International Journal of Molecular Sciences

Editorial

Jump to: Research, Review

2 pages, 166 KiB

Open AccessEditorial

Zebrafish: A Powerful Model for Genetics and Genomics

by Seong-Kyu Choe and Cheol-Hee Kim

Int. J. Mol. Sci. 2023, 24(9), 8169; https://doi.org/10.3390/ijms24098169 - 3 May 2023

Cited by 4 | Viewed by 1183

Abstract

Our understanding of fundamental biological mechanisms and the pathogenesis of human diseases has been greatly improved by studying the genetics and genomics of zebrafish [...] Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

Research

Jump to: Editorial, Review

16 pages, 9449 KiB

Open AccessArticle

Negative Elongation Factor (NELF) Inhibits Premature Granulocytic Development in Zebrafish

by Mengling Huang, Abrar Ahmed, Wei Wang, Xue Wang, Cui Ma, Haowei Jiang, Wei Li and Lili Jing

Int. J. Mol. Sci. 2022, 23(7), 3833; https://doi.org/10.3390/ijms23073833 - 30 Mar 2022

Cited by 4 | Viewed by 2346

Abstract

Gene expression is tightly regulated during hematopoiesis. Recent studies have suggested that RNA polymerase II (Pol II) promoter proximal pausing, a temporary stalling downstream of the promoter region after initiation, plays a critical role in regulating the expression of various genes in metazoans. [...] Read more.

Gene expression is tightly regulated during hematopoiesis. Recent studies have suggested that RNA polymerase II (Pol II) promoter proximal pausing, a temporary stalling downstream of the promoter region after initiation, plays a critical role in regulating the expression of various genes in metazoans. However, the function of proximal pausing in hematopoietic gene regulation remains largely unknown. The negative elongation factor (NELF) complex is a key factor important for this proximal pausing. Previous studies have suggested that NELF regulates granulocytic differentiation in vitro, but its in vivo function during hematopoiesis remains uncharacterized. Here, we generated the zebrafish mutant for one NELF complex subunit Nelfb using the CRISPR-Cas9 technology. We found that the loss of nelfb selectively induced excessive granulocytic development during primitive and definitive hematopoiesis. The loss of nelfb reduced hematopoietic progenitor cell formation and did not affect erythroid development. Moreover, the accelerated granulocytic differentiation and reduced progenitor cell development could be reversed by inhibiting Pol II elongation. Further experiments demonstrated that the other NELF complex subunits (Nelfa and Nelfe) played similar roles in controlling granulocytic development. Together, our studies suggested that NELF is critical in controlling the proper granulocytic development in vivo, and that promoter proximal pausing might help maintain the undifferentiated state of hematopoietic progenitor cells. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

17 pages, 1464 KiB

Open AccessArticle

Efficient Generation of Knock-In Zebrafish Models for Inherited Disorders Using CRISPR-Cas9 Ribonucleoprotein Complexes

by Erik de Vrieze, Suzanne E. de Bruijn, Janine Reurink, Sanne Broekman, Vince van de Riet, Marco Aben, Hannie Kremer and Erwin van Wijk

Int. J. Mol. Sci. 2021, 22(17), 9429; https://doi.org/10.3390/ijms22179429 - 30 Aug 2021

Cited by 13 | Viewed by 4894

Abstract

CRISPR-Cas9-based genome-editing is a highly efficient and cost-effective method to generate zebrafish loss-of-function alleles. However, introducing patient-specific variants into the zebrafish genome with CRISPR-Cas9 remains challenging. Targeting options can be limited by the predetermined genetic context, and the efficiency of the homology-directed DNA [...] Read more.

CRISPR-Cas9-based genome-editing is a highly efficient and cost-effective method to generate zebrafish loss-of-function alleles. However, introducing patient-specific variants into the zebrafish genome with CRISPR-Cas9 remains challenging. Targeting options can be limited by the predetermined genetic context, and the efficiency of the homology-directed DNA repair pathway is relatively low. Here, we illustrate our efficient approach to develop knock-in zebrafish models using two previously variants associated with hereditary sensory deficits. We employ sgRNA-Cas9 ribonucleoprotein (RNP) complexes that are micro-injected into the first cell of fertilized zebrafish eggs together with an asymmetric, single-stranded DNA template containing the variant of interest. The introduction of knock-in events was confirmed by massive parallel sequencing of genomic DNA extracted from a pool of injected embryos. Simultaneous morpholino-induced blocking of a key component of the non-homologous end joining DNA repair pathway, Ku70, improved the knock-in efficiency for one of the targets. Our use of RNP complexes provides an improved knock-in efficiency as compared to previously published studies. Correct knock-in events were identified in 3–8% of alleles, and 30–45% of injected animals had the target variant in their germline. The detailed technical and procedural insights described here provide a valuable framework for the efficient development of knock-in zebrafish models. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

16 pages, 13174 KiB

Open AccessArticle

Renal and Extra Renal Manifestations in Adult Zebrafish Model of Cystinosis

by Sante Princiero Berlingerio, Junling He, Lies De Groef, Harold Taeter, Tomas Norton, Pieter Baatsen, Sara Cairoli, Bianca Goffredo, Peter de Witte, Lambertus van den Heuvel, Hans J. Baelde and Elena Levtchenko

Int. J. Mol. Sci. 2021, 22(17), 9398; https://doi.org/10.3390/ijms22179398 - 30 Aug 2021

Cited by 3 | Viewed by 2866

Abstract

Cystinosis is a rare, incurable, autosomal recessive disease caused by mutations in the CTNS gene. This gene encodes the lysosomal cystine transporter cystinosin, leading to lysosomal cystine accumulation in all cells of the body, with kidneys being the first affected organs. The current [...] Read more.

Cystinosis is a rare, incurable, autosomal recessive disease caused by mutations in the CTNS gene. This gene encodes the lysosomal cystine transporter cystinosin, leading to lysosomal cystine accumulation in all cells of the body, with kidneys being the first affected organs. The current treatment with cysteamine decreases cystine accumulation, but does not reverse the proximal tubular dysfunction, glomerular injury or loss of renal function. In our previous study, we have developed a zebrafish model of cystinosis through a nonsense mutation in the CTNS gene and have shown that zebrafish larvae recapitulate the kidney phenotype described in humans. In the current study, we characterized the adult cystinosis zebrafish model and evaluated the long-term effects of the disease on kidney and extra renal organs through biochemical, histological, fertility and locomotor activity studies. We found that the adult cystinosis zebrafish presents cystine accumulation in various organs, altered kidney morphology, impaired skin pigmentation, decreased fertility, altered locomotor activity and ocular anomalies. Overall, our data indicate that the adult cystinosis zebrafish model reproduces several human phenotypes of cystinosis and may be useful for studying pathophysiology and long-term effects of novel therapies. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

13 pages, 5980 KiB

Open AccessArticle

Loss of Ift74 Leads to Slow Photoreceptor Degeneration and Ciliogenesis Defects in Zebrafish

by Panpan Zhu, Jingjin Xu, Yadong Wang and Chengtian Zhao

Int. J. Mol. Sci. 2021, 22(17), 9329; https://doi.org/10.3390/ijms22179329 - 28 Aug 2021

Cited by 5 | Viewed by 2193

Abstract

Cilia are microtubule-based structures projecting from the cell surface that perform diverse biological functions. Ciliary defects can cause a wide range of genetic disorders known collectively as ciliopathies. Intraflagellar transport (IFT) proteins are essential for the assembly and maintenance of cilia by transporting [...] Read more.

Cilia are microtubule-based structures projecting from the cell surface that perform diverse biological functions. Ciliary defects can cause a wide range of genetic disorders known collectively as ciliopathies. Intraflagellar transport (IFT) proteins are essential for the assembly and maintenance of cilia by transporting proteins along the axoneme. Here, we report a lack of Ift74, a core IFT-B protein, leading to ciliogenesis defects in multiple organs during early zebrafish development. Unlike rapid photoreceptor cell death in other ift-b mutants, the photoreceptors of ift74 mutants exhibited a slow degeneration process. Further experiments demonstrated that the connecting cilia of ift74 mutants were initially formed but failed to maintain, which resulted in slow opsin transport efficiency and eventually led to photoreceptor cell death. We also showed that the large amount of maternal ift74 transcripts deposited in zebrafish eggs account for the main reason of slow photoreceptor degeneration in the mutants. Together, our data suggested Ift74 is critical for ciliogenesis and that Ift proteins play variable roles in different types of cilia during early zebrafish development. To our knowledge, this is the first study to show ift-b mutant that displays slow photoreceptor degeneration in zebrafish. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

13 pages, 2633 KiB

Open AccessArticle

Zebrafish Bioassay for Screening Therapeutic Candidates Based on Melanotrophic Activity

by Ted I. Hong, Kyu-Seok Hwang, Tae-Ik Choi, Gunnar Kleinau, Patrick Scheerer, Jeong Kyu Bang, Seung-Hyun Jung and Cheol-Hee Kim

Int. J. Mol. Sci. 2021, 22(17), 9313; https://doi.org/10.3390/ijms22179313 - 27 Aug 2021

Cited by 2 | Viewed by 2879

Abstract

In this study, we used the zebrafish animal model to establish a bioassay by which physiological efficacy differential of alpha-melanocyte-stimulating hormone (α-MSH) analogues could be measured by melanosome dispersion in zebrafish larvae. Brain-skin connection research has purported the interconnectedness between the nervous system [...] Read more.

In this study, we used the zebrafish animal model to establish a bioassay by which physiological efficacy differential of alpha-melanocyte-stimulating hormone (α-MSH) analogues could be measured by melanosome dispersion in zebrafish larvae. Brain-skin connection research has purported the interconnectedness between the nervous system and skin physiology. Accordingly, the neuropeptide α-MSH is a key regulator in several physiological processes, such as skin pigmentation in fish. In mammals, α-MSH has been found to regulate motivated behavior, appetite, and emotion, including stimulation of satiety and anxiety. Several clinical and animal model studies of autism spectrum disorder (ASD) have already demonstrated the effectiveness of α-MSH in restoring the social deficits of autism. Therefore, we sought to analyze the effect of synthetic and naturally-occurring α-MSH variants amongst different species. Our results showed that unique α-MSH derivatives from several fish species produced differential effects on the degree of melanophore dispersion. Using α-MSH human form as a standard, we could identify derivatives that induced greater physiological effects; particularly, the synthetic analogue melanotan-II (MT-II) exhibited a higher capacity for melanophore dispersion than human α-MSH. This was consistent with previous findings in an ASD mouse model demonstrating the effectiveness of MT-II in improving ASD behavioral symptoms. Thus, the melanophore assay may serve as a useful screening tool for therapeutic candidates for novel drug discovery. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

18 pages, 3470 KiB

Open AccessArticle

Zebrafish as a Model to Evaluate a CRISPR/Cas9-Based Exon Excision Approach as a Future Treatment Option for EYS-Associated Retinitis Pigmentosa

by Renske Schellens, Erik de Vrieze, Pam Graave, Sanne Broekman, Kerstin Nagel-Wolfrum, Theo Peters, Hannie Kremer, Rob W. J. Collin and Erwin van Wijk

Int. J. Mol. Sci. 2021, 22(17), 9154; https://doi.org/10.3390/ijms22179154 - 25 Aug 2021

Cited by 6 | Viewed by 3534

Abstract

Retinitis pigmentosa (RP) is an inherited retinal disease (IRD) with an overall prevalence of 1 in 4000 individuals. Mutations in EYS (Eyes shut homolog) are among the most frequent causes of non-syndromic autosomal recessively inherited RP and act via a loss-of-function [...] Read more.

Retinitis pigmentosa (RP) is an inherited retinal disease (IRD) with an overall prevalence of 1 in 4000 individuals. Mutations in EYS (Eyes shut homolog) are among the most frequent causes of non-syndromic autosomal recessively inherited RP and act via a loss-of-function mechanism. In light of the recent successes for other IRDs, we investigated the therapeutic potential of exon skipping for EYS-associated RP. CRISPR/Cas9 was employed to generate zebrafish from which the region encompassing the orthologous exons 37-41 of human EYS (eys exons 40-44) was excised from the genome. The excision of these exons was predicted to maintain the open reading frame and to result in the removal of exactly one Laminin G and two EGF domains. Although the eys^Δexon40-44 transcript was found at levels comparable to wild-type eys, and no unwanted off-target modifications were identified within the eys coding sequence after single-molecule sequencing, Eys^Δexon40-44 protein expression could not be detected. Visual motor response experiments revealed that eys^Δexon40-44 larvae were visually impaired and histological analysis revealed a progressive degeneration of the retinal outer nuclear layer in these zebrafish. Altogether, the data obtained in our zebrafish model currently provide no indications for the skipping of EYS exons 37-41 as an effective future treatment strategy for EYS-associated RP. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

14 pages, 2387 KiB

Open AccessArticle

Optogenetic Manipulation of Olfactory Responses in Transgenic Zebrafish: A Neurobiological and Behavioral Study

by Yun-Mi Jeong, Tae-Ik Choi, Kyu-Seok Hwang, Jeong-Soo Lee, Robert Gerlai and Cheol-Hee Kim

Int. J. Mol. Sci. 2021, 22(13), 7191; https://doi.org/10.3390/ijms22137191 - 3 Jul 2021

Cited by 4 | Viewed by 3763

Abstract

Olfaction is an important neural system for survival and fundamental behaviors such as predator avoidance, food finding, memory formation, reproduction, and social communication. However, the neural circuits and pathways associated with the olfactory system in various behaviors are not fully understood. Recent advances [...] Read more.

Olfaction is an important neural system for survival and fundamental behaviors such as predator avoidance, food finding, memory formation, reproduction, and social communication. However, the neural circuits and pathways associated with the olfactory system in various behaviors are not fully understood. Recent advances in optogenetics, high-resolution in vivo imaging, and reconstructions of neuronal circuits have created new opportunities to understand such neural circuits. Here, we generated a transgenic zebrafish to manipulate olfactory signal optically, expressing the Channelrhodopsin (ChR2) under the control of the olfactory specific promoter, omp. We observed light-induced neuronal activity of olfactory system in the transgenic fish by examining c-fos expression, and a calcium indicator suggesting that blue light stimulation caused activation of olfactory neurons in a non-invasive manner. To examine whether the photo-activation of olfactory sensory neurons affect behavior of zebrafish larvae, we devised a behavioral choice paradigm and tested how zebrafish larvae choose between two conflicting sensory cues, an aversive odor or the naturally preferred phototaxis. We found that when the conflicting cues (the preferred light and aversive odor) were presented together simultaneously, zebrafish larvae swam away from the aversive odor. However, the transgenic fish with photo-activation were insensitive to the aversive odor and exhibited olfactory desensitization upon optical stimulation of ChR2. These results show that an aversive olfactory stimulus can override phototaxis, and that olfaction is important in decision making in zebrafish. This new transgenic model will be useful for the analysis of olfaction related behaviors and for the dissection of underlying neural circuits. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

22 pages, 5984 KiB

Open AccessArticle

Null cyp1b1 Activity in Zebrafish Leads to Variable Craniofacial Defects Associated with Altered Expression of Extracellular Matrix and Lipid Metabolism Genes

by Susana Alexandre-Moreno, Juan-Manuel Bonet-Fernández, Raquel Atienzar-Aroca, José-Daniel Aroca-Aguilar and Julio Escribano

Int. J. Mol. Sci. 2021, 22(12), 6430; https://doi.org/10.3390/ijms22126430 - 16 Jun 2021

Cited by 8 | Viewed by 3883

Abstract

CYP1B1 loss of function (LoF) is the main known genetic alteration present in recessive primary congenital glaucoma (PCG), an infrequent disease characterized by delayed embryonic development of the ocular iridocorneal angle; however, the underlying molecular mechanisms are poorly understood. To model CYP1B1 LoF [...] Read more.

CYP1B1 loss of function (LoF) is the main known genetic alteration present in recessive primary congenital glaucoma (PCG), an infrequent disease characterized by delayed embryonic development of the ocular iridocorneal angle; however, the underlying molecular mechanisms are poorly understood. To model CYP1B1 LoF underlying PCG, we developed a cyp1b1 knockout (KO) zebrafish line using CRISPR/Cas9 genome editing. This line carries the c.535_667del frameshift mutation that results in the 72% mRNA reduction with the residual mRNA predicted to produce an inactive truncated protein (p.(His179Glyfs*6)). Microphthalmia and jaw maldevelopment were observed in 23% of F0 somatic mosaic mutant larvae (144 hpf). These early phenotypes were not detected in cyp1b1-KO F3 larvae (144 hpf), but 27% of adult (four months) zebrafish exhibited uni- or bilateral craniofacial alterations, indicating the existence of incomplete penetrance and variable expressivity. These phenotypes increased to 86% in the adult offspring of inbred progenitors with craniofacial defects. No glaucoma-related phenotypes were observed in cyp1b1 mutants. Transcriptomic analyses of the offspring (seven dpf) of cyp1b1-KO progenitors with adult-onset craniofacial defects revealed functionally enriched differentially expressed genes related to extracellular matrix and cell adhesion, cell growth and proliferation, lipid metabolism (retinoids, steroids and fatty acids and oxidation–reduction processes that include several cytochrome P450 genes) and inflammation. In summary, this study shows the complexity of the phenotypes and molecular pathways associated with cyp1b1 LoF, with species dependency, and provides evidence for the dysregulation of extracellular matrix gene expression as one of the mechanisms underlying the pathogenicity associated with cyp1b1 disruption. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Graphical abstract

12 pages, 2231 KiB

Open AccessArticle

Apex Resection in Zebrafish (Danio rerio) as a Model of Heart Regeneration: A Video-Assisted Guide

by Ditte Gry Ellman, Ibrahim Mohamad Slaiman, Sabrina Bech Mathiesen, Kristian Skriver Andersen, Wolfgang Hofmeister, Elke Annette Ober and Ditte Caroline Andersen

Int. J. Mol. Sci. 2021, 22(11), 5865; https://doi.org/10.3390/ijms22115865 - 30 May 2021

Cited by 4 | Viewed by 3085

Abstract

Ischemic heart disease is one of the leading causes of deaths worldwide. A major hindrance to resolving this challenge lies in the mammalian hearts inability to regenerate after injury. In contrast, zebrafish retain a regenerative capacity of the heart throughout their lifetimes. Apex [...] Read more.

Ischemic heart disease is one of the leading causes of deaths worldwide. A major hindrance to resolving this challenge lies in the mammalian hearts inability to regenerate after injury. In contrast, zebrafish retain a regenerative capacity of the heart throughout their lifetimes. Apex resection (AR) is a popular zebrafish model for studying heart regeneration, and entails resecting 10–20% of the heart in the apex region, whereafter the regeneration process is monitored until the heart is fully regenerated within 60 days. Despite this popularity, video tutorials describing this technique in detail are lacking. In this paper we visualize and describe the entire AR procedure including anaesthesia, surgery, and recovery. In addition, we show that the concentration and duration of anaesthesia are important parameters to consider, to balance sufficient levels of sedation and minimizing mortality. Moreover, we provide examples of how zebrafish heart regeneration can be assessed both in 2D (immunohistochemistry of heart sections) and 3D (analyses of whole, tissue cleared hearts using multiphoton imaging). In summary, this paper aims to aid beginners in establishing and conducting the AR model in their laboratory, but also to spur further interest in improving the model and its evaluation. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

19 pages, 3110 KiB

Open AccessArticle

Generation of GCaMP6s-Expressing Zebrafish to Monitor Spatiotemporal Dynamics of Calcium Signaling Elicited by Heat Stress

by Fengyang Li, Yong Long, Juhong Xie, Jing Ren, Tong Zhou, Guili Song, Qing Li and Zongbin Cui

Int. J. Mol. Sci. 2021, 22(11), 5551; https://doi.org/10.3390/ijms22115551 - 24 May 2021

Cited by 8 | Viewed by 3367

Abstract

The ability of organisms to quickly sense and transduce signals of environmental stresses is critical for their survival. Ca²⁺ is a versatile intracellular messenger involved in sensing a wide variety of stresses and regulating the subsequent cellular responses. So far, our understanding [...] Read more.

The ability of organisms to quickly sense and transduce signals of environmental stresses is critical for their survival. Ca²⁺ is a versatile intracellular messenger involved in sensing a wide variety of stresses and regulating the subsequent cellular responses. So far, our understanding for calcium signaling was mostly obtained from ex vivo tissues and cultured cell lines, and the in vivo spatiotemporal dynamics of stress-triggered calcium signaling in a vertebrate remains to be characterized. Here, we describe the generation and characterization of a transgenic zebrafish line with ubiquitous expression of GCaMP6s, a genetically encoded calcium indicator (GECI). We developed a method to investigate the spatiotemporal patterns of Ca²⁺ events induced by heat stress. Exposure to heat stress elicited immediate and transient calcium signaling in developing zebrafish. Cells extensively distributed in the integument of the head and body trunk were the first batch of responders and different cell populations demonstrated distinct response patterns upon heat stress. Activity of the heat stress-induced calcium signaling peaked at 30 s and swiftly decreased to near the basal level at 120 s after the beginning of exposure. Inhibition of the heat-induced calcium signaling by LaCl₃ and capsazepine and treatment with the inhibitors for CaMKII (Ca²²/calmodulin-dependent protein kinase II) and HSF1 (Heat shock factor 1) all significantly depressed the enhanced heat shock response (HSR). Together, we delineated the spatiotemporal dynamics of heat-induced calcium signaling and confirmed functions of the Ca²⁺-CaMKII-HSF1 pathway in regulating the HSR in zebrafish. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

10 pages, 4068 KiB

Open AccessArticle

Generation of a Novel Transgenic Zebrafish for Studying Adipocyte Development and Metabolic Control

by Yousheng Mao, Kwang-Heum Hong, Weifang Liao, Li Li, Seong-Jin Kim, Yinyi Xiong, In-Koo Nam, Seong-Kyu Choe and Seong-Ae Kwak

Int. J. Mol. Sci. 2021, 22(8), 3994; https://doi.org/10.3390/ijms22083994 - 13 Apr 2021

Cited by 4 | Viewed by 2479

Abstract

Zebrafish have become a popular animal model for studying various biological processes and human diseases. The metabolic pathways and players conserved among zebrafish and mammals facilitate the use of zebrafish to understand the pathological mechanisms underlying various metabolic disorders in humans. Adipocytes play [...] Read more.

Zebrafish have become a popular animal model for studying various biological processes and human diseases. The metabolic pathways and players conserved among zebrafish and mammals facilitate the use of zebrafish to understand the pathological mechanisms underlying various metabolic disorders in humans. Adipocytes play an important role in metabolic homeostasis, and zebrafish adipocytes have been characterized. However, a versatile and reliable zebrafish model for long-term monitoring of adipose tissues has not been reported. In this study, we generated stable transgenic zebrafish expressing enhanced green fluorescent protein (EGFP) in adipocytes. The transgenic zebrafish harbored adipose tissues that could be detected using GFP fluorescence and the morphology of single adipocyte could be investigated in vivo. In addition, we demonstrated the applicability of this model to the long-term in vivo imaging of adipose tissue development and regulation based on nutrition. The transgenic zebrafish established in this study may serve as an excellent tool to advance the characterization of white adipose tissue in zebrafish, thereby aiding the development of therapeutic interventions to treat metabolic diseases in humans. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

24 pages, 7754 KiB

Open AccessArticle

Characterization of Biological Pathways Regulating Acute Cold Resistance of Zebrafish

by Jing Ren, Yong Long, Ran Liu, Guili Song, Qing Li and Zongbin Cui

Int. J. Mol. Sci. 2021, 22(6), 3028; https://doi.org/10.3390/ijms22063028 - 16 Mar 2021

Cited by 31 | Viewed by 4018

Abstract

Low temperature stress represents a major threat to the lives of both farmed and wild fish species. However, biological pathways determining the development of cold resistance in fish remain largely unknown. Zebrafish larvae at 96 hpf were exposed to lethal cold stress (10 [...] Read more.

Low temperature stress represents a major threat to the lives of both farmed and wild fish species. However, biological pathways determining the development of cold resistance in fish remain largely unknown. Zebrafish larvae at 96 hpf were exposed to lethal cold stress (10 °C) for different time periods to evaluate the adverse effects at organism, tissue and cell levels. Time series RNA sequencing (RNA-seq) experiments were performed to delineate the transcriptomic landscape of zebrafish larvae under cold stress and during the subsequent rewarming phase. The genes regulated by cold stress were characterized by progressively enhanced or decreased expression, whereas the genes associated with rewarming were characterized by rapid upregulation upon return to normal temperature (28 °C). Genes such as trib3, dusp5 and otud1 were identified as the representative molecular markers of cold-induced damages through network analysis. Biological pathways involved in cold stress responses were mined from the transcriptomic data and their functions in regulating cold resistance were validated using specific inhibitors. The autophagy, FoxO and MAPK (mitogen-activated protein kinase) signaling pathways were revealed to be survival pathways for enhancing cold resistance, while apoptosis and necroptosis were the death pathways responsible for cold-induced mortality. Functional mechanisms of the survival-enhancing factors Foxo1, ERK (extracellular signal-regulated kinase) and p38 MAPK were further characterized by inhibiting their activities upon cold stress and analyzing gene expression though RNA-seq. These factors were demonstrated to determine the cold resistance of zebrafish through regulating apoptosis and p53 signaling pathway. These findings have provided novel insights into the stress responses elicited by lethal cold and shed new light on the molecular mechanisms underlying cold resistance of fish. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

12 pages, 2151 KiB

Open AccessArticle

Comparative Proteome Research in a Zebrafish Model for Vanishing White Matter Disease

by Doeun Kim, Yu-Ri Lee, Tae-Ik Choi, Se-Hee Kim, Hoon-Chul Kang, Cheol-Hee Kim and Sangkyu Lee

Int. J. Mol. Sci. 2021, 22(5), 2707; https://doi.org/10.3390/ijms22052707 - 8 Mar 2021

Cited by 4 | Viewed by 3418

Abstract

Vanishing white matter (VWM) disease is a genetic leukodystrophy leading to severe neurological disease and early death. VWM is caused by bi-allelic mutations in any of the five genes encoding the subunits of the eukaryotic translation factor 2B (EIF2B). Previous studies have attempted [...] Read more.

Vanishing white matter (VWM) disease is a genetic leukodystrophy leading to severe neurological disease and early death. VWM is caused by bi-allelic mutations in any of the five genes encoding the subunits of the eukaryotic translation factor 2B (EIF2B). Previous studies have attempted to investigate the molecular mechanism of VWN by constructing models for each subunit of EIF2B that causes VWM disease. The underlying molecular mechanisms of the way in which mutations in EIF2B3 result in VWM are largely unknown. Based on our recent results, we generated an eif2b3 knockout (eif2b3^−/−) zebrafish model and performed quantitative proteomic analysis between the wild-type (WT) and eif2b3^−/− zebrafish, and identified 25 differentially expressed proteins. Four proteins were significantly upregulated, and 21 proteins were significantly downregulated in eif2b3^−/− zebrafish compared to WT. Lon protease and the neutral amino acid transporter SLC1A4 were significantly increased in eif2b3^−/− zebrafish, and crystallin proteins were significantly decreased. The differential expression of proteins was confirmed by the evaluation of mRNA levels in eif2b3^−/− zebrafish, using whole-mount in situ hybridization analysis. This study identified proteins which candidates as key regulators of the progression of VWN disease, using quantitative proteomic analysis in the first EIF2B3 animal model of VWN disease. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

Review

Jump to: Editorial, Research

15 pages, 647 KiB

Open AccessReview

Disease Modeling of Rare Neurological Disorders in Zebrafish

by Myeongjoo Son, Dae Yu Kim and Cheol-Hee Kim

Int. J. Mol. Sci. 2022, 23(7), 3946; https://doi.org/10.3390/ijms23073946 - 1 Apr 2022

Cited by 5 | Viewed by 3427

Abstract

Rare diseases are those which affect a small number of people compared to the general population. However, many patients with a rare disease remain undiagnosed, and a large majority of rare diseases still have no form of viable treatment. Approximately 40% of rare [...] Read more.

Rare diseases are those which affect a small number of people compared to the general population. However, many patients with a rare disease remain undiagnosed, and a large majority of rare diseases still have no form of viable treatment. Approximately 40% of rare diseases include neurologic and neurodevelopmental disorders. In order to understand the characteristics of rare neurological disorders and identify causative genes, various model organisms have been utilized extensively. In this review, the characteristics of model organisms, such as roundworms, fruit flies, and zebrafish, are examined, with an emphasis on zebrafish disease modeling in rare neurological disorders. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

18 pages, 1340 KiB

Open AccessReview

Using the Zebrafish as a Genetic Model to Study Erythropoiesis

by Yuhan Zhang, Mengying Chen and Caiyong Chen

Int. J. Mol. Sci. 2021, 22(19), 10475; https://doi.org/10.3390/ijms221910475 - 28 Sep 2021

Cited by 10 | Viewed by 4783

Abstract

Vertebrates generate mature red blood cells (RBCs) via a highly regulated, multistep process called erythropoiesis. Erythropoiesis involves synthesis of heme and hemoglobin, clearance of the nuclei and other organelles, and remodeling of the plasma membrane, and these processes are exquisitely coordinated by specific [...] Read more.

Vertebrates generate mature red blood cells (RBCs) via a highly regulated, multistep process called erythropoiesis. Erythropoiesis involves synthesis of heme and hemoglobin, clearance of the nuclei and other organelles, and remodeling of the plasma membrane, and these processes are exquisitely coordinated by specific regulatory factors including transcriptional factors and signaling molecules. Defects in erythropoiesis can lead to blood disorders such as congenital dyserythropoietic anemias, Diamond–Blackfan anemias, sideroblastic anemias, myelodysplastic syndrome, and porphyria. The molecular mechanisms of erythropoiesis are highly conserved between fish and mammals, and the zebrafish (Danio rerio) has provided a powerful genetic model for studying erythropoiesis. Studies in zebrafish have yielded important insights into RBC development and established a number of models for human blood diseases. Here, we focus on latest discoveries of the molecular processes and mechanisms regulating zebrafish erythropoiesis and summarize newly established zebrafish models of human anemias. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

13 pages, 3880 KiB

Open AccessReview

Mechanistic Insights into Axenfeld–Rieger Syndrome from Zebrafish foxc1 and pitx2 Mutants

by Curtis R. French

Int. J. Mol. Sci. 2021, 22(18), 10001; https://doi.org/10.3390/ijms221810001 - 16 Sep 2021

Cited by 12 | Viewed by 2296

Abstract

Axenfeld–Rieger syndrome (ARS) encompasses a group of developmental disorders that affect the anterior segment of the eye, as well as systemic developmental defects in some patients. Malformation of the ocular anterior segment often leads to secondary glaucoma, while some patients also present with [...] Read more.

Axenfeld–Rieger syndrome (ARS) encompasses a group of developmental disorders that affect the anterior segment of the eye, as well as systemic developmental defects in some patients. Malformation of the ocular anterior segment often leads to secondary glaucoma, while some patients also present with cardiovascular malformations, craniofacial and dental abnormalities and additional periumbilical skin. Genes that encode two transcription factors, FOXC1 and PITX2, account for almost half of known cases, while the genetic lesions in the remaining cases remain unresolved. Given the genetic similarity between zebrafish and humans, as well as robust antisense inhibition and gene editing technologies available for use in these animals, loss of function zebrafish models for ARS have been created and shed light on the mechanism(s) whereby mutations in these two transcription factors cause such a wide array of developmental phenotypes. This review summarizes the published phenotypes in zebrafish foxc1 and pitx2 loss of function models and discusses possible mechanisms that may be used to target pharmaceutical development and therapeutic interventions. Full article

(This article belongs to the Special Issue Zebrafish: A Powerful Model for Genetics and Genomics)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Zebrafish: A Powerful Model for Genetics and Genomics

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Related Special Issues

Published Papers (17 papers)

Editorial

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI