Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system

A simple and robust method for targeted mutagenesis in zebrafish has long been sought. Previous methods generate monoallelic mutations in the germ line of F0 animals, usually delaying homozygosity for the mutation to the F2 generation. Generation of robust biallelic mutations in the F0 would allow for phenotypic analysis directly in injected animals. Recently the type II prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system has been adapted to serve as a targeted genome mutagenesis tool. Here we report an improved CRISPR/Cas system in zebrafish with custom guide RNAs and a zebrafish codon-optimized Cas9 protein that efficiently targeted a reporter transgene Tg(-5.1mnx1:egfp) and four endogenous loci (tyr, golden, mitfa, and ddx19). Mutagenesis rates reached 75–99%, indicating that most cells contained biallelic mutations. Recessive null-like phenotypes were observed in four of the five targeting cases, supporting high rates of biallelic gene disruption. We also observed efficient germ-line transmission of the Cas9-induced mutations. Finally, five genomic loci can be targeted simultaneously, resulting in multiple loss-of-function phenotypes in the same injected fish. This CRISPR/Cas9 system represents a highly effective and scalable gene knockout method in zebrafish and has the potential for applications in other model organisms.     

Behavioral screening for cocaine sensitivity in mutagenized zebrafish

Understanding the molecular basis of addiction could be greatly aided by using forward genetic manipulation to lengthen the list of candidate genes involved in this complex process. Here, we report that zebrafish exhibit cocaine-induced conditioned place preference. In a pilot screen of 18 F(2) generation families of mutagenized fish, we found three with abnormally low responses to cocaine. This behavior was inherited by the F(3) generation in a manner that suggests the abnormalities were because of dominant mutations in single genes. Performance profiles in secondary behavioral screens measuring visual dark-adaptation and learning suggest that the defects were the result of mutations in distinct genes that affect dopaminergic signaling in the retina and brain.     

New Insight into the Molecular Basis of Hemophilia A

Since publication of the sequence of the factor VIII gene (F8) in 1984, a large number of mutations that cause hemophilia A (HA) have been identified. With the technical advances associated with mutation screenings, it is now possible to identify a putative F8 sequence alteration in the great majority of HA patients. The mutation spectrum includes 2 inversion hot spots (intron 1 and intron 22 inversions) mediated by intrachromosomal recombination between 2 copies of long inverted repeats, one of which lies within the F8 gene whereas the other is extragenic. Point mutations are distributed over all of the exons, and deletions or insertions of different sizes and mutations affecting splice sites account for the rest of the known mutations. In a small number of cases, however, we are unable to find any disease-determining DNA changes in the coding regions of the F8 gene. This fact points to possibilities of unknown gene rearrangements that disrupt the F8 gene or mutations in other genes that play a role in the processing/secretion of the factor VIII protein. Moreover, the proof of an absence of F8 messenger RNA (mRNA) in one patient points to either a defect in the expression of F8 mRNA or its rapid degradation, which may represent a novel mechanism leading to HA.     

Highly aneuploid zebrafish malignant peripheral nerve sheath tumors have genetic alterations similar to human cancers

Aneuploidy is a hallmark of human cancers, but most mouse cancer models lack the extensive aneuploidy seen in many human tumors. The zebrafish is becoming an increasingly popular model for studying cancer. Here we report that malignant peripheral nerve sheath tumors (MPNSTs) that arise in zebrafish as a result of mutations in either ribosomal protein (rp) genes or in p53 are highly aneuploid. Karyotyping reveals that these tumors frequently harbor near-triploid numbers of chromosomes, and they vary in chromosome number from cell to cell within a single tumor. Using array comparative genomic hybridization, we found that, as in human cancers, certain fish chromosomes are preferentially overrepresented, whereas others are underrepresented in many MPNSTs. In addition, we obtained evidence for recurrent subchromosomal amplifications and deletions that may contain genes involved in cancer initiation or progression. These focal amplifications encompassed several genes whose amplification is observed in human tumors, including met, cyclinD2, slc45a3, and cdk6. One focal amplification included fgf6a. Increasing fgf signaling via a mutation that overexpresses fgf8 accelerated the onset of MPNSTs in fish bearing a mutation in p53, suggesting that fgf6a itself may be a driver of MPNSTs. Our results suggest that the zebrafish is a useful model in which to study aneuploidy in human cancer and in which to identify candidate genes that may act as drivers in fish and potentially also in human tumors.     

Major histocompatibility complex class II genes of zebrafish.

Twenty cDNA clones derived from beta-chain-encoding class II genes of the zebrafish (Brachydanio rerio) major histocompatibility complex (MHC) have been sequenced. They fall into three groups identifying three loci of expressed genes. The length and organization of these genes are similar to those of their mammalian homologs. Amplification by polymerase chain reaction and sequencing of genomic DNA from zebrafish collected at different locations in India indicate the existence of a fourth group of sequences (fourth locus). A high degree of polymorphism at the B. rerio MHC loci and concentration of variability to the putative peptide-binding region of the beta 1-domain-encoding part of the gene are also indicated. Large genetic distances between alleles suggest trans-specific evolution of fish MHC polymorphism. Zebrafish genes appear to be derived from a different ancestor than the various class II gene families of other vertebrates. In spite of great sequence divergence between fish and mammalian MHC genes, there seems to be a striking conservation in their overall organization.     

Cloning of the gene and complete cDNA encoding a type 2 deiodinase from Fundulus heteroclitus

Recently, we reported the cloning of a cDNA fragment from Fundulus heteroclitus liver encoding the open reading frame of type 2 deiodinase (FhD2). We here report the cloning of 14 kb of genomic sequence from F. heteroclitus that includes the previously reported coding region of the F. heteroclitus Dio2 gene (FhDio2), the 5(') and 3(') untranslated regions, and flanking regions and introns. This FhDio2 gene comprises two exons divided by a 4.8-kb intron. The position of the intron is similar to that of introns in other Dio2 genes. The analysis of approximately 1.3 kb of genomic sequence upstream of the mRNA start site revealed that, in contrast to mammalian Dio2 genes, there were no apparent TATA or CRE sequences. Nevertheless, a putative Sp1 site was found, similar to that in other F. heteroclitus TATA-less promoters. We have also cloned the complete FhD2 cDNA, which spans 4652 bp and contains a sequence adjacent to its poly(A) tail that is highly similar to the selenocysteine insertion sequence (SECIS) found in human D2 cDNA. The expression of a construct containing the FhD2 ORF plus the native SECIS resulted in a protein with deiodinase activity similar to that of the native FhD2. Analysis of the regulation of this gene, combined with ongoing studies of the F. heteroclitus D1 gene, will allow us to elucidate the functions of the colocalized deiodinases in teleost liver.     

The zebrafish stress axis: Molecular fallout from the teleost-specific genome duplication event

The teleost-specific whole genome duplication event 350 million years ago resulted in a variety of duplicated genes that exist in fish today. In this review, we examine whether molecular components involved in the functioning of the hypothalamus-pituitary-interrenal (HPI) axis are present as single or duplicate genes. Specifically, we looked at corticotropin releasing hormone (CRH), adrenocorticotropic hormone (ACTH) and the glucocorticoid receptor (GR). The focus is on zebrafish but a variety of species are covered whenever data is available through literature or genomic database searches. Duplicate CRH genes are retained in the salmoniformes and cypriniformes, and the peptide sequences are very similar or identical. Zebrafish, along with the Acanthopterygii, are the exceptions as they have a single CRH gene. Also, two copies of the proopiomelanocortin (POMC) gene, which encodes for ACTH and other peptides, have been observed in all teleosts except tilapia and sea bass. In zebrafish, ACTH is derived from only one POMC gene, since the cleavage site is mutated in the other gene. All teleosts examined to date have two GRs, including the recent discoveries of duplicate GRs in two species of cyprinids (carp and fathead minnow). Zebrafish are the only known exception with one GR gene. The loss of duplicate genes is not a general feature of the zebrafish genome, but zebrafish have lost the duplicate CRH, ACTH and GR genes in the past 33 million years, after possessing two of each for the previous 300 million years. The evolutionary pressures underlying the rapid loss of these HPI axis genes, and the implications on the development and the functioning of the evolutionarily conserved cortisol stress response in zebrafish are currently unknown.     

Neurokinin Bs and neurokinin B receptors in zebrafish-potential role in controlling fish reproduction

The endocrine regulation of vertebrate reproduction is achieved by the coordinated actions of several peptide neurohormones, tachykinin among them. To study the evolutionary conservation and physiological functions of neurokinin B (NKB), we identified tachykinin (tac) and tac receptor (NKBR) genes from many fish species, and cloned two cDNA forms from zebrafish. Phylogenetic analysis showed that piscine Tac3s and mammalian neurokinin genes arise from one lineage. High identity was found among different fish species in the region encoding the NKB; all shared the common C-terminal sequence. Although the piscine Tac3 gene encodes for two putative tachykinin peptides, the mammalian ortholog encodes for only one. The second fish putative peptide, referred to as neurokinin F (NKF), is unique and found to be conserved among the fish species when tested in silico. tac3a was expressed asymmetrically in the habenula of embryos, whereas in adults zebrafish tac3a-expressing neurons were localized in specific brain nuclei that are known to be involved in reproduction. Zebrafish tac3a mRNA levels gradually increased during the first few weeks of life and peaked at pubescence. Estrogen treatment of prepubertal fish elicited increases in tac3a, kiss1, kiss2, and kiss1ra expression. The synthetic zebrafish peptides (NKBa, NKBb, and NKF) activated Tac3 receptors via both PKC/Ca(2+) and PKA/cAMP signal-transduction pathways in vitro. Moreover, a single intraperitoneal injection of NKBa and NKF significantly increased leuteinizing hormone levels in mature female zebrafish. These results suggest that the NKB/NKBR system may participate in neuroendocrine control of fish reproduction.     

Microarray-based rapid cloning of an ion accumulation deletion mutant in Arabidopsis thaliana

Here we describe the development of a microarray-based mapping strategy to rapidly isolate deletion mutant genes. The presented approach is particularly useful for mapping mutant genes that are difficult to phenotype. This strategy uses masking bulk segregant analysis to mask unrelated deletions, thus allowing identification of target deletions by microarray hybridization of pooled genomic DNA from both WT and mutant F2 populations. Elemental profiling has proven to be a powerful tool for isolation of nutrient and toxic metal accumulation mutants in Arabidopsis. Using microarray mapping, a sodium overaccumulation mutant FN1148 was identified as having a 523-bp genomic deletion within the second exon and intron of the AtHKT1 gene. Further cosegregation, complementation, and comparative analyses among different salt-sensitive mutants confirmed that the deletion within the AtHKT1 gene is responsible for the sodium overaccumulation in shoots and leaf sodium sensitivity of the FN1148 mutant. These results demonstrate that microarray-based cloning is an efficient and powerful tool to rapidly clone ion accumulation or other genetic deletion mutants that are otherwise difficult to phenotype for mapping, such as metabolic or cell signaling mutants.     

Computational and molecular approaches for predicting unreported causal missense mutations in Belgian patients with haemophilia A

Haemophilia A (HA) is caused by widespread mutations in the factor VIII gene. The high spontaneous mutation rate of this gene means that roughly 40% of HA mutations are private. This study aimed to describe the approaches used to confirm private disease-causing mutations in a cohort of Belgian HA patients. We studied 148 unrelated HA families for the presence of intron 22 and intron 1 inversion by Southern blotting and polymerase chain reaction (PCR). Multiplex ligation-dependent probe amplification (MLPA) assay was used to detect large genomic rearrangements. Detection of point mutations was performed by DNA sequencing. Predicting the causal impact of new non-synonymous changes was studied by two general strategies: (i) molecular approaches such as family cosegregation, evaluation of the implicated codon based on phylogenic separated species and absence of the mutation in the general Belgian population, and (ii) bioinformatics approaches to analyse the potential functional consequences of missense mutations. Among the 148 HA patients, in addition to common intron 22 and intron 1 inversions as well as large deletions or duplications, 67 different point mutations were identified, of which 42 had been reported in the HAMSTeRS database, and 25 were novel including 10 null variants for which RNA analyses confirmed the causal effect of mutations located in a splice site consensus and 15 missense mutations whose causality was demonstrated by molecular approaches and bioinformatics. This article reports several strategies to evaluate the deleterious consequences of unreported F8 substitutions in a large cohort of HA patients.     

Bone morphogenetic protein-15 in the zebrafish ovary: complementary deoxyribonucleic acid cloning, genomic organization, tissue distribution, and role in oocyte maturation

Bone morphogenetic protein-15 (BMP-15) is a member of the TGFbeta family known to regulate ovarian functions in mammals. The structure and function of BMP-15 in lower vertebrates are less known. In this study, we cloned the zebrafish BMP-15 (zfBMP-15) cDNA and depicted its genomic organization. The zfBMP-15 cDNA encodes a protein of 384 amino acids. The mature protein has 46-51% sequence identities to fugu, chicken, and mammalian BMP-15. It also shares 38-46% homology with growth and differentiation factor-9 in fishes, chicken, and mammals. Phylogenetic analysis further confirms that the zfBMP-15 is most closely related to BMP-15 from other species, whereas the growth and differentiation factor-9 peptides from fish to mammals form a distinct branch. Comparison of zfBMP-15 cDNA with zebrafish genome database revealed that zfBMP-15 is encoded by a gene with two exons and one intron, located on chromosome 6. BMP-15 mRNA is expressed in the ovary and testis and, to a lesser extent, brain, liver, gut, heart, and muscle. Real-time PCR revealed that BMP-15 is expressed in follicles at all stages of development with no significant changes over the course of folliculogenesis. Using in situ hybridization and immunocytochemistry, we detected BMP-15 in both oocytes and follicular cells. Incubation of follicles with antiserum against zfBMP15 increased oocyte maturation, whereas incubation with recombinant human BMP-15 suppressed human chorionic gonadotropin-induced oocyte maturation. These findings suggest that BMP-15 plays a role in regulating gonadal functions in fish, in particular oocyte maturation.     

Intron self-complementarity enforces exon inclusion in a yeast pre-mRNA

Skipping of internal exons during removal of introns from pre-mRNA must be avoided for proper expression of most eukaryotic genes. Despite significant understanding of the mechanics of intron removal, mechanisms that ensure inclusion of internal exons in multi-intron pre-mRNAs remain mysterious. Using a natural two-intron yeast gene, we have identified distinct RNA–RNA complementarities within each intron that prevent exon skipping and ensure inclusion of internal exons. We show that these complementarities are positioned to act as intron identity elements, bringing together only the appropriate 5′ splice sites and branchpoints. Destroying either intron self-complementarity allows exon skipping to occur, and restoring the complementarity using compensatory mutations rescues exon inclusion, indicating that the elements act through formation of RNA secondary structure. Introducing new pairing potential between regions near the 5′ splice site of intron 1 and the branchpoint of intron 2 dramatically enhances exon skipping. Similar elements identified in single intron yeast genes contribute to splicing efficiency. Our results illustrate how intron secondary structure serves to coordinate splice site pairing and enforce exon inclusion. We suggest that similar elements in vertebrate genes could assist in the splicing of very large introns and in the evolution of alternative splicing.     

Identification of 315 genes essential for early zebrafish development

We completed a large insertional mutagenesis screen in zebrafish to identify genes essential for embryonic and early larval development. We isolated 525 mutants, representing lesions in approximately 390 different genes, and we cloned the majority of these. Here we describe 315 mutants and the corresponding genes. Our data suggest that there are roughly 1,400 embryonic-essential genes in the fish. Thus, we have mutations in approximately 25% of these genes and have cloned approximately 22% of them. Re-screens of our collection to identify mutants with specific developmental defects suggest that approximately 50 genes are essential for the development of some individual organs or cell types. Seventy-two percent of the embryonic-essential fish genes have homologues in yeast, 93% have homologues in invertebrates (fly or worm), and 99% have homologues in human. Yeast and worm orthologues of genes that are essential for early zebrafish development have a strong tendency to be essential for viability in yeast and for embryonic development in the worm. Thus, the trait of being a genetically essential gene is conserved in evolution. This mutant collection should be a valuable resource for diverse studies of cell and developmental biology.     

Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature

The evolutionary transition of the fins of fish into tetrapod limbs involved genetic changes to developmental systems that resulted in novel skeletal patterns and functions. Approaches to understanding this issue have entailed the search for antecedents of limb structure in fossils, genes, and embryos. Comparative genetic analyses have produced ambiguous results: although studies of posterior Hox genes from homology group 13 (Hoxa-13 and Hoxd-13) reveal similarities in gene expression between the distal segments of fins and limbs, this functional homology has not been supported by genomic comparisons of the activity of their cis-regulatory elements, namely the Hoxd Global Control Region. Here, we show that cis-regulatory elements driving Hoxd gene expression in distal limbs are present in fish. Using an interspecies transgenesis approach, we find functional conservation between gnathostome Hoxd enhancers, demonstrating that orthologous sequences from tetrapods, zebrafish and skate can drive reporter gene expression in mouse limbs and zebrafish fins. Our results support the notion that some of the novelties associated with tetrapod limbs arose by modification of deeply conserved cis- and trans-acting mechanisms of Hox regulation in gnathostomes.