Consequences of depleting TNRC6, AGO, and DROSHA proteins on expression of microRNAs

Effect of loss of TNRC6 paralogs on mature miRNA expression. (A) Scheme showing interactions of TNRC6 protein during miRNA-mediated silencing. Tryptophan residues on the TNRC6 protein are indicated as “W” in a circle. (B) Volcano plot of global differential miRNA expression of miRNAs annotated on MirGeneDB from small-RNA-seq in TNRC6AB^−/− relative to WT (pink) and TNRC6AB^−/− + siTNRC6C cells relative to WT HCT116 transfected with siGL2 negative control (red). (All sequencing performed in three biological replicates. Differential expression and significance [P-adj] calculated with edgeR, and dotted lines represent two log₂ fold-change. Read cutoff of 1 TPM for all displayed miRNAs.) (C) Volcano plot of differential miRNA expression from small-RNA-seq in TNRC6AB^−/− relative to WT and TNRC6AB^−/− + siTNRC6C (pink) cells relative to WT HCT116 transfected with siGL2 negative control (red) showing only the top 100 miRNAs associated with AGO2 from AGO2-eCLIP from HCT116. (D) Volcano plot where red dots represent differential expression of miRNAs that were reported as Drosha-dependent (Kim et al. 2021) in TNRC6AB^−/− HCT116 transfected with siTNRC6C relative to WT HCT116 transfected with siGL2 negative control. (E) TPM for all miRBase miRNAs with expression levels above the read cutoff of 1 TPM in WT transfected with siGL2 negative control and TNRC6AB^−/− transfected with siTNRC6C. The color of each point represents significance, −log₁₀ adjusted P-value.