mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay.

As model organism-based research shifts from forward to reverse genetics approaches, largely due to the ease of genome editing technology, a low frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein. In zebrafish, this low frequency is in part explained by compensation by genes of redundant or similar function, often resulting from the additional round of teleost-specific whole genome duplication within vertebrates. Here we offer additional explanations for the low frequency of mutant phenotypes. We analyzed mRNA processing in seven zebrafish lines with mutations expected to disrupt gene function, generated by CRISPR/Cas9 or ENU mutagenesis methods. Five of the seven lines showed evidence of altered mRNA processing: one through a skipped exon that did not lead to a frame shift, one through nonsense-associated splicing that did not lead to a frame shift, and three through the use of cryptic splice sites. These results highlight the need for a methodical analysis of the mRNA produced in mutant lines before making conclusions or embarking on studies that assume loss of function as a result of a given genomic change. Furthermore, recognition of the types of adaptations that can occur may inform the strategies of mutant generation.

Knockdown of a galectin-1-like protein in zebrafish (Danio rerio) causes defects in skeletal muscle development.

We previously identified and characterized four galectin-1-like proteins in zebrafish, Drgal1-L1, Drgal1-L2, Drgal1-L3, and one splice variant of Drgal1-L2, of distinct ontogenic expression. Drgal1-L1 is maternal; Drgal1-L2 is zygotic and strongly expressed in the notochord, while Drgal1-L3 is both maternal and zygotic. Knockdown experiments in zebrafish embryos using a morpholino-modified antisense oligo targeted to the 5'-UTR sequence of Drgal1-L2 resulted in a phenotype with a bent tail and disorganized muscle fibers. This effect was dose-dependent as follows: 62-66% at 17 ng, 29-35% at 5.7 ng, 21-28% at 1.9 ng, and 14-17% at 0.6 ng. However, no (or a negligible number of) Drgal1-L1 knockdown embryos showed similar morphological defects, indicating that the observed effects are sequence-specific, and not due to the toxicity of the morpholino-modified oligos. Further, ectopic expression of native Drgal1-L2 specifically rescued the phenotype, as co-injection of the full-length sense Drgal1-L2 mRNA with Drgal1-L2-MO yielded 60-62% normal embryos. As the notochord serves as the primary source of signaling molecules required for proper patterning of adjacent tissues, such as neural tube, somites, and heart, these results suggest that galectins produced by the notochord play a key role in somitic cell differentiation and development.

Biochemical and molecular characterization of galectins from zebrafish (Danio rerio): notochord-specific expression of a prototype galectin during early embryogenesis.

Galectins are a family of beta-galactoside-binding lectins that on synthesis are either translocated into the nucleus or released to the extracellular space. Their developmentally regulated expression, extracellular location, and affinity for extracellular components (such as laminin and fibronectin) suggest a role in embryonic development, but so far this has not been unequivocally established. Zebrafish constitute an ideal model for developmental studies because of their external fertilization, transparent embryos, rapid growth, and availability of a large collection of mutants. As a first step in addressing the biological roles in zebrafish embryogenesis, we identified and characterized members of the three galectin types: three protogalectins (Drgal1-L1, Drgal1-L2, Drgal1-L3), one chimera galectin (Drgal3), and one tandem-repeat galectin (Drgal9-L1). Like mammalian prototype galectin-1, Drgal1-L2 preferentially binds to N-acetyllactosamine. Genomic structure of Drgal1-L2 revealed four exons, with the exon-intron boundaries conserved with the mammalian galectin-1. Interestingly, this gene also encodes an alternatively spliced form of Drgal1-L2 that lacks eight amino acids near the carbohydrate-binding domain. Zebrafish galectins exhibited distinct patterns of temporal expression during embryo development. Drgal1-L2 is expressed postbud stage, and its expression is strikingly specific to the notochord. In contrast, Drgal1-L1 is expressed maternally in the oocytes. Drgal1-L3, Drgal3, and Drgal9-L1 are expressed both maternally and zygotically, ubiquitously in the adult tissues. The distinct temporal and spatial patterns of expression of members of the zebrafish galectin repertoire suggest that each may play distinct biological roles during early embryogenesis.

Galectins in teleost fish: Zebrafish (Danio rerio) as a model species to address their biological roles in development and innate immunity.

Cell surface glycans, such as glycocoproteins and glycolipids, encode information that modulates interactions between cells, or between cells and the extracellular matrix, by specifically regulating the binding to cell surface-associated or soluble carbohydrate-binding receptors, such as lectins. Rapid modifications of exposed carbohydrate moieties by glycosidases and glycosyltransferases, and the equally dynamic patterns of expression of their receptors during early development, suggest that both play important roles during embryogenesis. Among a variety of biological roles, galectins have been proposed to mediate developmental processes, such as embryo implantation and myogenesis. However, the high functional "redundancy" of the galectin repertoire in mammals has hindered the rigorous characterization of their specific roles by gene knockout approaches in murine models. In recent years, the use of teleost fish as alternative models for addressing developmental questions in mammals has expanded dramatically, and we propose their use for the elucidation of biological roles of galectins in embryogenesis and innate immunity. All three major galectin types, proto, chimera, and tandem-repeat, are present in teleost fish, and phylogenetic topologies confirm the expected clustering with their mammalian orthologues. As a model organism, the zebrafish (Danio rerio) may help to overcome limitations imposed by the murine models because it offers substantial advantages: external fertilization, transparent embryos that develop rapidly in vitro, a diverse toolbox of established methods to manipulate early gene expression, a growing collection of mutations that affect early embryonic development, availability of cell lines, and most importantly, an apparently less diversified galectin repertoire.