Fig. 4: Post-transcriptional Z-upregulation through elevated translation rate. | Nature Communications

Fig. 4: Post-transcriptional Z-upregulation through elevated translation rate.

From: Multi-layered dosage compensation of the avian Z chromosome by increased transcriptional burst frequency and elevated translational rates

Fig. 4

a Bar plot showing the number of unique autosomal (chrA; green) and Z-linked (chrZ; purple) proteins identified using tandem mass spectrometry (MS2) or triple-stage mass spectrometry (MS3) in chicken embryonic fibroblast (CEF) lines (n = 2 female, n = 2 male and n = 1 triploid intersex samples, average of 3 technical replicates). b Scatterplots of RNA expression (y-axis, bulk RNA-seq) and protein abundance (x-axis; MS2) in CEFs, per sample, with coloured by density. Spearman’s Rho and p-value based on a two-tailed Spearman rank correlation test shown for each sample. c Scatterplot of Male:Female ratios of protein abundances based on MS2 (x-axis) and MS3 (y-axis) proteomic measurements for proteins detected in both MS2 and MS3 datasets (n = 1002), with histograms of distributions shown for MS3 (y-axis) and MS2 (x-axis). Spearman’s Rho and p-value based on a two-tailed Spearman rank correlation test shown over the scatter. d Boxplot over violin plots of Male:Female ratios, of protein abundances (MS3) per chromosome in CEFs. The number of genes included in the analysis per chromosome is shown in grey. Purple vertical lines indicate median Male:Female ratios of gene expression based on bulk RNA-seq in CEFs. Data shown as median (center line), first and third quartiles (box limits) and 1.5x interquartile range (whiskers). μ denotes grouped micro-chromosomes 9-33. Data collected from 3 technical replicates. Number of samples (n) defined as: CEF lines derived from n = 2 female and n = 2 male embryos. e Bar plots displaying the percentage of ribosomal P-sites in 5’ untranslated region (UTR), coding sequence (CDS) and 3’ UTR of mRNA transcripts per sample, with the expected read distribution based on random fragmentation displayed on the right. f Female:Male and Intersex:Male ratios of translation efficiency, calculated as gene expression-normalised ribosome-protected footprint (RPF) FPKM counts for autosomes and chrZ. Based only on expressed genes (RPF > 1 & RNA FPKM > 1; number of genes shown in panel). Number of samples (n) defined as: CEF lines derived from n = 2 female, n = 2 male and n = 1 triploid embryos. P-values based on two-tailed Mann-Whitney-U test. Data shown as median, first and third quartiles and 1.5x interquartile range (IQR).

Back to article page