Zebrafish embryogenesis – A framework to study regulatory RNA elements in development and disease

Translational control of furina by an RNA regulon is important for left-right patterning, heart morphogenesis and cardiac valve function

Heart development is a complex process that requires asymmetric positioning of the heart, cardiac growth and valve morphogenesis. The mechanisms controlling heart morphogenesis and valve formation are not fully understood. The pro-convertase FurinA functions in heart development across vertebrates. How FurinA activity is regulated during heart development is unknown. Through computational analysis of the zebrafish transcriptome, we identified an RNA motif in a variant FurinA transcript harbouring a long 3' untranslated region (3'UTR). The alternative 3'UTR furina isoform is expressed prior to organ positioning. Somatic deletions in the furina 3'UTR lead to embryonic left-right patterning defects. Reporter localisation and RNA-binding assays show that the furina 3'UTR forms complexes with the conserved RNA-binding translational repressor, Ybx1. Conditional ybx1 mutant embryos show premature and increased Furin reporter expression, abnormal cardiac morphogenesis and looping defects. Mutant ybx1 hearts have an expanded atrioventricular canal, abnormal sino-atrial valves and retrograde blood flow from the ventricle to the atrium. This is similar to observations in humans with heart valve regurgitation. Thus, the furina 3'UTR element/Ybx1 regulon is important for translational repression of FurinA and regulation of heart development.

Proteomic analysis of zebrafish (Danio rerio) embryos exposed to benzyl benzoate

Benzyl benzoate (BB) is widely used in the food, cosmetics, agriculture, and pharmaceutical industries and is discharged into the aquatic environment via various water sources, including wastewater. Research on the bioaccumulation and possible toxicity of BB has been conducted, but the biochemical responses to BB toxicity are not fully understood, and the specific molecular pathways by which BB causes toxicity remain unknown. In this study, label-free quantitative proteomics based on mass spectrometry was applied to investigate protein profiles in zebrafish (Danio rerio) embryos exposed to BB (1 µg/mL) for 7 days. A total of 83 differentially expressed proteins (DEPs) were identified, including 49 up-regulated and 34 down-regulated proteins. The biological functions of proteins regulated by BB were grouped into functional categories and subcategories, including the biosynthesis of organonitrogen compound biosynthetic process, translation, amide biosynthetic process, lipid transport, stress response, and cytoskeletal activity. The results provide novel insight into the molecular basis of the ecotoxicity of BB in aquatic ecosystems.

Identification of embryonic RNA granules that act as sites of mRNA translation after changing their physical properties

Fertilized eggs begin to translate mRNAs at appropriate times and placements to control development, but how the translation is regulated remains unclear. Here, we found that pou5f3 mRNA encoding a transcriptional factor essential for development formed granules in a dormant state in zebrafish oocytes. Although the number of pou5f3 granules remained constant, Pou5f3 protein accumulated after fertilization. Intriguingly, signals of newly synthesized peptides and a ribosomal protein became colocalized with pou5f3 granules after fertilization and, moreover, nascent Pou5f3 was shown to be synthesized in the granules. This functional change was accompanied by changes in the state and internal structure of granules. Dissolution of the granules reduced the rate of protein synthesis. Similarly, nanog and sox19b mRNAs in zebrafish and Pou5f1/Oct4 mRNA in mouse assembled into granules. Our results reveal that subcellular compartments, termed embryonic RNA granules, function as activation sites of translation after changing physical properties for directing vertebrate development.

Differential gene expression associated with behavioral variation in ecotypes of Lake Superior brook trout (Salvelinus fontinalis)

Associations between behaviors and the development of different life history tactics have been documented in several species of salmon, trout, and charr. While it is well known that such behaviors are heritable the genes and molecular pathways connected to these behaviors remain unknown. We used an RNA-seq approach to identify genes and molecular pathways differentially regulated in brain tissue between "shy" and "bold" brook trout (Salvelinus fontinalis). A small number of genes were differentially expressed between the behavioral types at several months after hatching and two years of age. Pathway analysis revealed that EIF2 signaling differed consistently between shy and bold individuals suggesting large-scale differences in protein synthesis between behavioral types in the brain. Additionally, the RNA-seq data were used to find polymorphisms within the brook trout genome and a GWAS approach was used to test for statistical associations between genetic variants and behavior type. One allele located in a transcription factor (TSHZ3) contained a protein-coding non-synonymous SNP suggesting that functional variation within TSHZ3 is connected to the development of different behaviors. These results suggest that the molecular basis of behavioral development is complex and due to the differential expression of many genes involved in a wide-range of different molecular pathways.

Investigating the molecular guts of endoderm formation using zebrafish

The vertebrate endoderm makes major contributions to the respiratory and gastrointestinal tracts and all associated organs. Zebrafish and humans share a high degree of genetic homology and strikingly similar endodermal organ systems. Combined with a multitude of experimental advantages, zebrafish are an attractive model organism to study endoderm development and disease. Recent functional genomics studies have shed considerable light on the gene regulatory programs governing early zebrafish endoderm development, while advances in biological and technological approaches stand to further revolutionize our ability to investigate endoderm formation, function and disease. Here, we discuss the present understanding of endoderm specification in zebrafish compared to other vertebrates, how current and emerging methods will allow refined and enhanced analysis of endoderm formation, and how integration with human data will allow modeling of the link between non-coding sequence variants and human disease.

Packaging development: how chromatin controls transcription in zebrafish embryogenesis

How developmental gene expression is activated, co-ordinated and maintained is one of the biggest questions in developmental biology. While transcription factors lead the way in directing developmental gene expression, their accessibility to the correct repertoire of genes can depend on other factors such as DNA methylation, the presence of particular histone variants and post-translational modifications of histones. Collectively, factors that modify DNA or affect its packaging and accessibility contribute to a chromatin landscape that helps to control the timely expression of developmental genes. Zebrafish, perhaps better known for their strength as a model of embryology and organogenesis during development, are coming to the fore as a powerful model for interpreting the role played by chromatin in gene expression. Several recent advances have shown that zebrafish exhibit both similarities and differences to other models (and humans) in the way that they employ chromatin mechanisms of gene regulation. Here, I review how chromatin influences developmental transcriptional programmes during early zebrafish development, patterning and organogenesis. Lastly, I briefly highlight the importance of zebrafish chromatin research towards the understanding of human disease and transgenerational inheritance.