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Transcriptional programming of lipid and amino acid metabolism by the skeletal muscle circadian clock

Fig 2

Transcriptional reprogramming of metabolic pathways in mKO muscles.

(A) REACTOME pathway enrichment analysis of 931 differentially expressed genes from mKO TA muscles. (B) Diurnal expression profiles of selected BMAL1-dependent circadian genes in TA determined by microarray and plotted as absolute expression levels (n = 3 × timepoint; mean ± SEM *p = 0.05, **p = 0.01, ***p = 0.001, 2-way ANOVA with Bonferroni correction). (C) Diurnal REV-ERBα and REV-ERBβ protein levels determined by western blot in vastus lateralis; GAPDH used as loading control. (D-F) Diurnal expression profiles in TA muscle of selected (D) REV-ERBα and HDAC3 target genes, (E) PPARα/δ-regulated mediators of lipid catabolism and oxidation, (F) GR-regulated mediators of protein turnover (n = 3 × timepoint; mean ± SEM *p = 0.05, **p = 0.01, ***p = 0.001, 2-way ANOVA with Bonferroni correction). (G) Venn diagram showing relative overlap and pathway enrichment of differentially regulated mKO genes with BMAL1 and REV-ERBα ChIP-seq peaks. Underlying data can be found in supporting files S1 Data, S1 Table, and at Gene Expression Omnibus (accession number GSE43071). BMAL1, brain and muscle ARNT-like protein 1; ChIP-seq, chromatin immunoprecipitation followed by next-generation sequencing; CLOCK, circadian locomotor output cycles kaput; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; GR, glucocorticoid receptor; HDAC3, histone deacetylase 3; MAPK, mitogen-activated protein kinase; MEF2, myocyte enhancer binding factor 2; mKO, myocyte-specific loss of BMAL1; NFκB, nuclear factor kappa B; NPAS2, neuronal PAS domain protein 2; PPARα/δ, peroxisome proliferator–activated receptor alpha/delta; RORα, RAR-related orphan receptor alpha; TA, tibialis anterior; TGFβ, transforming growth factor beta; WT, wild type; ZT, Zeitgeber time.

Fig 2