrafish use has accelerated more recently in genetic toxicology, high throughput screening (HTS), and behavioral testing. This review describes major advances in these testing methods that have positioned the zebrafish as a highly applicable model in chemical safety evaluations and sustainable chemistry efforts. Many toxic responses have been shown to be shared among fish and mammals owing to their generally well-conserved development, cellular networks, and organ systems. These shared responses have been observed for chemicals that impair endocrine functioning, development, and reproduction, as well as those that elicit cardiotoxicity and carcinogenicity, among other diseases. HTS technologies with zebrafish enable screening large chemical libraries for bioactivity that provide opportunities for testing early in product development. A compelling attribute of the zebrafish centers on being able to characterize toxicity mechanisms across multiple levels of biological organization from the genome to receptor interactions and cellular processes leading to phenotypic changes such as developmental malformations. Finally, there is a growing recognition of the links between human and wildlife health and the need for approaches that allow for assessment of real world multi-chemical exposures. The zebrafish is poised to be an important model in bridging these two conventionally separate areas of toxicology and characterizing the biological effects of chemical mixtures that could augment its role in sustainable chemistry.
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Affiliation(s)
- Pamela D. Noyes
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Gloria R. Garcia
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Robert L. Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331
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27
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Yang A, Zhou Z, Pan Y, Jiang J, Dong Y, Guan X, Sun H, Gao S, Chen Z. RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus. BMC Genomics 2016; 17:459. [PMID: 27296384 PMCID: PMC4906609 DOI: 10.1186/s12864-016-2810-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/02/2016] [Indexed: 12/14/2022] Open
Abstract
Background Sea cucumber Apostichopus japonicus is an important economic species in China, which is affected by various diseases; skin ulceration syndrome (SUS) is the most serious. In this study, we characterized the transcriptomes in A. japonicus challenged with Vibrio splendidus to elucidate the changes in gene expression throughout the three stages of SUS progression. Results RNA sequencing of 21 cDNA libraries from various tissues and developmental stages of SUS-affected A. japonicus yielded 553 million raw reads, of which 542 million high-quality reads were generated by deep-sequencing using the Illumina HiSeq™ 2000 platform. The reference transcriptome comprised a combination of the Illumina reads, 454 sequencing data and Sanger sequences obtained from the public database to generate 93,163 unigenes (average length, 1,052 bp; N50 = 1,575 bp); 33,860 were annotated. Transcriptome comparisons between healthy and SUS-affected A. japonicus revealed greater differences in gene expression profiles in the body walls (BW) than in the intestines (Int), respiratory trees (RT) and coelomocytes (C). Clustering of expression models revealed stable up-regulation as the main pattern occurring in the BW throughout the three stages of SUS progression. Significantly affected pathways were associated with signal transduction, immune system, cellular processes, development and metabolism. Ninety-two differentially expressed genes (DEGs) were divided into four functional categories: attachment/pathogen recognition (17), inflammatory reactions (38), oxidative stress response (7) and apoptosis (30). Using quantitative real-time PCR, twenty representative DEGs were selected to validate the sequencing results. The Pearson’s correlation coefficient (R) of the 20 DEGs ranged from 0.811 to 0.999, which confirmed the consistency and accuracy between these two approaches. Conclusions Dynamic changes in global gene expression occur during SUS progression in A. japonicus. Elucidation of these changes is important in clarifying the molecular mechanisms associated with the development of SUS in sea cucumber. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2810-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aifu Yang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China.
| | - Yongjia Pan
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Jingwei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Xiaoyan Guan
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Hongjuan Sun
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Shan Gao
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Zhong Chen
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
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28
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Xu H, Li C, Zeng Q, Agrawal I, Zhu X, Gong Z. Genome-wide identification of suitable zebrafish Danio rerio reference genes for normalization of gene expression data by RT-qPCR. JOURNAL OF FISH BIOLOGY 2016; 88:2095-2110. [PMID: 27126589 DOI: 10.1111/jfb.12915] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 01/18/2016] [Indexed: 06/05/2023]
Abstract
In this study, to systematically identify the most stably expressed genes for internal reference in zebrafish Danio rerio investigations, 37 D. rerio transcriptomic datasets (both RNA sequencing and microarray data) were collected from gene expression omnibus (GEO) database and unpublished data, and gene expression variations were analysed under three experimental conditions: tissue types, developmental stages and chemical treatments. Forty-four putative candidate genes were identified with the c.v. <0·2 from all datasets. Following clustering into different functional groups, 21 genes, in addition to four conventional housekeeping genes (eef1a1l1, b2m, hrpt1l and actb1), were selected from different functional groups for further quantitative real-time (qrt-)PCR validation using 25 RNA samples from different adult tissues, developmental stages and chemical treatments. The qrt-PCR data were then analysed using the statistical algorithm refFinder for gene expression stability. Several new candidate genes showed better expression stability than the conventional housekeeping genes in all three categories. It was found that sep15 and metap1 were the top two stable genes for tissue types, ube2a and tmem50a the top two for different developmental stages, and rpl13a and rp1p0 the top two for chemical treatments. Thus, based on the extensive transcriptomic analyses and qrt-PCR validation, these new reference genes are recommended for normalization of D. rerio qrt-PCR data respectively for the three different experimental conditions.
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Affiliation(s)
- H Xu
- Pearl River Fisheries Research Institute, Chinese Academic of Fishery Sciences, Guangzhou 510380, China
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - C Li
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Q Zeng
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - I Agrawal
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - X Zhu
- Pearl River Fisheries Research Institute, Chinese Academic of Fishery Sciences, Guangzhou 510380, China
| | - Z Gong
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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29
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Bicskei B, Taggart JB, Glover KA, Bron JE. Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression. Genet Sel Evol 2016; 48:20. [PMID: 26987528 PMCID: PMC4797325 DOI: 10.1186/s12711-016-0200-6] [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: 07/07/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Due to selective breeding, domesticated and wild Atlantic salmon are genetically diverged, which raises concerns about farmed escapees having the potential to alter the genetic composition of wild populations and thereby disrupting local adaptation. Documenting transcriptional differences between wild and domesticated stocks under controlled conditions is one way to explore the consequences of domestication and selection. We compared the transcriptomes of wild and domesticated Atlantic salmon embryos, by using a custom 44k oligonucleotide microarray to identify perturbed gene pathways between the two stocks, and to document the inheritance patterns of differentially-expressed genes by examining gene expression in their reciprocal hybrids. RESULTS Data from 24 array interrogations were analysed: four reciprocal cross types (W♀ × W♂, D♀ × W♂; W♀ × D♂, D♀ × D♂) × six biological replicates. A common set of 31,491 features on the microarrays passed quality control, of which about 62 % were assigned a KEGG Orthology number. A total of 6037 distinct genes were identified for gene-set enrichment/pathway analysis. The most highly enriched functional groups that were perturbed between the two stocks were cellular signalling and immune system, ribosome and RNA transport, and focal adhesion and gap junction pathways, relating to cell communication and cell adhesion molecules. Most transcripts that were differentially expressed between the stocks were governed by additive gene interaction (33 to 42 %). Maternal dominance and over-dominance were also prevalent modes of inheritance, with no convincing evidence for a stock effect. CONCLUSIONS Our data indicate that even at this relatively early developmental stage, transcriptional differences exist between the two stocks and affect pathways that are relevant to wild versus domesticated environments. Many of the identified differentially perturbed pathways are involved in organogenesis, which is expected to be an active process at the eyed egg stage. The dominant effects are more largely due to the maternal line than to the origin of the stock. This finding is particularly relevant in the context of potential introgression between farmed and wild fish, since female escapees tend to have a higher spawning success rate compared to males.
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Affiliation(s)
- Beatrix Bicskei
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.
| | - John B Taggart
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Kevin A Glover
- Institute of Marine Research, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - James E Bron
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
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30
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Yang KY, Chen Y, Zhang Z, Ng PKS, Zhou WJ, Zhang Y, Liu M, Chen J, Mao B, Tsui SKW. Transcriptome analysis of different developmental stages of amphioxus reveals dynamic changes of distinct classes of genes during development. Sci Rep 2016; 6:23195. [PMID: 26979494 PMCID: PMC4793263 DOI: 10.1038/srep23195] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 02/29/2016] [Indexed: 01/05/2023] Open
Abstract
Vertebrates diverged from other chordates approximately 500 million years ago and have adopted several modifications of developmental processes. Amphioxus is widely used in evolutionary developmental biology research, such as on the basic patterning mechanisms involved in the chordate body plan and the origin of vertebrates. The fast development of next-generation sequencing has advanced knowledge of the genomic organization of amphioxus; however, many aspects of gene regulation during amphioxus development have not been fully characterized. In this study, we applied high-throughput sequencing on the transcriptomes of 13 developmental stages of Chinese amphioxus to gain a comprehensive understanding of transcriptional processes occurring from the fertilized egg to the adult stage. The expression levels of 3,423 genes were significantly changed (FDR ≤ 0.01). All of these genes were included in a clustering analysis, and enrichment of biological functions associated with these clusters was determined. Significant changes were observed in several important processes, including the down-regulation of the cell cycle and the up-regulation of translation. These results should build a foundation for identifying developmentally important genes, especially those regulatory factors involved in amphioxus development, and advance understanding of the developmental dynamics in vertebrates.
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Affiliation(s)
- Kevin Yi Yang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuan Chen
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina, USA
| | - Zuming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Patrick Kwok-Shing Ng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wayne Junwei Zhou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yinfeng Zhang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Minghua Liu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junyuan Chen
- Nanjing Institute of Paleontology and Geology, Chinese Academy of Sciences, Nanjing, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
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31
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Vanhauwaert S, Lefever S, Coucke P, Speleman F, De Paepe A, Vandesompele J, Willaert A. RT-qPCR gene expression analysis in zebrafish: Preanalytical precautions and use of expressed repetitive elements for normalization. Methods Cell Biol 2016; 135:329-42. [PMID: 27443934 DOI: 10.1016/bs.mcb.2016.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Gene expression analysis is increasingly important in many fields of biological research. Understanding patterns of expressed genes is assumed to provide insight into complex regulatory networks and can lead to the identification of genes relevant to specific biological processes, including disease. Among different techniques, reverse transcription quantitative polymerase chain reaction (RT-qPCR) is currently regarded as the gold standard for targeted quantification of RNA gene expression, especially because of its high sensitivity, specificity, accuracy, and precision, and also because of its practical simplicity and processing speed. However, different critical factors can influence the outcome of RT-qPCR studies, including isolation of RNA, reverse transcription to cDNA, and data analysis. These factors need to be addressed in order to obtain biologically meaningful results. In this chapter, we describe how RT-qPCR can be used in a reliable way to successfully study differential gene expression in zebrafish. Hereby, we especially focus on how expressed repetitive elements can be employed as reference targets in zebrafish RT-qPCR studies and how they can further improve the quality of the data.
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Affiliation(s)
| | | | - P Coucke
- Ghent University, Ghent, Belgium
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32
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Hu Y, Xie S, Yao J. Identification of Novel Reference Genes Suitable for qRT-PCR Normalization with Respect to the Zebrafish Developmental Stage. PLoS One 2016; 11:e0149277. [PMID: 26891128 PMCID: PMC4758726 DOI: 10.1371/journal.pone.0149277] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/29/2016] [Indexed: 12/20/2022] Open
Abstract
Reference genes used in normalizing qRT-PCR data are critical for the accuracy of gene expression analysis. However, many traditional reference genes used in zebrafish early development are not appropriate because of their variable expression levels during embryogenesis. In the present study, we used our previous RNA-Seq dataset to identify novel reference genes suitable for gene expression analysis during zebrafish early developmental stages. We first selected 197 most stably expressed genes from an RNA-Seq dataset (29,291 genes in total), according to the ratio of their maximum to minimum RPKM values. Among the 197 genes, 4 genes with moderate expression levels and the least variation throughout 9 developmental stages were identified as candidate reference genes. Using four independent statistical algorithms (delta-CT, geNorm, BestKeeper and NormFinder), the stability of qRT-PCR expression of these candidates was then evaluated and compared to that of actb1 and actb2, two commonly used zebrafish reference genes. Stability rankings showed that two genes, namely mobk13 (mob4) and lsm12b, were more stable than actb1 and actb2 in most cases. To further test the suitability of mobk13 and lsm12b as novel reference genes, they were used to normalize three well-studied target genes. The results showed that mobk13 and lsm12b were more suitable than actb1 and actb2 with respect to zebrafish early development. We recommend mobk13 and lsm12b as new optimal reference genes for zebrafish qRT-PCR analysis during embryogenesis and early larval stages.
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Affiliation(s)
- Yu Hu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuying Xie
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jihua Yao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
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Duran I, Csukasi F, Taylor S, Krakow D, Becerra J, Bombarely A, Marí-Beffa M. Collagen duplicate genes of bone and cartilage participate during regeneration of zebrafish fin skeleton. Gene Expr Patterns 2015; 19:60-9. [DOI: 10.1016/j.gep.2015.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/14/2015] [Accepted: 07/31/2015] [Indexed: 11/17/2022]
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Liu J, Hou J, Jiang C, Li G, Lu H, Meng F, Shi L. Deep Sequencing of the Scutellaria baicalensis Georgi Transcriptome Reveals Flavonoid Biosynthetic Profiling and Organ-Specific Gene Expression. PLoS One 2015; 10:e0136397. [PMID: 26317778 PMCID: PMC4552754 DOI: 10.1371/journal.pone.0136397] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 08/04/2015] [Indexed: 12/22/2022] Open
Abstract
Scutellaria baicalensis Georgi has long been used in traditional medicine to treat various such widely varying diseases and has been listed in the Chinese Pharmacopeia, the Japanese Pharmacopeia, the Korean Pharmacopoeia and the European Pharmacopoeia. Flavonoids, especially wogonin, wogonoside, baicalin, and baicalein, are its main functional ingredients with various pharmacological activities. Although pharmaological studies for these flavonoid components have been well conducted, the molecular mechanism of their biosynthesis remains unclear in S. baicalensis. In this study, Illumina/Solexa deep sequencing generated more than 91 million paired-end reads and 49,507 unigenes from S. baicalensis roots, stems, leaves and flowers. More than 70% unigenes were annotated in at least one of the five public databases and 13,627 unigenes were assigned to 3,810 KEGG genes involved in 579 different pathways. 54 unigenes that encode 12 key enzymes involved in the pathway of flavonoid biosynthesis were discovered. One baicalinase and three baicalein 7-O-glucuronosyltransferases genes potentially involved in the transformation between baicalin/wogonoside and baicalein/wogonin were identified. Four candidate 6-hydroxylase genes for the formation of baicalin/baicalein and one candidate 8-O-methyltransferase gene for the biosynthesis of wogonoside/wogonin were also recognized. Our results further support the conclusion that, in S. baicalensis, 3,5,7-trihydroxyflavone was the precursor of the four above compounds. Then, the differential expression models and simple sequence repeats associated with these genes were carefully analyzed. All of these results not only enrich the gene resource but also benefit research into the molecular genetics and functional genomics in S. baicalensis.
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Affiliation(s)
- Jinxin Liu
- Key Laboratory of Traditional Chinese Medicine Research and Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde, 067000, China; Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, 100875, China; State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijng, 100700, China
| | - Jingyi Hou
- Key Laboratory of Traditional Chinese Medicine Research and Development of Hebei Province, Institute of Traditional Chinese Medicine, Chengde Medical University, Chengde, 067000, China; Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, 100875, China; State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijng, 100700, China
| | - Chao Jiang
- Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, 100875, China; State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijng, 100700, China
| | - Geng Li
- Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, 100875, China; State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijng, 100700, China
| | - Heng Lu
- Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, 100875, China; State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijng, 100700, China
| | - Fanyun Meng
- Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, 100875, China; State Key Laboratory Breeding Base of Dao-di Herbs, China Academy of Chinese Medical Sciences, Beijng, 100700, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
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Sundström G, Zamani N, Grabherr MG, Mauceli E. Whiteboard: a framework for the programmatic visualization of complex biological analyses. Bioinformatics 2015; 31:2054-5. [PMID: 25661541 DOI: 10.1093/bioinformatics/btv078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/01/2015] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED Whiteboard is a class library implemented in C++ that enables visualization to be tightly coupled with computation when analyzing large and complex datasets. AVAILABILITY AND IMPLEMENTATION the C++ source code, coding samples and documentation are freely available under the Lesser General Public License from http://whiteboard-class.sourceforge.net/.
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Affiliation(s)
- Görel Sundström
- Department of Medical Biochemistry and Microbiology, Bioinformatics Infrastructure for Life Sciences, Uppsala University, 75123 Uppsala, Sweden, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden and Parabase Genomics, 27 Drydock Avenue, Boston MA 02210, USA
| | - Neda Zamani
- Department of Medical Biochemistry and Microbiology, Bioinformatics Infrastructure for Life Sciences, Uppsala University, 75123 Uppsala, Sweden, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden and Parabase Genomics, 27 Drydock Avenue, Boston MA 02210, USA Department of Medical Biochemistry and Microbiology, Bioinformatics Infrastructure for Life Sciences, Uppsala University, 75123 Uppsala, Sweden, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden and Parabase Genomics, 27 Drydock Avenue, Boston MA 02210, USA
| | - Manfred G Grabherr
- Department of Medical Biochemistry and Microbiology, Bioinformatics Infrastructure for Life Sciences, Uppsala University, 75123 Uppsala, Sweden, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden and Parabase Genomics, 27 Drydock Avenue, Boston MA 02210, USA
| | - Evan Mauceli
- Department of Medical Biochemistry and Microbiology, Bioinformatics Infrastructure for Life Sciences, Uppsala University, 75123 Uppsala, Sweden, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden and Parabase Genomics, 27 Drydock Avenue, Boston MA 02210, USA
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Li Z, Long Y, Zhong L, Song G, Zhang X, Yuan L, Cui Z, Dai H. RNA sequencing provides insights into the toxicogenomic response of ZF4 cells to methyl methanesulfonate. J Appl Toxicol 2015; 36:94-104. [DOI: 10.1002/jat.3147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/10/2015] [Accepted: 02/10/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Zhouquan Li
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
- University of Chinese Academy of Sciences; Yuquan Road 19A Beijing 100039 People's Republic of China
| | - Yong Long
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Liqiao Zhong
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
- University of Chinese Academy of Sciences; Yuquan Road 19A Beijing 100039 People's Republic of China
| | - Guili Song
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Xiaohua Zhang
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Li Yuan
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Zongbin Cui
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Heping Dai
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
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Vanhauwaert S, Van Peer G, Rihani A, Janssens E, Rondou P, Lefever S, De Paepe A, Coucke PJ, Speleman F, Vandesompele J, Willaert A. Expressed repeat elements improve RT-qPCR normalization across a wide range of zebrafish gene expression studies. PLoS One 2014; 9:e109091. [PMID: 25310091 PMCID: PMC4195698 DOI: 10.1371/journal.pone.0109091] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 09/01/2014] [Indexed: 11/29/2022] Open
Abstract
The selection and validation of stably expressed reference genes is a critical issue for proper RT-qPCR data normalization. In zebrafish expression studies, many commonly used reference genes are not generally applicable given their variability in expression levels under a variety of experimental conditions. Inappropriate use of these reference genes may lead to false interpretation of expression data and unreliable conclusions. In this study, we evaluated a novel normalization method in zebrafish using expressed repetitive elements (ERE) as reference targets, instead of specific protein coding mRNA targets. We assessed and compared the expression stability of a number of EREs to that of commonly used zebrafish reference genes in a diverse set of experimental conditions including a developmental time series, a set of different organs from adult fish and different treatments of zebrafish embryos including morpholino injections and administration of chemicals. Using geNorm and rank aggregation analysis we demonstrated that EREs have a higher overall expression stability compared to the commonly used reference genes. Moreover, we propose a limited set of ERE reference targets (hatn10, dna15ta1 and loopern4), that show stable expression throughout the wide range of experiments in this study, as strong candidates for inclusion as reference targets for qPCR normalization in future zebrafish expression studies. Our applied strategy to find and evaluate candidate expressed repeat elements for RT-qPCR data normalization has high potential to be used also for other species.
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Affiliation(s)
| | - Gert Van Peer
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Ali Rihani
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Els Janssens
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Pieter Rondou
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Steve Lefever
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Anne De Paepe
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Paul J. Coucke
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Frank Speleman
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Andy Willaert
- Center of Medical Genetics, Ghent University, Ghent, Belgium
- * E-mail:
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Balmer NV, Klima S, Rempel E, Ivanova VN, Kolde R, Weng MK, Meganathan K, Henry M, Sachinidis A, Berthold MR, Hengstler JG, Rahnenführer J, Waldmann T, Leist M. From transient transcriptome responses to disturbed neurodevelopment: role of histone acetylation and methylation as epigenetic switch between reversible and irreversible drug effects. Arch Toxicol 2014; 88:1451-68. [PMID: 24935251 PMCID: PMC4067541 DOI: 10.1007/s00204-014-1279-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 05/19/2014] [Indexed: 01/17/2023]
Abstract
The superordinate principles governing the transcriptome response of differentiating cells exposed to drugs are still unclear. Often, it is assumed that toxicogenomics data reflect the immediate mode of action (MoA) of drugs. Alternatively, transcriptome changes could describe altered differentiation states as indirect consequence of drug exposure. We used here the developmental toxicants valproate and trichostatin A to address this question. Neurally differentiating human embryonic stem cells were treated for 6 days. Histone acetylation (primary MoA) increased quickly and returned to baseline after 48 h. Histone H3 lysine methylation at the promoter of the neurodevelopmental regulators PAX6 or OTX2 was increasingly altered over time. Methylation changes remained persistent and correlated with neurodevelopmental defects and with effects on PAX6 gene expression, also when the drug was washed out after 3-4 days. We hypothesized that drug exposures altering only acetylation would lead to reversible transcriptome changes (indicating MoA), and challenges that altered methylation would lead to irreversible developmental disturbances. Data from pulse-chase experiments corroborated this assumption. Short drug treatment triggered reversible transcriptome changes; longer exposure disrupted neurodevelopment. The disturbed differentiation was reflected by an altered transcriptome pattern, and the observed changes were similar when the drug was washed out during the last 48 h. We conclude that transcriptome data after prolonged chemical stress of differentiating cells mainly reflect the altered developmental stage of the model system and not the drug MoA. We suggest that brief exposures, followed by immediate analysis, are more suitable for information on immediate drug responses and the toxicity MoA.
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Affiliation(s)
- Nina V. Balmer
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Stefanie Klima
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Eugen Rempel
- Department of Statistics, TU Dortmund, Dortmund, Germany
| | - Violeta N. Ivanova
- Chair for Bioinformatics and Information Mining, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | | | - Matthias K. Weng
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Kesavan Meganathan
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Margit Henry
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Agapios Sachinidis
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Michael R. Berthold
- Chair for Bioinformatics and Information Mining, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), 44139 Dortmund, Germany
| | | | - Tanja Waldmann
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Marcel Leist
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
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Wang L, Cao C, Ma Q, Zeng Q, Wang H, Cheng Z, Zhu G, Qi J, Ma H, Nian H, Wang Y. RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications. BMC PLANT BIOLOGY 2014; 14:169. [PMID: 24939556 PMCID: PMC4070088 DOI: 10.1186/1471-2229-14-169] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 06/05/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND Soybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is also an excellent model for studying evolution of duplicated genes. However, relative to the model plants Arabidopsis and rice, the present knowledge about soybean transcriptome is quite limited. RESULTS In this study, we employed RNA-seq to investigate transcriptomes of 11 soybean tissues, for genome-wide discovery of truly expressed genes, and novel and alternative transcripts, as well as analyses of conservation and divergence of duplicated genes and their functional implications. We detected a total of 54,132 high-confidence expressed genes, and identified 6,718 novel transcriptional regions with a mean length of 372 bp. We also provided strong evidence for alternative splicing (AS) events for ~15.9% of the genes with two or more exons. Among them, 1,834 genes exhibited stage-dependent AS, and 202 genes had tissue-biased exon-skipping events. We further defined the conservation and divergence in expression patterns between duplicated gene pairs from recent whole genome duplications (WGDs); differentially expressed genes, tissue preferentially expressed genes, transcription factors and specific gene family members were identified for shoot apical meristem and flower development. CONCLUSIONS Our results significantly improved soybean gene annotation, and also provide valuable resources for functional genomics and studies of the evolution of duplicated genes from WGDs in soybean.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
| | - Chenlong Cao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
| | - Qibin Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, 510642 Guangzhou, China
- Guangdong Sub-Center of National Soybean Improvement Center, South China Agricultural University, 510642 Guangzhou, China
| | - Qiaoying Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, 510642 Guangzhou, China
- Guangdong Sub-Center of National Soybean Improvement Center, South China Agricultural University, 510642 Guangzhou, China
| | - Haifeng Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
- Institute of Biomedical Sciences, Fudan University, 200032 Shanghai, China
| | - Zhihao Cheng
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
| | - Genfeng Zhu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
- Institute of Biomedical Sciences, Fudan University, 200032 Shanghai, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
- Institute of Biomedical Sciences, Fudan University, 200032 Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
- Institute of Biomedical Sciences, Fudan University, 200032 Shanghai, China
- Institute of Biodiversity Sciences, Fudan University, 200433 Shanghai, China
| | - Hai Nian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, 510642 Guangzhou, China
- Guangdong Sub-Center of National Soybean Improvement Center, South China Agricultural University, 510642 Guangzhou, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
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Wang Z, Gao J, Song H, Wu X, Sun Y, Qi J, Yu H, Wang Z, Zhang Q. Sexually dimorphic expression of vasa isoforms in the tongue sole (Cynoglossus semilaevis). PLoS One 2014; 9:e93380. [PMID: 24671276 PMCID: PMC3966880 DOI: 10.1371/journal.pone.0093380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 03/03/2014] [Indexed: 11/19/2022] Open
Abstract
The vasa gene encodes an ATP-dependent RNA helicase of the DEAD box protein family that functions in a broad range of molecular events involving duplex RNA. In most species, the germline specific expression of vasa becomes a molecular marker widely used in the visualization and labeling of primordial germ cells (PGCs) and a tool in surrogate broodstock production through PGC transplantation. The vasa gene from tongue sole (Cynoglossus semilaevis) was characterized to promote the development of genetic breeding techniques in this species. Three C. semilaevis vasa transcripts were isolated, namely vas-l, vas-m, and vas-s. Quantitative real-time PCR results showed that C. semilaevis vasa transcripts were prevalently expressed in gonads, with very weak expression of vas-s in other tissues. Embryonic development expression profiles revealed the onset of zygotic transcription of vasa mRNAs and the maternal deposit of the three transcripts. The genetic ZW female juvenile fish was discriminated from genetic ZZ males by a pair of female specific primers. Only the expression of vas-s can be observed in both sexes during early gonadal differentiation. Before PGCs started mitosis, there was sexually dimorphic expression of vas-s with the ovary showing higher levels and downward trend. The results demonstrated the benefits of vasa as a germline specific marker for PGCs during embryonic development and gonadal differentiation. This study lays the groundwork for further application of C. semilaevis PGCs in fish breeding.
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Affiliation(s)
- Zhongkai Wang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jinning Gao
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Huayu Song
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaomeng Wu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yan Sun
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jie Qi
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Haiyang Yu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhigang Wang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- * E-mail:
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Anavy L, Levin M, Khair S, Nakanishi N, Fernandez-Valverde SL, Degnan BM, Yanai I. BLIND ordering of large-scale transcriptomic developmental timecourses. Development 2014; 141:1161-6. [PMID: 24504336 DOI: 10.1242/dev.105288] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA-Seq enables the efficient transcriptome sequencing of many samples from small amounts of material, but the analysis of these data remains challenging. In particular, in developmental studies, RNA-Seq is challenged by the morphological staging of samples, such as embryos, since these often lack clear markers at any particular stage. In such cases, the automatic identification of the stage of a sample would enable previously infeasible experimental designs. Here we present the 'basic linear index determination of transcriptomes' (BLIND) method for ordering samples comprising different developmental stages. The method is an implementation of a traveling salesman algorithm to order the transcriptomes according to their inter-relationships as defined by principal components analysis. To establish the direction of the ordered samples, we show that an appropriate indicator is the entropy of transcriptomic gene expression levels, which increases over developmental time. Using BLIND, we correctly recover the annotated order of previously published embryonic transcriptomic timecourses for frog, mosquito, fly and zebrafish. We further demonstrate the efficacy of BLIND by collecting 59 embryos of the sponge Amphimedon queenslandica and ordering their transcriptomes according to developmental stage. BLIND is thus useful in establishing the temporal order of samples within large datasets and is of particular relevance to the study of organisms with asynchronous development and when morphological staging is difficult.
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Affiliation(s)
- Leon Anavy
- Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
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42
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Aanes H, Collas P, Aleström P. Transcriptome dynamics and diversity in the early zebrafish embryo. Brief Funct Genomics 2013; 13:95-105. [PMID: 24335756 DOI: 10.1093/bfgp/elt049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent years advances in high-throughput sequencing have improved our understanding of how transcripts regulate early vertebrate development. Here, we review the transcriptome dynamics and diversity during early stages of zebrafish embryogenesis. Transcriptome dynamics is characterized by different patterns of mRNA degradation, activation of dormant transcripts and onset of transcription. Several studies have shown a striking diversity of both coding and non-coding transcripts. However, in the aftermath of this immense increase in data, functional studies of both protein-coding and non-coding transcripts are lagging behind. We anticipate that the forthcoming years will see studies relying on different high-throughput sequencing technologies and genomic tools developed for zebrafish embryos to further pin down yet un-annotated transcript-function relationships.
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Affiliation(s)
- Håvard Aanes
- BasAM, Norwegian School of Veterinary Science, Dep., 0033 Oslo, Norway.
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Abstract
In this review, we present an overview of the recent advances of genomic technologies applied to studies of fish species belonging to the superclass of Osteichthyes (bony fish) with a major emphasis on the infraclass of Teleostei, also called teleosts. This superclass that represents more than 50% of all known vertebrate species has gained considerable attention from genome researchers in the last decade. We discuss many examples that demonstrate that this highly deserved attention is currently leading to new opportunities for answering important biological questions on gene function and evolutionary processes. In addition to giving an overview of the technologies that have been applied for studying various fish species we put the recent advances in genome research on the model species zebrafish and medaka in the context of its impact for studies of all fish of the superclass of Osteichthyes. We thereby want to illustrate how the combined value of research on model species together with a broad angle perspective on all bony fish species will have a huge impact on research in all fields of fundamental science and will speed up applications in many societally important areas such as the development of new medicines, toxicology test systems, environmental sensing systems and sustainable aquaculture strategies.
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