Journal article
Expression patterns of dscam and sdk gene paralogs in developing zebrafish retina
Molecular vision, Vol.24, pp.443-458
2018
Handle:
https://hdl.handle.net/2376/115912
PMCID: PMC6054835
PMID: 30078982
Abstract
The differential adhesion hypothesis states that a cell adhesion code provides cues that direct the specificity of nervous system development. The Down syndrome cell adhesion molecule (DSCAM) and sidekick (SDK) proteins belong to the immunoglobulin superfamily of cell adhesion molecules (CAMs) and provide both attractive and repulsive cues that help to organize the nervous system during development, according to the differential adhesion hypothesis. The zebrafish genome is enriched in
and
genes, making the zebrafish an excellent model system to further test this hypothesis. The goal of this study is to describe the phylogenetic relationships of the paralogous CAM genes and their spatial expression and co-expression patterns in the embryonic zebrafish retina.
Exon-intron structures, karyotypic locations, genomic context, and amino acid sequences of the zebrafish CAM genes (
,
,
,
,
,
, and
) were obtained from the Ensembl genome database. The Prosite and SMART programs were used to determine the number and identity of protein domains for each CAM gene. The randomized axelerated maximum likelihood (RaxML) program was used to perform a phylogenetic analysis of the zebrafish CAM genes and orthologs in other vertebrates. A synteny analysis of regions surrounding zebrafish CAM paralogs was performed. Digoxigenin (dig)-labeled cRNA probes for each CAM gene were generated to perform in situ hybridization of retinal cryosections from zebrafish embryos and larvae. Dual in situ hybridization of retinal cryosections from zebrafish larvae was performed with dig- and fluorescein-labeled cRNA probes.
We found the studied zebrafish CAM genes encode similar protein domain structures as their corresponding orthologs in mammals and possess similar intron-exon organizations. CAM paralogs were located on different chromosomes. Phylogenetic and synteny analyses provided support for zebrafish
and
paralogs having originated during the teleost genome duplication. We found that
and
are co-expressed in the ganglion cell layer (GCL) and the basal portion of the inner nuclear layer (INL), with weak expression in the photoreceptor-containing outer nuclear layer (ONL). Of the
genes, only
was strongly expressed in ONL.
and
were co-expressed in the GCL and the basal portion of the INL.
and
also showed co-expression in the GCL and basal portion of the INL. All
genes were expressed in the ciliary marginal zone (CMZ). Dual in situ hybridizations revealed alternating patterns of co-expression and exclusive expression for the
and
paralogs in cells of the GCL and the INL. The same alternating pattern was observed between
and
paralogs and between
and
paralogs. The expression of
was observed in the INL and the GCL, with some cells in the basal portion of the INL showing co-expression of
and
.
These findings suggest that zebrafish
and
paralogs were likely the result of the teleost whole genome duplication and that all CAM duplicates show some differential expression patterns. We also demonstrate that the comparative expression patterns of CAM genes in the zebrafish are distinct from the exclusive expression patterns observed in chick retina, in which retinal ganglion cells express one of the four chick
or
genes only. The patterns in zebrafish are more similar to those of mice, in which co-expression of
and
genes is observed. These findings provide the groundwork for future functional analysis of the roles of the CAM paralogs in zebrafish.
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Details
- Title
- Expression patterns of dscam and sdk gene paralogs in developing zebrafish retina
- Creators
- Carlos A Galicia - University of Idaho, Department of Biological Sciences, Moscow, IDJoshua M Sukeena - University of Idaho, Department of Biological Sciences, Moscow, IDDeborah L Stenkamp - University of Idaho, Department of Biological Sciences, Moscow, IDPeter G Fuerst - University of Washington School of Medicine, WWAMI Medical Education Program, Moscow, ID
- Publication Details
- Molecular vision, Vol.24, pp.443-458
- Academic Unit
- Center for Reproductive Biology
- Publisher
- United States
- Grant note
- R21 EY026814 / NEI NIH HHS
- Identifiers
- 99900547519601842
- Language
- English
- Resource Type
- Journal article