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Angiosarcoma is a clinically aggressive tumor with a high rate of mortality. It can arise in vascular or lymphatic tissues, involve any part of the body, and aggressively spread locally or metastasize. Angiosarcomas spontaneously develop in the tp53 deleted (tp53del/del) zebrafish mutant. However, established protocols for tumor dissection and transplantation of single cell suspensions of angiosarcoma tumors result in inferior implantation rates. To resolve these complications, we developed a new tumor grafting technique for engraftment of angiosarcoma and similar tumors in zebrafish, which maintains the tumor microenvironment and has superior rates of engraftment.

Although recent advances in the treatment of acute coronary heart disease have reduced mortality rates, few therapeutic strategies exist to mitigate the progressive loss of cardiac function that manifests as heart failure. Nuclear factor, erythroid 2 like 2 (Nfe2l2, Nrf2) is a transcriptional regulator that is known to confer transient myocardial cytoprotection following acute ischemic insult; however, its sustained activation paradoxically causes a reductive environment characterized by excessive antioxidant activity. We previously identified a subset of 16 microRNAs (miRNA) significantly diminished in Nrf2-ablated (Nrf2−/−) mouse hearts, leading to the hypothesis that increasing levels of Nrf2 activation augments miRNA induction and post-transcriptional dysregulation. Here, we report the identification of distinct miRNA signatures (i.e. “reductomiRs”) associated with Nrf2 overexpression in a cardiac-specific and constitutively active Nrf2 transgenic (caNrf2-Tg) mice expressing low (TgL) and high (TgH) levels. We also found several Nrf2 dose-responsive miRNAs harboring proximal antioxidant response elements (AREs), implicating these “reductomiRs” as putative meditators of Nrf2-dependent post-transcriptional regulation. Analysis of mRNA-sequencing identified a complex network of miRNAs and effector mRNAs encoding known pathological hallmarks of cardiac stress-response. Altogether, these data support Nrf2 as a putative regulator of cardiac miRNA expression and provide novel candidates for future mechanistic investigation to understand the relationship between myocardial reductive stress and cardiac pathophysiology.

The development of the heart follows a synergic action of several signaling pathways during gestational, pre- & postnatal stages. The current study aimed to investigate whether the myocardium experiences transcriptional changes during the transition from post-natal to adulthood stages. Herein, we used C57/Bl6/J mice at 4 (28- days; post-natal/PN) and 20 weeks (adulthood/AH) of ages and employed the next generation RNAseq (NGS) to profile the transcriptome and echocardiography analysis to monitor the structural/functional changes in the heart. NGS-based RNA-seq revealed that 1215 genes were significantly upregulated and 2549 were down regulated in the AH versus PN hearts, indicating a significant transcriptional change during this transition. A synchronized cardiac transcriptional regulation through cell cycle, growth hormones, redox homeostasis, and metabolic pathways was noticed in both PN and AH hearts. Echocardiography revealed significant structural and functional (i.e. systolic/diastolic) changes during the transition of PN to adult stage. Particularly, a progressive decline in ejection fraction and cardiac output was observed in AH hearts. These structural adaptations are in line with critical signaling pathways that drive the maturation of heart during AH. Overall, we have presented a comprehensive transcriptomic analysis along with a structural-functional relationship during the myocardial development in adult mice.

Graphical abstract Abstract The development of gene editing technologies, especially the CRISPR-Cas9 system, has been pivotal for understanding the functional role of proteins. Rapid and efficient genotyping methods are necessary to screen for generated mutations and streamline the isolation of homozygotes. CRISPR-Cas9 system targeting a single site in the gene typically results in small indels. Many genotyping methods utilize the heteroduplex that is formed when wild-type and mutant amplicons with small indels anneal during PCR creating a bubble due to mismatched strands. These methods include T7 endonuclease/Cel-I assay, high resolution melting (HRM) analysis, and heteroduplex mobility assay (HMA). Our protocol explains a simple, two step method of a mixing HMA (mHMA) to identify homozygous mutants, a modification of the previously published HMA. We have utilized the mHMA for screening and genotyping numerous CRISPR generated models. The mHMA method to differentiate homozygous wild type from homozygous mutant animals eliminates - • DNA sequencing, even with small indels that can be difficult to discern on a gel. • additional enzymatic reaction steps, such as with the T7EI/Cel-I assay. • specialized equipment and analysis tools, such as with HRM analysis.

Mice with disruptions of growth hormone‐releasing hormone (GHRH) or growth hormone receptor (GHR) exhibit similar phenotypes of prolonged lifespan and delayed age‐related diseases. However, these two models respond differently to calorie restriction indicating that they might carry different and/or independent mechanisms for improved longevity and healthspan. In order to elucidate these mechanisms, we generated GHRH and GHR double‐knockout mice (D‐KO). In the present study, we focused specifically on the characteristics of female D‐KO mice. The D‐KO mice have reduced body weight and enhanced insulin sensitivity compared to wild‐type (WT) controls. Growth retardation in D‐KO mice is accompanied by decreased GH expression in pituitary, decreased circulating IGF‐1, increased high‐molecular‐weight (HMW) adiponectin, and leptin hormones compared to WT controls. Generalized linear model‐based regression analysis, which controls for body weight differences between D‐KO and WT groups, shows that D‐KO mice have decreased lean mass, bone mineral density, and bone mineral content, but increased adiposity. Indirect calorimetry markers including oxygen consumption, carbon dioxide production, and energy expenditure were significantly lower in D‐KO mice relative to the controls. In comparison with WT mice, the D‐KO mice displayed reduced respiratory exchange ratio (RER) values only during the light cycle, suggesting a circadian‐related metabolic shift toward fat utilization. Interestingly, to date survival data suggest extended lifespan in D‐KO female mice., In comparison with WT mice, the D‐KO mice displayed reduced respiratory exchange ratio (RER) values only during the light cycle, suggesting a circadian‐related metabolic shift towards fat utilization.

The development of the heart follows a synergic action of several signaling pathways during gestational, pre- & postnatal stages. The current study aimed to investigate whether the myocardium experiences transcriptional changes during the transition from post-natal to adult hood stages. Herein, we used C57/Bl6/J mice at 4 (28-days; post-natal/PN) and 20 weeks (adulthood/AH) of ages and employed the next generation RNAseq (NGS) to profile the transcriptome and echocardiography analysis to monitor the structural/functional changes in the heart. NGS-based RNA-seq revealed that 1215 genes were significantly upregulated and 2549 were down regulated in the AH versus PN hearts, indicating a significant transcriptional change during this transition. A synchronized cardiac transcriptional regulation through cell cycle, growth hormones, redox homeostasis and metabolic pathways was noticed in both PN and AH hearts. Echocardiography reveals significant structural and functional (i.e. systolic/diastolic) changes during the transition of PN to adult stage. Particularly, a progressive decline in ejection fraction (EF) and cardiac output was observed in AH hearts. These structural adaptations are in line with critical signaling pathways that drive the maturation of heart during AH. Overall, we have presented a comprehensive transcriptomic analysis along with structural-functional relationship during the myocardial development in adult mice.

Our previous study demonstrated that the loss of growth hormone releasing hormone (GHRH) results in increased lifespan and improved metabolic homeostasis in the mouse model generated by classical embryonic stem cell based gene-targeting method. In this study, we targeted the GHRH gene using the CRISPR/Cas9 technology to avoid passenger alleles/mutations and performed in-depth physiological and metabolic characterization. In agreement with our previous observation, male and female GHRH-/- mice have significantly reduced body weight and enhanced insulin sensitivity when compared to wild type littermates. Dual-energy X-ray absorptiometry showed that there were significant decreases in lean mass, bone mineral content and density, and a dramatic increase in fat mass of GHRH-/- mice when compared to wild type littermates. Indirect calorimetry measurements including oxygen consumption, carbon dioxide production and energy expenditure were dramatically reduced in GHRH-/- mice compared to wild type mice. Respiratory exchange ratio was significantly lower in GHRH-/- mice during the light cycle, but not during the dark cycle, indicating a circadian related metabolic shift towards fat utilization in the growth hormone deficient mice. The novel CRISPR/Cas9 GHRH-/- mice are exhibiting the consistent and unique physiological and metabolic characteristics, which might mediate the longevity effects of growth hormone deficiency in mice.

The key negative regulatory gene of the RAS pathway, NF1, is mutated or deleted in numerous cancer types and is associated with increased cancer risk and drug resistance. Even though women with neurofibromatosis (germline NF1 mutations) have a substantially increased breast cancer risk at a young age and NF1 is commonly mutated in sporadic breast cancers, we have a limited understanding of the role of NF1 in breast cancer. We utilized CRISPR–Cas9 gene editing to create Nf1 rat models to evaluate the effect of Nf1 deficiency on tumorigenesis. The resulting Nf1 indels induced highly penetrant, aggressive mammary adenocarcinomas that express estrogen receptor (ER) and progesterone receptor (PR). We identified distinct Nf1 mRNA and protein isoforms that were altered during tumorigenesis. To evaluate NF1 in human breast cancer, we analyzed genomic changes in a data set of 2000 clinically annotated breast cancers. We found NF1 shallow deletions in 25% of sporadic breast cancers, which correlated with poor clinical outcome. To identify biological networks impacted by NF1 deficiency, we constructed gene co-expression networks using weighted gene correlation network analysis (WGCNA) and identified a network connected to ESR1 (estrogen receptor). Moreover, NF1-deficient cancers correlated with established RAS activation signatures. Estrogen-dependence was verified by estrogen-ablation in Nf1 rats where rapid tumor regression was observed. Additionally, Nf1 deficiency correlated with increased estrogen receptor phosphorylation in mammary adenocarcinomas. These results demonstrate a significant role for NF1 in both NF1-related breast cancer and sporadic breast cancer, and highlight a potential functional link between neurofibromin and the estrogen receptor., Genetics: Mutant tumor suppressor linked to estrogen receptor signaling Mutations in a tumor suppressor gene called NF1 may be an important prognostic indicator for women with breast cancer and a therapeutic target for tumors resistant to hormone therapy. A team led by Carrie Graveel and Matthew Steensma from the Van Andel Research Institute in Grand Rapids, Michigan, USA, studied a large dataset of well-characterized breast cancer cases. They showed that 25% harbored mutations in NF1, a genetic alteration that correlated with diminished survival. Gene network analyses revealed links between NF1 deficiency, RAS oncogene activity, and signaling through the estrogen receptor, including with genes known to mediate resistance to hormone therapy. The researchers also describe a newly created rat model of NF1-mutant breast cancer that they say could help further interrogate the importance of these genetic connections.

Nodal-related protein (ndr2) is a member of the transforming growth factor type $$\upbeta $$ superfamily of factors and is required for ventral midline patterning of the embryonic central nervous system in zebrafish. In humans, mutations in the gene encoding nodal cause holoprosencephaly and heterotaxy. Mutations in the ndr2 gene in the zebrafish (Danio rerio) lead to similar phenotypes, including loss of the medial floor plate, severe deficits in ventral forebrain development and cyclopia. Alleles of the ndr2 gene have been useful in studying patterning of ventral structures of the central nervous system. Fifteen different ndr2 alleles have been reported in zebrafish, of which eight were generated using chemical mutagenesis, four were radiation-induced and the remaining alleles were obtained via random insertion, gene targeting (TALEN) or unknown methods. Therefore, most mutation sites were random and could not be predicted a priori. Using the CRISPR-Cas9 system from Streptococcus pyogenes, we targeted distinct regions in all three exons of zebrafish ndr2 and observed cyclopia in the injected ( $$\hbox {G}_{0}$$ ) embryos. We show that the use of sgRNA-Cas9 ribonucleoprotein (RNP) complexes can cause penetrant cyclopic phenotypes in injected ( $$\hbox {G}_{0}$$ ) embryos. Targeted polymerase chain reaction amplicon analysis using Sanger sequencing showed that most of the alleles had small indels resulting in frameshifts. The sequence information correlates with the loss of ndr2 activity. In this study, we validate multiple CRISPR targets using an in vitro nuclease assay and in vivo analysis using embryos. We describe one specific mutant allele resulting in the loss of conserved terminal cysteine-coding sequences. This study is another demonstration of the utility of the CRISPR-Cas9 system in generating domain-specific mutations and provides further insights into the structure–function of the ndr2 gene.

Ciliopathies are genetic disorders arising from dysfunction of microtubule-based cellular appendages called cilia. Different cilia types possess distinct stereotypic microtubule doublet arrangements with non-motile or ‘primary’ cilia having a 9+0 and motile cilia have a 9+2 array of microtubule doublets. Primary cilia are critical sensory and signaling centers needed for normal mammalian development. Defects in their structure/function result in a spectrum of clinical and developmental pathologies including abnormal neural tube and limb patterning. Altered patterning phenotypes in the limb and neural tube are due to perturbations in the hedgehog (Hh) signaling pathway. Motile cilia are important in fluid movement and defects in motility result in chronic respiratory infections, altered left-right asymmetry, and infertility. These features are the hallmarks of Primary Ciliary Dyskinesia (PCD, OMIM 244400). While mutations in several genes are associated with PCD in patients and animal models, the genetic lesion in many cases is unknown. We assessed the in vivo functions of Growth Arrest Specific 8 (GAS8). GAS8 shares strong sequence similarity with the Chlamydomonas Nexin-Dynein Regulatory Complex (NDRC) protein 4 (DRC4) where it is needed for proper flagella motility. In mammalian cells, the GAS8 protein localizes not only to the microtubule axoneme of motile cilia, but also to the base of non-motile cilia. Gas8 was recently implicated in the Hh signaling pathway as a regulator of Smoothened trafficking into the cilium. Here, we generate the first mouse with a Gas8 mutation and show that it causes severe PCD phenotypes; however, there were no overt Hh pathway phenotypes. In addition, we identified two human patients with missense variants in Gas8. Rescue experiments in Chlamydomonas revealed a subtle defect in swim velocity compared to controls. Further experiments using CRISPR/Cas9 homology driven repair (HDR) to generate one of these human missense variants in mice demonstrated that this allele is likely pathogenic., Author Summary Growth-Arrest Specific 8 (Gas8) is implicated in dual roles at both the primary cilium to regulate hedgehog signaling and in motile cilia to coordinate cilia movement. To investigate these roles in vivo, we created a Gas8 genetrap mutant mouse. Though no overt primary cilia phenotypes were evident in the Gas8 genetrap mutant mice, there were severe motility defects and the mice presented with Primary Ciliary Dyskinesia (PCD) like symptoms including situs inversus and hydrocephalus. We also identified two potential disease causing GAS8 missense variants (A391V and E199K) in humans. Utilizing CRISPR/Cas9 we generated a mouse to mimic the A391V allele. When we crossed the Gas8AV mutants with the Gas8GT mutant, the compound Gas8GT/AV heterozygous animals developed mild hydrocephalus. Rescue experiments using Chlamydomonas with mutations in the Gas8 homolog revealed only a modest decrease in swim velocity raising the possibility that the E199K allele is not pathogenic.

Tyrosinase is a key enzyme in melanin biosynthesis. Mutations in the gene encoding tyrosinase (Tyr) cause oculocutaneous albinism (OCA1) in humans. Alleles of the Tyr gene have been useful in studying pigment biology and coat color formation. Over 100 different Tyr alleles have been reported in mice, of which ≈24% are spontaneous mutations, ≈60% are radiation-induced, and the remaining alleles were obtained by chemical mutagenesis and gene targeting. Therefore, most mutations were random and could not be predicted a priori. Using the CRISPR-Cas9 system, we targeted two distinct regions of exon 1 to induce pigmentation changes and used an in vivo visual phenotype along with heteroduplex mobility assays (HMA) as readouts of CRISPR-Cas9 activity. Most of the mutant alleles result in complete loss of tyrosinase activity leading to an albino phenotype. In this study, we describe two novel in-frame deletion alleles of Tyr, dhoosara (Sanskrit for gray) and chandana (Sanskrit for sandalwood). These alleles are hypomorphic and show lighter pigmentation phenotypes of the body and eyes. This study demonstrates the utility of CRISPR-Cas9 system in generating domain-specific in-frame deletions and helps gain further insights into structure-function of Tyr gene.

Neurofibromatosis type 1 (NF1) is a common tumor predisposition syndrome caused by germline mutations in the NF1 gene that affects1 in 3,000 births. The NF1 gene encodes for neurofibromin, a GTPase that negatively regulates RAS. Women with NF1 have a 10-fold increased risk of developing breast cancer under the age of 40 and an overall lifetime risk of 18%. NF1-related breast cancers are associated with higher grade, poor prognostic factors, and poor survival (5-year survival is 68%). Comprehensive genomic analyses have also revealed that NF1 is commonly mutated in sporadic breast cancers and is a suspected driver gene. Much of our understanding of the mechanisms underlying the functional loss of NF1 comes from genetically engineered mouse models that do not completely recapitulate the phenotypes of human NF1. To examine the effect of functional NF1 loss on tumorigenesis, we induced a deletion in the NF1 GAP-related domain (GRD) in Sprague-Dawley rats using a CRISPR-Cas9 editing strategy. Because CRISPR modification results in variability at the guide site, two classes of Nf1-deficient rats were generated: larger “in-frame” indels (i.e., 63 bp) and smaller “premature stop” indels (i.e., -11). Both types of Nf1 indels induced highly penetrant and aggressive mammary adenocarcinomas in multiple rat founder lines. Mammary tumors were observed in 100% (11/11) of G0 females in mammary glands 1-5 at the average age of 51 days. Notably, two male founders also developed mammary adenocarcinomas at 14-16 months of age. This aggressive mammary phenotype was highly penetrant and multifocal mammary tumors were observed in the subsequent F1 and F2 generations from each of the Nf1 lines. Histopathologic analysis of the mammary tumors revealed that both Nf1 in-frame deletions and premature stop indels induced a wide variety of histopathologic mammary tumor types (i.e., acinar, solid, ductular, and cystic). To understand how the distinct Nf1 indels affect disease burden and survival, we examined the overall survival of females with in-frame indels (n=35) compared to premature stop indels (n=24) in three lines (Nf1IF-57/+, Nf1IF-57/PS-8, Nf1IF-54/PS 11). Kaplan-Meier analysis revealed that animals with a premature stop codon in exon 20 died due to tumor burden significantly faster than animals with an in-frame deletion (p < 0.0002). These results suggest that the Nf1 in-frame deletions may maintain some functional activity (compared to premature stop indels) that delays tumorigenesis. To our knowledge, this is the first model of NF1-related breast cancer and one of the few animal models of male breast cancer. Moreover, the Nf1 CRISPR rat is a novel model in which to explore the role of NF1 and deregulated Ras signaling in breast cancer initiation and progression. To examine the frequency of NF1 alterations in sporadic human breast cancer, we analyzed the METABRIC breast cancer dataset. NF1 mutations were identified in 3.8% of patients, whereas 24.5% of cancers harbored shallow deletions in NF1. Survival analysis (accounting for ER status and age at diagnosis) revealed that patients with NF1 shallow deletions are 1.65X (p < 1.6e-05) more likely to die within the first 10 years after diagnosis. These results reveal that NF1 deficiency may drive a more aggressive breast cancer phenotype in approximately 25% of all sporadic breast cancers. Citation Format: Patrick Dischinger, Elizabeth Tovar, Curt Essenburg, Eve Gardner, Megan Callaghan, Megan Bowman, Zachary Madaj, Ashley Turner, Anil Challa, Tristan Kempston, Bryn Eagleson, Roderick Bronson, Robert Kesterson, Matthew Steensma, Carrie Graveel. NF1 deficiency induces aggressive mammary carcinomas in a CRISPR rat model and correlates with poor outcome in sporadic human breast cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr B43.

Zebrafish embryos are well suited as a model system to perform chemical biology experiments effectively in educational settings. We studied the effect of caffeine on heart rate (HR) and other phenotypes of zebrafish embryos using visual microscopy and simple imaging. Acute treatment with millimolar concentrations of caffeine in embryo medium caused a dose-dependent decrease in HR in 2-3-day-old zebrafish embryos, ultimately resulting in complete HR cessation. A characteristic pattern of decrease in HR was observed, with an initial acute drop in HR and a period of stabilization followed by complete cessation. The effects of caffeine were not reversed by cotreatment with ruthenium red and adenosine, agents known to be antagonistic to caffeine, or by changes in calcium concentration in embryo medium. Apparent cardiac arrhythmia and a typical kinking effect in the trunk/tail region were also observed because of caffeine treatment. Our results, taken together with previous reports, raise the possibility that caffeine exerts its effects on embryonic HR of zebrafish by inhibition of ether-a-go-go potassium channels. However, further experimentation is required to dissect the molecular basis of caffeine action. We demonstrate that such experiments can be used to explore the effect of small molecules, such as caffeine, on cardiovascular phenotypes and to encourage experimental design in chemical biology.

Sialic acids are sometimes 9-O-acetylated in a developmentally regulated and cell-type-specific manner. Cells naturally expressing the disialoganglioside GD3 often O-acetylate the terminal sialic acid residue, giving 9-O-acetyl-GD3 (9AcGD3), a marker of neural differentiation and malignant transformation. We also reported that Chinese hamster ovary cells transfected with GD3 synthase can spontaneously O-acetylate some of the newly synthesized GD3. It is unclear whether such phenomena result from induction of the 9-O-acetylation machinery and whether induction is caused by the GD3 synthase protein or by the GD3 molecule itself. We now show that exogenously added GD3 rapidly incorporates into the plasma membrane of Chinese hamster ovary cells, and 9AcGD3 is detected after ∼6 h. The incorporated GD3 and newly synthesized 9AcGD3 have a half-life of ∼24 h. This phenomenon is also seen in other cell types, such as human diploid fibroblasts. Inhibitors of gene transcription, protein translation, or endoplasmic reticulum-to-Golgi transport each prevent induction of 9-O-acetylation, without affecting GD3 incorporation. Inhibition of the initial clathrin-independent internalization of incorporated GD3 also blocks induction of 9-O-acetylation. Thus, new synthesis of one or more components of the 9-O-acetylation machinery is induced by incorporation and internalization of GD3. Prepriming with structurally related gangliosides fails to accelerate the onset of 9-O-acetylation of subsequently added GD3, indicating a requirement for specific recognition of GD3. To our knowledge, this is the first example wherein a newly expressed or exogenously introduced ganglioside induces de novo synthesis of an enzymatic machinery to modify itself, and the first evidence for a mechanism of induction of sialic acid O-acetylation.

The Roundabout (Robo) family of receptors and their extracellular ligands, the Slit protein family, play important roles in repulsive axon guidance. First identified in Drosophila, Robo receptors form an evolutionarily conserved sub-family of the immunoglobulin (Ig) superfamily that are characterized by the presence of five Ig repeats and three fibronectin-type III repeats in the extracellular domain, a transmembrane domain, and a cytoplasmic domain with several conserved motifs that play important roles in Robo-mediated signaling (Cell 92 (1998) 205; Cell 101 (2000) 703). Robo family members have now been identified in C. elegans, Xenopus, rat, mouse, and human (Cell 92 (1998) 205; Cell 92 (1998) 217; Cell 96 (1999) 807; Dev. Biol. 207 (1999) 62). Furthermore, multiple robo genes have been described in Drosophila, rat, mouse and humans, raising the possibility of potential redundancy and diversity in robo gene function. As a first step in elucidating the role of Robo receptors during vertebrate development, we identified and characterized two Robo family members from zebrafish. We named these zebrafish genes robo1 and robo3, reflecting their amino acid sequence similarity to other vertebrate robo genes. Both genes are dynamically expressed in the developing nervous system in distinct patterns. robo3 is expressed during the first day of development in the hindbrain and spinal cord and is later expressed in the tectum and retina. robo1 nervous system expression appears later in development and is more restricted. Moreover, both genes are expressed in non-neuronal tissues consistent with additional roles for these genes during development.

Tyrosine kinases have significant roles in cell growth, apoptosis, development, and disease. To explore the use of zebrafish as a vertebrate model for tyrosine kinase signaling and to better understand their roles, we have identified all of the tyrosine kinases encoded in the zebrafish genome and quantified RNA expression of selected tyrosine kinases during early development. Using profile hidden Markov model analysis, we identified 122 zebrafish tyrosine kinase genes and proposed unambiguous gene names where needed. We found them to be organized into 39 nonreceptor and 83 receptor type, and 30 families consistent with human tyrosine kinase family assignments. We found five human tyrosine kinase genes (epha1, bmx, fgr, srm, and insrr) with no identifiable zebrafish ortholog, and one zebrafish gene (yrk) with no identifiable human ortholog. We also found that receptor tyrosine kinase genes were duplicated more often than nonreceptor tyrosine kinase genes in zebrafish. We profiled expression levels of 30 tyrosine kinases representing all families using direct digital detection at different stages during the first 24 hours of development. The profiling experiments clearly indicate regulated expression of tyrosine kinases in the zebrafish, suggesting their role during early embryonic development. In summary, our study has resulted in the first comprehensive description of the zebrafish tyrosine kinome.

Roundabout (Robo) receptors and their secreted ligand Slits have been shown to function in a number of developmental events both inside and outside of the nervous system. We previously cloned zebrafish robo orthologs to gain a better understanding of Robo function in vertebrates. Further characterization of one of these orthologs, robo3 , has unveiled the presence of two distinct isoforms, robo3 variant 1 ( robo3var1 ) and robo3 variant 2 ( robo3var2 ). These two isoforms differ only in their 5′-ends with robo3var1 , but not robo3var2 , containing a canonical signal sequence. Despite this difference, both forms accumulate on the cell surface. Both isoforms are contributed maternally and exhibit unique and dynamic gene expression patterns during development. Functional analysis of robo3 isoforms using an antisense gene knockdown strategy suggests that Robo3var1 functions in motor axon pathfinding, whereas Robo3var2 appears to function in dorsoventral cell fate specification. This study reveals a novel function for Robo receptors in specifying ventral cell fates during vertebrate development.