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Epigenetics, Transcriptome and Proteome Analysis of Zebrafish
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Epigenetics, Transcriptome and Proteome Analysis of Zebrafish

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (31 July 2021) | Viewed by 8124

Special Issue Editor

Dr. Beatrice Gagnaire

E-Mail Website
Guest Editor
Laboratory of Ecotoxicology of Radionuclides, Institut de Radioprotection et de Sureté Nucléaire (IRSN), 13115 Saint-Paul-lez-Durance, France
Interests: ecotoxicology; radioactive pollutants; fish, biomarkers; immune system; oxidative stress; neurology; transcriptomic

Special Issue Information

Dear Colleagues,

This Special Issue will be focused on the use of zebrafish, Danio rerio, and the use of new tools to assess modifications of its health status. Zebrafish is a classical model used in toxicology and ecotoxicology. Its genome and proteome are entirely sequenced and well annotated, which helps the development of new screening tools using global analysis approaches. This issue will cover the use of epigenetics, transcriptome, and/or proteome analysis (for example, RNAseq, proteomics, metabolomics) as relevant tools in order to monitor response to organisms to a stressful environment (for example, global warming, exposure to a chemical or a mixture of chemicals).

Dr. Beatrice Gagnaire
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • zebrafish
  • Danio rerio
  • epigenetics
  • transcriptome analysis
  • proteome analysis

Published Papers (3 papers)

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Research

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12 pages, 1604 KiB  
Article
The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression
by Marco Spreafico, Eleonora Mangano, Mara Mazzola, Clarissa Consolandi, Roberta Bordoni, Cristina Battaglia, Silvio Bicciato, Anna Marozzi and Anna Pistocchi
Int. J. Mol. Sci. 2020, 21(24), 9719; https://doi.org/10.3390/ijms21249719 - 19 Dec 2020
Cited by 1 | Viewed by 2209
Abstract
Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity, such as the cohesin genes and their regulator NIPBL. In our previous studies, using a zebrafish [...] Read more.
Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity, such as the cohesin genes and their regulator NIPBL. In our previous studies, using a zebrafish model for nipblb knockdown, we described the effect of nipblb loss-of-function in specific contexts, such as central nervous system development and hematopoiesis. However, the genome-wide transcriptional impact of nipblb loss-of-function in zebrafish embryos at diverse developmental stages remains under investigation. By RNA-seq analyses in zebrafish embryos at 24 h post-fertilization, we examined genome-wide effects of nipblb knockdown on transcriptional programs. Differential gene expression analysis revealed that nipblb loss-of-function has an impact on gene expression at 24 h post fertilization, mainly resulting in gene inactivation. A similar transcriptional effect has also been reported in other organisms, supporting the use of zebrafish as a model to understand the role of Nipbl in gene regulation during early vertebrate development. Moreover, we unraveled a connection between nipblb-dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes, enforcing our previous evidence on the involvement of NIPBL-related transcriptional dysregulation in hematological malignancies. Full article
(This article belongs to the Special Issue Epigenetics, Transcriptome and Proteome Analysis of Zebrafish)
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23 pages, 8319 KiB  
Article
Ionising Radiation Induces Promoter DNA Hypomethylation and Perturbs Transcriptional Activity of Genes Involved in Morphogenesis during Gastrulation in Zebrafish
by Sophia Murat El Houdigui, Christelle Adam-Guillermin and Olivier Armant
Int. J. Mol. Sci. 2020, 21(11), 4014; https://doi.org/10.3390/ijms21114014 - 04 Jun 2020
Cited by 6 | Viewed by 2892
Abstract
Embryonic development is particularly vulnerable to stress and DNA damage, as mutations can accumulate through cell proliferation in a wide number of cells and organs. However, the biological effects of chronic exposure to ionising radiation (IR) at low and moderate dose rates (< [...] Read more.
Embryonic development is particularly vulnerable to stress and DNA damage, as mutations can accumulate through cell proliferation in a wide number of cells and organs. However, the biological effects of chronic exposure to ionising radiation (IR) at low and moderate dose rates (< 6 mGy/h) remain largely controversial, raising concerns for environmental protection. The present study focuses on the molecular effects of IR (0.005 to 50 mGy/h) on zebrafish embryos at the gastrula stage (6 hpf), at both the transcriptomics and epigenetics levels. Our results show that exposure to IR modifies the expression of genes involved in mitochondrial activity from 0.5 to 50 mGy/h. In addition, important developmental pathways, namely, the Notch, retinoic acid, BMP and Wnt signalling pathways, were altered at 5 and 50 mGy/h. Transcriptional changes of genes involved in the morphogenesis of the ectoderm and mesoderm were detected at all dose rates, but were prominent from 0.5 to 50 mGy/h. At the epigenetic level, exposure to IR induced a hypomethylation of DNA in the promoter of genes that colocalised with both H3K27me3 and H3Kme4 histone marks and correlated with changes in transcriptional activity. Finally, pathway enrichment analysis demonstrated that the DNA methylation changes occurred in the promoter of important developmental genes, including morphogenesis of the ectoderm and mesoderm. Together, these results show that the transcriptional program regulating morphogenesis in gastrulating embryos was modified at dose rates greater than or equal to 0.5 mGy/h, which might predict potential neurogenesis and somitogenesis defects observed at similar dose rates later in development. Full article
(This article belongs to the Special Issue Epigenetics, Transcriptome and Proteome Analysis of Zebrafish)
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Review

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16 pages, 1254 KiB  
Review
The Zebrafish Model to Understand Epigenetics in Renal Diseases
by Nina Sopel and Janina Müller-Deile
Int. J. Mol. Sci. 2021, 22(17), 9152; https://doi.org/10.3390/ijms22179152 - 25 Aug 2021
Cited by 3 | Viewed by 2319
Abstract
Epigenetic modifications are able to alter gene expression and include DNA methylation, different histone variants, and post-transcriptional modifications (PTMs), such as acetylation or phosphorylation, and through short/long RNAs, respectively. In this review, we focus on current knowledge concerning epigenetic modifications in gene regulation. [...] Read more.
Epigenetic modifications are able to alter gene expression and include DNA methylation, different histone variants, and post-transcriptional modifications (PTMs), such as acetylation or phosphorylation, and through short/long RNAs, respectively. In this review, we focus on current knowledge concerning epigenetic modifications in gene regulation. We describe different forms of epigenetic modifications and explain how epigenetic changes can be detected. The relevance of epigenetics in renal diseases is highlighted with multiple examples and the use of the zebrafish model to study glomerular diseases in general and epigenetics in renal diseases in particular is discussed. We end with an outlook on how to use epigenetic modifications as a therapeutic target for different diseases. Here, the zebrafish model can be employed as a high-throughput screening tool not only to discover epigenetic alterations contributing to disease, but also to test novel substances that change epigenetic signatures in vivo. Therefore, the zebrafish model harbors the opportunity to find novel pathogenic pathways allowing a pre-selection of potential targets and compounds to be tested for renal diseases. Full article
(This article belongs to the Special Issue Epigenetics, Transcriptome and Proteome Analysis of Zebrafish)
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