Abstract
BackgroundThe purpose of this study was to identify transcripts of retinal rod photoreceptors of the zebrafish. The zebrafish is an important animal model for vision science due to rapid and tractable development, persistent neurogenesis of rods throughout the lifespan, and capacity for functional retinal regeneration.ResultsZebrafish rods, and non-rod retinal cells of the xops:eGFP transgenic line, were separated by cell dissociation and fluorescence-activated cell sorting (FACS), followed by RNA-seq. At a false discovery rate of < 0.01, 597 transcripts were upregulated (“enriched”) in rods vs. other retinal cells, and 1032 were downregulated (“depleted”). Thirteen thousand three hundred twenty four total transcripts were detected in rods, including many not previously known to be expressed by rods. Forty five transcripts were validated by qPCR in FACS-sorted rods vs. other retinal cells. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas, and were also enriched in rods sorted from retinas subjected to a neurotoxic lesion and allowed to regenerate. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration.ConclusionsWe report the generation and validation of an RNA-seq dataset describing the rod transcriptome of the zebrafish, which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics.
Highlights
The purpose of this study was to identify transcripts of retinal rod photoreceptors of the zebrafish
To verify enrichment of our sorted populations, a separate sample from one fish was used to collect GFP+ cells using the same fluorescence-activated cell sorting (FACS)-sorting parameters as those used for RNA-seq, and we subsequently examined the sorted population by fluorescence microscopy and by post-sort analysis (Fig. 1c)
This transcriptome appears stable across the zebrafish lifespan, and similar in regenerated rods as compared with undamaged rods
Summary
The purpose of this study was to identify transcripts of retinal rod photoreceptors of the zebrafish. Within the vertebrate neural retina, photoreceptor cells are the sensory neurons that detect photons and convert this physical information into electrochemical signals. Rod photoreceptors contain the visual pigment rhodopsin, are highly sensitive to light, and provide predominantly convergent information to downstream neurons to maximize light detectability in low-light situations. Cone photoreceptors contain cone visual pigments (cone opsins) with distinct peak spectral sensitivities, and provide convergent and divergent information to downstream neurons, which process differential input to discriminate color and provide high acuity vision. Rod photoreceptors in humans are sensitive to genetic changes in structural and functional components; such defects cause hereditary retinal degenerations, which typically involve rod cell death, followed by cone cell death and loss of vision [3]. There is great interest in increasing our depth of understanding of rod photoreceptor biology, health, the factors leading to cell death, and the discovery of strategies for promoting rod survival and/or rod replacement
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