Differentially expressed genes (DEGs) in retinas of cep290^−/− and bbs2^−/− versus wild-type zebrafish regulate similar biological processes. (A) Upregulated (red) and downregulated (blue) DEGs in retinas from 6 mpf bbs2^−/− and cep290^−/− mutants compared to wild-type siblings. (B) Heat map showing the standardized gene counts of DEGs in all samples (n = 5,522) and hierarchically clustered by sample. The length of the branch is proportional to the difference in transcript levels between samples. (C) Heat map of all downregulated PANTHER Biological processes based on DEGs from cep290 and bbs2 mutant retinas. (D) Heat map of all upregulated PANTHER Biological processes based on DEGs from cep290 and bbs2 mutant retinas.

Enrichment of differentially expressed genes in biological processes of interest in cep290 and bbs2 mutants. (A) Log/log plot of DEG fold changes of common DEGs in cep290^−/− and bbs2^−/− datasets. Blue circles represent downregulated DEGs. Red circles represent common upregulated DEGs. Purple circles are DEGs upregulated in bbs2^−/− retina but downregulated in cep290^−/− retinas. Green circles are DEGs downregulated in bbs2^−/− retinas but upregulated in cep290^−/− retinas. (B) Heat map of the log₂ fold change in the top 50 most abundantly expressed of the 815 DEGs in common by read count. Most DEGs were downregulated. (C) Heat map of the log₂ fold change in the top 50 DEGs with greatest fold change in expression.

PANTHER Overrepresentation Analysis of the molecular function of the DEGs shared by cep290 and bbs2 mutants with a |log₂ > 0.5| fold change in expression. (A) GO Molecular Function analysis to identify the molecular functions that were over- or underrepresented for the common DEGs. (B) Cone-specific genes expressed at lower levels in both mutants (C) PANTHER Pathway analysis to identify signaling pathways that are over- or underrepresented for common DEGS.

PANTHER Overrepresentation Analysis of the signaling pathways of the DEGs shared by cep290 and bbs2 mutants with a |log₂ > 0.5| fold change in expression. (A) The DEGs shared between mutant retinas had an overabundance of genes in inflammatory and stress response signaling pathways. Genes of the apoptosis, PDGF, and gonadotropin-releasing hormone receptor pathway were also overrepresented. (B) The DEGs from the apoptosis signaling pathway were upregulated. (C) Genes of the platelet derived growth factor (PDGF) signaling pathway include the Stat transcription factors and were largely upregulated. The transcription factor nin was downregulated. (D) Genes of the gonadotropin-releasing hormone receptor pathway were largely upregulated and include stat3. Three transcription factors were downregulated.

Fold change of gene expression in cep290 and bbs2 mutant retinas compared to wild-type animals. qRT-PCR of selected genes involved in inflammatory signaling and apoptosis processes in 6 mpf mutants. Gene expression was normalized to 18S reference gene expression and plotted relative to expression in wild-type siblings. Data are plotted as the mean ± S.D. Three technical replicates were conducted on each of four distinct biological samples of RNA. At least 2 retinas were pooled for each biological sample. *p < 0.05 by way of two-way Mann Whitney tests.

cep290 and bbs2 mutant gene expression as compared to a regeneration time series. (A) Differentially expressed genes across a 28-day retinal regeneration versus expression in cep290 and bbs2 versus wild-type. Expression in the mutants did not reach the levels seen between 24 h post-lesion and 5 days post-lesion and was most comparable to animals 10–28 days post-lesion. (B) 179 of the DEGs shared between cep290 and bbs2 were also differentially expressed between 24 and 72 h post-lesion, and the expression of these genes closely paralleled that of the actively regenerating animals.