Fig. 7: Genome-wide contribution of RS-mediated functions of PGC-1α at promoter-binding, transcriptome and proteome levels.

a Pie chart representing the relative distribution and diversity of promoters bound by PGC-1α. b Venn diagram representing promoters bound by PGC-1α and PGC-1α-ΔRS. c Bar charts representing KEGG pathways enriched in the promoters bound by PGC-1α. The statistical analysis uses a modified Fisher’s Exact test within the DAVID package⁸². d Combined sizes of whole-cell transcriptomes (WCT) and cytoplasmic transcriptomes (CyT) for quantified annotated and protein-coding transcripts at gene level. e Volcano plots representing the genome-wide distribution of differentially-expressed transcripts according to p-values and fold changes upon loss-of-function of the RS domain (ΔRS-res versus WT-res). NS (black): non-significant; FC (green): fold changes >1.41, p-values > 0.05; P (blue): p-values < 0.05, fold changes <1.41; P & FC (red): significant p-values (<0.05) & fold changes (>1.41). Red labels indicate the numbers of significantly down- or up-regulated annotated transcripts in the whole cell and cytoplasmic transcriptomes. The DESeq2 package was used to statistically estimate the differential expression (Supplementary Method 6). f Pie chart representing annotated transcripts differentially expressed upon loss of the RS domain of PGC-1α in the whole cell and cytoplasmic transcriptomes. g Bar charts representing KEGG pathways enriched cytoplasmic mRNAs down-regulated upon loss-of-function of the RS domain. The statistical analysis uses a modified Fisher’s Exact test within the DAVID package⁸². h Volcano plot representing differentially expressed proteins with adjusted p-values < 0.05. The LIMMA package was used to statistically estimate the differential expression (Supplementary Method 7). i Bar chart representing KEGG pathways enriched in proteins down-regulated upon loss-of-function of the RS domain. The statistical analysis uses a modified Fisher’s Exact test within the DAVID ontology package⁸². j Venn diagram comparing the lists of down-regulated total/cytoplasmic mRNAs and proteins upon loss-of-function of the RS domain.