Microarray analysis of XOPS-mCFP zebrafish retina identifies genes associated with rod photoreceptor degeneration and regeneration.

PURPOSE: XOPS-mCFP transgenic zebrafish experience a continual cycle of rod photoreceptor development and degeneration throughout life, making them a useful model for investigating the molecular determinants of rod photoreceptor regeneration. The purpose of this study was to compare the gene expression profiles of wild-type and XOPS-mCFP retinas and identify genes that may contribute to the regeneration of the rods. METHODS: Adult wild-type and XOPS-mCFP retinal mRNA was subjected to microarray analysis. Pathway analysis was used to identify biologically relevant processes that were significantly represented in the dataset. Expression changes were verified by RT-PCR. Selected genes were further examined during retinal development and in adult retinas by in situ hybridization and immunohistochemistry and in a transgenic fluorescent reporter line. RESULTS: More than 600 genes displayed significant expression changes in XOPS-mCFP retinas compared with expression in wild-type controls. Many of the downregulated genes were associated with phototransduction, whereas upregulated genes were associated with several biological functions, including cell cycle, DNA replication and repair, and cell development and death. RT-PCR analysis of a subset of these genes confirmed the microarray RESULTS: Three transcription factors (sox11b, insm1a, and c-myb), displaying increased expression in XOPS-mCFP retinas, were also expressed throughout retinal development and in the persistently neurogenic ciliary marginal zone. CONCLUSIONS: This study identified numerous gene expression changes in response to rod degeneration in zebrafish and further suggests a role for the transcriptional regulators sox11b, insm1a, and c-myb in both retinal development and rod photoreceptor regeneration.

Expressed sequence tag analysis of zebrafish eye tissues for NEIBank.

PURPOSE: To characterize gene expression patterns in various tissues of the zebrafish (Danio rerio) eye and identify zebrafish orthologs of human genes by expressed sequence tag (EST) analysis for NEIBank. METHODS: mRNA was extracted from adult zebrafish eye tissues, including lenses, anterior segments (minus lens), retinas, posterior segments lacking retinas, and whole eyes. Five different cDNA libraries were constructed in the pCMVSport6 vector. Approximately 4,000 clones from each library were sequenced and analyzed using various bioinformatics programs. RESULTS: The analysis yielded approximately 2,500 different gene clusters for each library. Combining data from the five libraries produced 10,392 unique gene clusters. GenBank accession numbers were identified for 37.6% (3,906) of the total gene clusters in the combined libraries and approximately 50% were linked to Unigene clusters in the current database. Several new crystallin genes, including two gammaN-crystallins, and a second major intrinsic protein (MIP) were identified in the lens library. In addition, a zebrafish homolog of cochlin (COCH), a gene that may play a role in the pathogenesis of human glaucoma, was identified in the anterior segment library. Surprisingly, no clear ortholog of the major retinal transcription factor Nrl was identified. CONCLUSIONS: The zebrafish eye tissue cDNA libraries are a useful resource for comparative gene expression analysis. These libraries will complement the cDNA libraries made for the Zebrafish Gene Collection (ZGC) and provide an additional source for gene identification and characterization in the vertebrate eye.

Developmental expression of the POU domain transcription factor Brn-3b (Pou4f2) in the lateral line and visual system of zebrafish.

Members of the class IV POU domain transcription factors are important regulators of neural development. In mouse, Brn-3b (Pou4f2, Brn3.2) and Brn-3c (Pou4f3, Brn3.1) are essential for the normal differentiation and maturation of retinal ganglion cells (RGCs) and hair cells of the auditory system, respectively. In this report, the cloning and expression profile of brn-3b in the zebrafish (Danio rerio) were assessed as the first step for understanding its role in the development of sensory systems. Two brn-3b alternative transcripts exhibited different onset of expression during development but shared overlapping expression domains in the adult visual system. The brn-3b expression in the zebrafish retina was consistent with a conserved role in differentiation and maintenance of RGCs. Expression was also observed in the optic tectum. Unexpectedly, brn-3b was prominently expressed in the migrating posterior lateral line primordium and larval neuromasts. For comparison, brn-3c expression was limited to the otic vesicle and was not detected in the lateral line during embryonic development. The expression of brn-3b in the mechanosensory lateral line of fish suggests a conserved function of a class IV POU domain transcription factor in sensory system development.

Retina-specific expression of 5A11/Basigin-2, a member of the immunoglobulin gene superfamily.

PURPOSE: 5A11/Basigin has recently been identified as a critical glycoprotein for full maturity and function of the mouse retina. However, the biological function of 5A11/Basigin has yet to be determined. Previous reports indicate the presence of multiple 5A11/Basigin polypeptides within the retina. Therefore, in an effort to determine the function of 5A11/Basigin, the molecular diversity of its expression was evaluated. METHODS: Northern blot and immunoblot techniques were used to evaluate the number of forms of 5A11/Basigin in the mouse retina. cDNA cloning, using a mouse retina library or RT-PCR from rat, chicken, zebrafish, and human retina, was performed to determine the sequence of 5A11/Basigin transcripts. A peptide was generated, based on the deduced amino acid sequence, for subsequent antibody production. Localization of 5A11/Basigin expression was evaluated by immunoblot, immunohistochemistry, and real-time RT-PCR. RESULTS: Two 5A11/Basigin transcripts of approximately 1.5 kb and approximately 1.8 kb, which correspond to glycosylated proteins of approximately 45 and approximately 55 kDa, respectively, were identified in mouse retina. The shorter form was previously cloned. However, the longer form, a splice variant of mouse 5A11/Basigin, is a member of the immunoglobulin gene superfamily and has been named 5A11/Basigin-2. Homologous transcripts were also cloned from rat, chicken, zebrafish, and human retina. 5A11/Basigin-2 expression was limited to the retina, specifically to photoreceptor cells, where it appeared to be most concentrated in the inner segments. CONCLUSIONS: The specific and limited expression of 5A11/Basigin-2 explicitly within photoreceptor cells implies that this glycoprotein plays a fundamental role within the retina. However, its role remains to be determined.

Spatial and temporal expression of the 5A11/HT7 antigen in the chick embryo : Association with morphogenetic events and tissue maturation.

The 5AII/HT7 antigen is the avian homologue of a 45-50X103 M r plasma membrane glycoprotein of the immunoglobulin super-gene family also identified in mammalian species (basigin, mouse gp42, MRC OX-47 antigen, M6 antigen). We had previously demonstrated that antibodies to this antigen interfere with heterotypic cell-to-cell interaction-dependent glial cell maturation in vitro. In this report, we sought to gain insight into its developmental role through an analysis of its distribution at various stages of avian embryogenesis. The primary mode of expression progresses from generalized staining of the undifferentiated tissue to intense labelling of specific cell types coincident with biochemical or morphological differentiation. In the retina, expression progresses from the generalized staining of the neural ectoderm, then, during neurogenesis, becomes restricted to Müller cells, photoreceptor cell bodies, the retina pigmented epithelium, the pigmented cells of the ciliary membrane and endothelia of the pecten. Similarly, the uniform staining of undifferentiated skin ectoderm progressively becomes confined to the germinative cells of the epidermis during biochemical differentiation of scutate and reticulate scales and formation of the feather follicle. During mesonephric and metanephric tubule development, labeling appears on those cells induced to form epithelia from the unlabeled mesenchyme and persists on the basal-lateral membranes of the convoluted tubules. Western blot analysis of NP-40 solubilized proteins from hatchling chicken identifies an immunoreactive polypeptide of 45-50X103 M r in tissues stained immunohistochemically and an additional band of 69X103 M r in the neural retina and pineal gland. The localization of the 5A11 antigen at boundaries typically associated with inductive interactions between cells and tissues suggests broad involvement in cell-to-cell interactions associated with cellular maturation.