Fig. 8: Genome-wide relevance of the splicing and mRNA nuclear export function of PGC-1α.
From: The master energy homeostasis regulator PGC-1α exhibits an mRNA nuclear export function
a Bar charts representing KEGG pathways enriched in the list of PGC-1α-dependent mRNA nuclear export (NE) targets. The statistical analysis uses a modified Fisher’s Exact test within the DAVID ontology package82. b Bar charts representing Biological Processes (BP Direct) enriched in the list of PGC-1α-dependent mRNA nuclear export targets. The statistical analysis uses a modified Fisher’s Exact test within the DAVID ontology package82. c Venn diagram comparing the lists of PGC-1α ΔRS-dependent down-regulation of cytoplasmic mRNAs, up- and down-regulation of cytoplasmic mRNAs (all altered) and PGC-1α mRNA nuclear export targets. d Bar chart representing the number of alternative spliced events for annotated transcripts and pre-mRNAs. The following alternative splicing types were identified: TE Tandem alternative polyadenylation site, TS Tandem transcription start site, CE Cassette exon, AA Alternative Acceptor splice site, AD Alternative Donor splice site, RI Retained intron, AF Alternative First exon, AL Alternative Last exon. DESeq2 was used within the Whippet package81 to statistically estimate the differential expression (Supplementary Method 6). e Bar charts representing KEGG pathways enriched in the list of pre-mRNAs with altered alternative splicing upon loss-of-function of the RS domain. The statistical analysis uses a modified Fisher’s Exact test within the DAVID ontology package82. f Venn diagram comparing the lists of PGC-1α-bound protein-coding promoters, PGC-1α-dependent mRNA nuclear export targets and RS domain-mediated alteration of pre-mRNA splicing. g Venn diagram comparing the lists of PGC-1α-bound protein-coding promoters, PGC-1α-dependent mRNA nuclear export targets and RS domain-dependent down-regulation of proteins. h Heat map comparing the enrichment scores of major pathways for the RS-mediated down-regulation of proteins/mRNAs levels and altered splicing with the PGC-1α-dependent mRNA nuclear export targets and PGC-1α-bound protein-coding promoters. A scale of light to dark green depicts pathways with increased enrichment scores while orange highlights those not identified in the gene ontology analysis (Supplementary Data 6).
