RNAseq analysis of skeletal muscle transcriptomes from wild type and MLL4SETf/fHSA-Cre mice

Enhancers play central role in controlling gene expression in time and space. Primed enhancers are marked by histone H3 lysine 4 (H3K4) mono/di-methylation (H3K4me1/2). Mixed-lineage leukemia 4 (MLL4/KMT2D) is an evolutionarily conserved H3K4me1/2 methyltransferase that is required for enhancer activation. To investigate the physiological importance of MLL4 in skeletal muscle nutrient handling, skeletal muscle-specific Mll4-knockout (MLL4SETf/fHSA-Cre) and wild-type (WT) littermates were placed on HFD (60% kcal from fat). Remarkably, muscle-specific deletion of MLL4 protects against high-fat diet-induced obesity and improves systemic glucose homeostasis. To dissect the underline mechanism, we conducted a comprehensive study of the muscle transcriptome induced by MLL4 deletion, HFD feeding, or the combination. Comparison of gene expression profiles in MLL4SETf/f muscle revealed 638 genes in total whose expression was significantly regulated by HFD, and comparison between WT and MLL4SETf/fHSA-Cre muscle showed 1430 and 1490 genes that were influenced by MLL4 abrogation on CD and HFD, respectively. Categorized into four subgroups, gene ontology (GO) pathway analysis not only showed HFD-induced immune and inflammatory pathways that were suppressed by MLL4 deficiency, but also revealed muscle metabolic and contractile gene networks that were substantially altered by MLL4 abrogation. Overall design: Gastrocnemius muscle mRNA profiles of 20-week-old WT and MLL4SETf/fHSA-Cre mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000.