Role of miR-2954-3p in dosage compensation. (A) Expression of miR-2954-3p in chicken tissues. Raw read counts were normalized with DESeq2. (B) Proportion of Z-linked genes among the genes that were predicted to be targets of miR-2954-3p and autosomal miRNAs. Target prediction was performed with TargetScan and only 8-mer sites were considered. (C) Log2-transformed M:F expression ratios for Z-linked target genes of miR-2954-3p or autosomal miRNAs. (D) Proportion of annotated ohnologs between Z-linked targets of miR-2954-3p and autosomal miRNAs. (E) Log2-transformed expression ratios for protein-coding genes following miR-2954-3p knockdown compared to control. Genes that are down-regulated by miR-2954-3p are expected to have positive ratios. The first panel shows Z-linked genes in purple and autosomal genes in gray. The following two panels show Z-linked genes predicted to be more (light purple) or less (dark purple) dosage-sensitive based on chicken expression data and ohnolog annotations. Only genes that were 1-to-1 orthologs and located on the Z Chromosome in both chicken and zebra finch were included in the analyses. Statistical significance: (*) P < 0.05; (**) P < 0.01; (***) P < 0.001.
