Insights into the evolutionary history of the vertebrate zic3 locus from a teleost-specific zic6 gene in the zebrafish, Danio rerio
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- Keller, M.J. & Chitnis, A.B. Dev Genes Evol (2007) 217: 541. doi:10.1007/s00427-007-0161-4
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The Zic gene family of zinc-finger transcription factors includes five orthologues, zic1–5, that are common to the Euteleostian vertebrates (fish, frogs, birds, and mammals). The Zic genes have been implicated as regulators of a number of critical developmental processes, including neurulation, neuronal differentiation, neural crest specification, the establishment of left–right asymmetry, and regulation of cell proliferation. The different Zic genes encode proteins that are expressed in broadly overlapping spatial domains, have conserved DNA-binding domains that recognize a common motif, are capable of physical interactions, and can co-regulate one another’s transcription. Thus, the transcriptional regulation of individual proteins and their effects on downstream targets must be assessed within the context of co-expression with other family members. We describe a novel gene, zic6, that is specific to the teleost fishes and lacks the lateral and rostral expression domains typical of the other Zic family members. We present evidence that zic6 is an ancestral locus arising by chromosomal duplication early in the Euteleostomi that was subsequently lost in the terrestrial vertebrates.
The Zic gene family encodes a group of C2H2 zinc-finger transcription factors, which are important regulators of early vertebrate development. They are part of a larger Gli/Zic/NKL gene superfamily and, together with the Gli genes, are thought to provide positional information within the developing embryo (Brewster et al. 1998). The Zic genes are typically expressed in ectodermal tissues contributing to the nervous system and neural crest, as well as somitic mesoderm (Grinblat and Sive 2001; Toyama et al. 2004). There is strong experimental support for a combined role of the Zic genes in neurulation, neurogenesis, neural crest specification, and establishment of left–right asymmetry (reviewed by Aruga 2004). Deficits in Zic gene family members have been linked to developmental defects such as spina-bifida, holoprosencephaly, and X-linked heterotaxia (reviewed by Grinberg and Millen 2005).
Understanding the significance of Zic gene function during embryonic development is confounded by their broadly overlapping expression with the potential for competition for DNA-binding, sites as well as cross-regulatory and physical interactions among orthologues (Grinblat and Sive 2001; Koyabu et al. 2001; Mizugishi et al. 2001; Nakata et al. 2000; Toyama et al. 2004). It is therefore essential to define the combined expression of the Zic gene family members and understand their evolutionary relationships. Although there is significant conservation in the structure of the Zic protein DNA-binding domain, consisting of five zinc-fingers, there is also considerable divergence in other parts of the protein that may be correlated with altered post-translational regulation, protein–protein interactions and repressor/activator activities (Aruga et al. 2006). The evolutionary diversification among family members may, however, be constrained by their physical arrangement as paired genes (bigenes) of divergent orientation in the genome that share a limited amount of “upstream” DNA. Four known vertebrate homologues occur as zic1/zic4 and zic2/zic5 bigenes, with the exception being zic3, which is a single-gene locus, located on the X-chromosome in mammals (Aruga et al. 2006).
We describe in this paper the structure, genomic context, and embryonic expression of zebrafish zic6 and use those pieces of evidence to infer the evolutionary relationships of the Zic family members in the Euteleostomi. The zic6 gene was found to be teleost-specific, occurring among a broad range of fishes, but absent from the genomes of frogs, birds, and mammals. Genomic analysis established that zic6 is paired with zic3, in opposite orientation, as is the case with the zic1/zic4 and zic2a/zic5 gene pairs. Synteny of flanking genes confirmed that the zic3 loci of fish and the other vertebrate taxa are true homologues, supporting the conclusion that zic6 was the product of a chromosomal duplication before the divergence of fishes and tetrapods and was subsequently lost in the tetrapod lineage. The expression of zic6 in the neural plate lacked the lateral and rostral domains typical of the other Zic gene orthologues, indicating it has evolved a highly derivative if not entirely new regulatory role during early embryonic development of fish.
Materials and methods
Zebrafish, Danio rerio (strain AB*), were maintained at 28.5°C on a 14:10 light/dark cycle. All fish were housed at a density of ≤15 individuals per 2-l tank on a recirculating water system and fed daily with dry flake/krill and live brine. Embryos were fixed overnight at 4°C in 4% paraformaldehyde/phosphate-buffered saline (PBS), manually dechorionated and stored in absolute methanol at −20°C. Procedures were approved by the NIH ACUC.
Comparisons of conservative domains among Zic protein family members, exclusive of the zinc-finger domains
Accession numbers for amino acid sequences based on cDNA
Ensembl-predicted genes from fish genome projects used to determine amino acid sequences of homologues used in the maximum likelihood analysis
Ensembl Gene IDa
cDNA cloning and in situ hybridization
The zebrafish zic6 coding region was amplified from total RNA of 24-h post-fertilization embryos by polymerase chain reaction (PCR) with the Qiagen One-Step enzyme mix, gel-purified with Qiagen Qiaquick columns and TA cloned into pCRII-TOPO vector (Invitrogen). Primers were designed from assembled genomic sequences (Fwd, 5′-cctcagccaagcttgcaacaaaac-3′; Rev, 5′-atgggaagcaactcacgactgtc-3′). The cloned complementary DNA (cDNA) was sequenced from plasmid by MWG (Gaithersburg, MD). DIG- and FITC-labeled riboprobes for zic6 and deltaA (Haddon et al. 1998) were in vitro synthesized and used for in situ hybridization essentially as described by Thisse and Thisse (1998) and Liang et al. (2000), using 1% Roche blocking reagent in PBS + 0.1% Tween-20 with Roche alkaline phosphatase-labeled antibodies and either Roche BM Purple or Fast Red substrates. In situ hybridization results were imaged with a ProgRes C14 camera mounted on a Leica MZ12 binocular microscope and post-processed with Adobe Photoshop CS.
Results and discussion
Zebrafish zic6 is a novel member of the Zic gene family
A thorough analysis of the zebrafish expressed sequence tag (EST) and genomic DNA sequence databases predicted a novel member of the Zic gene family in addition to homologues of zic1–5 from frog, chick, and mammals. The predicted 525 amino acid sequence of the coding region from cDNA matched that from the genomic sequences. This novel locus was also cloned independently by Parinov et al. (2004) from a Tol2 retrotransposon insertion screen for developmental enhancer traps and designated as zic6.
The zic6 gene is specific to teleosts
A survey of available genome databases yielded open reading frames (ORFs) for predicted proteins with 78–93% identity to the zebrafish zic6 gene in other teleosts, including medaka (Oryzias latipes), stickleback (Gasterosteus aculeatus), fugu (Takifugu rubripes), and pufferfish (Tetraodon nigroviridis). In each of the fishes, the zic6 gene structure consisted of two exons with conserved exon–intron boundaries. This organization is shared with zic4 and zic5 and contrasts with the conserved three-exon architecture of zic1–3 (Aruga et al. 2006). No homologue of zic6 was found in frogs (X. laevis and X. tropicalis), birds (Gallus gallus), or mammals (Bos taurus, Canis familiaris, Homo sapiens, and Mus musculus). Unfortunately, the limited data available for the Chondrichthyan fishes or agnathans precluded analyses of gene complements in vertebrates basal to the Euteleostomi. However, only a single Zic gene homologue is known from the basal chordate, amphioxius (Branchiostoma floridae), indicating that the radiation of zic1–6 occurred within the vertebrate lineage. The next closest living chordate group, the tunicates, experienced a separate radiation of the Zic genes (Aruga et al. 2006).
The teleost zic3/zic6 locus is syntenic to the tetrapod zic3 locus
The early expression of zic6 is limited to the intermediate neurogenic domain
A range of critical developmental processes occur during the open neural plate stage after gastrulation but before formation of the neural tube, including progenitor cell maintenance, neurogenesis, neural crest differentiation, and somitogenesis. In zebrafish, the common vertebrate Zic genes are all expressed to varying degrees in the lateral plate, forebrain/midbrain of the neural plate, and to a lesser extent in the hindbrain (Fig. 4a–e,g). The expression of zebrafish Zic family members in these domains is consistent with the patterns of their homologues in other vertebrates. The overlap between zic1–5 in the neural plate border region underscores their critical function in the differentiation of neural crest (reviewed by Aruga 2004; Fujimi et al. 2006). In comparison, zic6 is absent from the lateral and forebrain/midbrain regions and has very restricted hindbrain expression (Fig. 4f). The zic3 gene is also expressed broadly in the hindbrain; therefore, the restricted expression of zic6 could involve elements shared with zic3 in the bigene promoter region. In general, however, the expression of zic6 is highly derived and may reflect reduced- or neo-functionalization of the locus. After 1 day of development, however, zic6 is expressed in the dorsal neural tube in a pattern similar to the other orthologues (Parinov et al. 2004).
Given the similarities among the various Zic gene family members, both among orthologues and across species, the highly restricted and very specific expression of zic6 in the intermediate neurogenic domain of the zebrafish embryonic hindbrain is exceptional. This suggests that the expression of zic6 may be a derived feature within the teleost fish lineage, possibly associated with a teleost-specific developmental feature. The fact that the other bigene pairs (zic1/zic4 and zic2a/zic5) tend to exhibit similar expression patterns leads us to predict that the ancestral zic3/zic6 bigene may also have shared regulatory elements. In that case, the loss of zic6 in the tetrapods may not have been of great consequence if there was substantial redundancy of zic3. Alternatively, the novel expression pattern of zic6 may have arisen in a common ancestor of the Euteleostomi and reflects a regulatory program that was subsequently lost in the Tetrapoda. However, the development of the intermediate neurogenic domain is very similar between zebrafish, which have zic6, and Xenopus, which lack zic6. This indicates that the function of zic6 in that domain is not critical to its specification or development in vertebrates in general.