arl3, arl13b and unc119b are upregulated in MZcep290 mutants. (A) RNAseq workflow for the identification of candidate cep290 compensating genes. RNAseq gene expression analysis was performed with 3-dpf cep290ex25 morphants, cep290 mutants and sibling wild-type (WT) embryos (NCBI GEO accession GSE175491), with three biological replicates. Upregulated genes in each group were identified, and genes specifically upregulated in MZcep290−/− mutants were selected for further analysis. MZcep290 upregulated genes were compared to a cilia proteome database to identify candidate cep290 compensating cilia-related genes. (B) RNAseq results showing upregulation of cilia-related genes arl3, arl13b and unc119b in 72-hpf embryos. (C) RT-qPCR quantification of arl3, arl13b and unc119b from MZcep290 mutant adult eye samples. n=3 biological replicates per condition; technical triplicates. (D) The upregulation of arl3, arl13b and unc119b was not detected at 3 dpf in cep290ex25 morphants embryos. n=20 embryos pooled per condition; technical triplicates. (E) The upregulation of arl3, arl13b and unc119b also was not detected at 3 dpf in cep290 zygotic mutants embryos. n=20 embryos pooled per condition; technical triplicates. (F) The ciliary mutants smh (ccdc103) and oval (ift88) did not show upregulation of arl3, arl13b and unc119b at 3 dpf. n=20 embryos pooled per condition; technical triplicates. All RT-qPCR data are expressed as fold change (2−ΔΔCt) compared with age-matched control embryos. Data are mean±s.d.
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