Fig. 7
From: Essential roles of mitochondrial biogenesis regulator Nrf1 in retinal development and homeostasis
RNA-seq identifies genes involved in neurite outgrowth, mitochondrial functions, and energy production in Nrf1f/f;Six3-Cre retina. (a) qRT-PCR analysis of the 22 top affected genes identified in Nrf1f/f;Six3-Cre retinas, confirming changes in mRNA expression detected by RNA-seq. (b, c) Representative images of retinal explant cultures from E13.5 wildtype (b) and Nrf1f/f;Six3-Cre (c) embryos. (d) Schematic mapping of mitochondrial and functional annotation of upregulated (red) and downregulated (green) genes in Nrf1f/f;Six3-Cre retinas detected by RNA-seq. (e) Heatmap from Nrf1f/f; Six3-Cre RNA-seq showing 30 mitochondrial and 5 glycolytic genes whose expression changed. Mitochondrial genes are labeled in black, and glycolytic genes are labeled in red. (f, g) COX activity in E13.5 wildtype (f) and Nrf1f/f;Six3-Cre (g) retinas. Insets show higher magnification images of the indicated areas. Arrows indicate COX activities in the future photoreceptor layer; arrowheads indicate COX activities in ganglion cell layer. (h) qRT-PCR analysis of a subset of affected mitochondria genes between wildtype and Nrf1f/f;Six3-Cre retinas confirming changes of mRNA expression detected by RNA-seq. (i–p) In situ hybridization of mitochondrion-associated genes on E13.5 wildtype (i, k, m, and o) and Nrf1f/f;Six3-Cre (j, l, n, and p) retinal sections. Arrowheads indicate increased expression of Cpt1a in the central area of Nrf1f/f;Six3-Cre retina. (q) qRT-PCR analysis of glycolytic genes of wildtype and Nrf1f/f;Six3-Cre retinas. Scale bars: 100 μm in f and g, 20 μm in insets and 50 μm in i–j. WT: wildtype