Fig. 1: Transcriptional upregulation of the female Z chromosome.
a Schematic representation of the experimental set up. RNA from brain, kidney, liver, skin, ovary and testis tissues was isolated from purebred WL (White Leghorn; blue) or RJF (Red Junglefowl; red) or F1 crossbred chickens (F1-Forward: RJFmat x WLpat or F1-Reverse: WLmat x RJFpat) and used for allele-resolved RNA-sequencing using bulk UMI Smartseq2. b Male:Female ratios of gene expression per tissue shown as boxplots over violin plots. Number of samples per tissue (n) shown in respective panels. Only expressed genes (average FPKM > 1; chr1 = 2055, chr2 = 1355, chr3 = 1219, chr4 = 1118, chr5 = 957, chr6 = 545, chr7 = 513, chr8 = 513, μ = 6045, chrZ=710 genes) were included in the analysis. μ denotes grouped micro-chromosomes 9-33. Data shown as median (center line), first and third quartiles (box limits) and 1.5x interquartile range (whiskers). c Male:Female gene expression ratios along chromosomes 4 and Z per tissue. Average ratio per gene shown in green, with a rolling average (LOESS) ± 95% confidence interval shown in pink. On the bottom panel, Male:Female (M-F) 5mC (5-methylcytosine) enrichment based on bisulfite is shown for chromosomes 4 and Z, with male hypermethylated regions denoted in red. d Z:autosome ratios of bulk RNA-seq of WL, RJF and F1 chicken tissues. Each line and dot represents individual samples. Number samples (n) per tissue type shown in respective panels. Only expressed genes (FPKM > 1; chrA: n = 266-936, chrZ: n = 351) were included in the analysis. Female and male samples coloured in pink and green respectively. e Boxplots of allelic expression (FPKM) in female and male samples for each chromosome for F1 tissue samples (see a). RJF and WL alleles are shown in red and blue, respectively. μ denotes grouped micro-chromosomes 9-33. Number of samples (n) shown in respective panels. Only expressed genes (average FPKM > 1; 7047 (chr1 = 936, 2 = 628, 3 = 567, 4 = 554, 5 = 424, 6 = 301, 7 = 261, 8 = 266, 9-33 = 2758, Z = 351) were included in the analysis. Data shown as median (center line), first and third quartiles (box limits) and 1.5x interquartile range (whiskers).
