Evidence of regional specializations in regenerated zebrafish retina

Stenkamp, Deborah L.; Viall, Derek D; Mitchell, Diana

doi:10.1016/j.exer.2021.108789

Cited by 6 publications

(3 citation statements)

References 61 publications

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“…While the presence of vax2 in larval zebrafish retina is not surprising and likely is involved in the regulation of many genes, vax2 expression in adult zebrafish was unexpected as vax2 is not expressed in adult mouse retina (Barbieri et al, 1999). We speculate that vax2 may be important in the maintenance of correct topography of cone subtypes in the adult zebrafish, perhaps even after regeneration (Stenkamp et al, 2021).…”

Section: Lws1 and Lws2 Cones Differ At The Transcriptional Level Beyo...mentioning

confidence: 83%

“…Another feature of the DE list that represents a possible limitation of the FACS-RNA-Seq approach is the abundance of DE transcripts encoding components of the proteasome (37 of the 185 transcripts enriched in LWS2 cones; Datasets 1, 2). Correspondingly, GO analysis returned numerous overrepresented categories, including one KEGG category related to proteasomal function (Supplementary Figure 2A) The "RFP" in lws:PAC(H) is dsRedExpress (Tsujimura et al, 2010), which has been noted to misfold and/or aggregate (Stenkamp et al, 2021), and engage cell stress pathways (Zhou et al, 2011), and so this is a potential explanation for the enriched presence of proteasome components.…”

Section: Transcriptome Analysis Of Lws1 Vs Lws2 Cones: Facs-bulk-rna-seqmentioning

confidence: 99%

“…Curiously, opn1lw1 was not detected as DE by either the RNA-Seq analysis, or by qPCR of Sort #2 (Supplementary Figure 1). Although we only rarely observe co-expression of GFP and RFP reporters in adult lws:PAC(H) retinas (Tsujimura et al, 2010;Mitchell et al, 2015;Stenkamp et al, 2021), we tested whether co-expression was more common for the native transcripts, using multiplex fluorescence in situ hybridization. These studies confirmed that a small fraction of the adult LWS cones indeed express both lws transcripts.…”

Section: Transcriptome Analysis Of Lws1 Vs Lws2 Cones: Facs-bulk-rna-seqmentioning

confidence: 99%

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Long wavelength-sensing cones of zebrafish retina exhibit multiple layers of transcriptional heterogeneity

Farre

Sun

Starostik

et al. 2023

Front. Cell. Neurosci.

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IntroductionUnderstanding how photoreceptor genes are regulated is important for investigating retinal development and disease. While much is known about gene regulation in cones, the mechanism by which tandemly-replicated opsins, such as human long wavelength-sensitive and middle wavelength-sensitive opsins, are differentially regulated remains elusive. In this study, we aimed to further our understanding of transcriptional heterogeneity in cones that express tandemly-replicated opsins and the regulation of such differential expression using zebrafish, which express the tandemly-replicated opsins lws1 and lws2.MethodsWe performed bulk and single cell RNA-Seq of LWS1 and LWS2 cones, evaluated expression patterns of selected genes of interest using multiplex fluorescence in situ hybridization, and used exogenous thyroid hormone (TH) treatments to test selected genes for potential control by thyroid hormone: a potent, endogenous regulator of lws1 and lws2 expression.ResultsOur studies indicate that additional transcriptional differences beyond opsin expression exist between LWS1 and LWS2 cones. Bulk RNA-Seq results showed 95 transcripts enriched in LWS1 cones and 186 transcripts enriched in LWS2 cones (FC > 2, FDR < 0.05). In situ hybridization results also reveal underlying heterogeneity within the lws1- and lws2-expressing populations. This heterogeneity is evident in cones of mature zebrafish, and further heterogeneity is revealed in transcriptional responses to TH treatments.DiscussionWe found some evidence of coordinate regulation of lws opsins and other genes by exogenous TH in LWS1 vs. LWS2 cones, as well as evidence of gene regulation not mediated by TH. The transcriptional differences between LWS1 and LWS2 cones are likely controlled by multiple signals, including TH.

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Section: Lws1 and Lws2 Cones Differ At The Transcriptional Level Beyo...mentioning

confidence: 83%