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Fig. 1 | Journal of Biomedical Science

Fig. 1

From: Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy

Fig. 1

Preferential downregulation of highly expressed photoreceptor identity genes in SCA7. A MA-plot of RNA-seq analysis depicting differentially expressed protein coding genes in 12-week-old SCA7140Q/140Q retina compared to age-matched WT. Red and blue dots represent upregulated (FC > 1.3; adj. p < 0.05) and downregulated (FC < 0.7; adj. p < 0.05) genes, respectively, and black dots correspond to non-deregulated genes. B Enrichment of Gene Ontology (GO) terms for biological processes (BP) and cellular components (CC) (log10(adjusted p value) ≤ 10–3) among the 907 downregulated genes and 1421 upregulated genes in SCA7 retina. A subset of 371 downregulated genes (out of 907) accounted for almost all retrieved vision GO terms, while the remaining 536 downregulated genes retrieved only one enriched GO term. C Violin plots comparing the expression levels of different subsets of and upregulated and downregulated genes in WT and SCA7 retina. In WT retina, the 371-subset of downregulated genes has higher expression level than the 536-subset. Among the 371-subset, 54 photoreceptor (PR) specific genes are highly expressed, as compared to housekeeping (HK) genes. In contrast, 187 upregulated genes associated to immune system process have very low expression level in WT retina, when compared to entire population of expressed retinal genes. Data were analyzed using Mann–Whitney test. D Violin plots showing the relative expression level of the subset of 371 genes downregulated in SCA7 and associated with vision functions, at different stages of retinogenesis in WT retina (RNA-seq data source from [64]). Expression level of each gene is normalized relative to its lowest (0) and highest (1) value across mouse retina development. P, post-natal day

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