Crowther LM, Wang SCM, Eriksson NA, Myers SA, Murray LA, Muscat GEO. Chicken ovalbumin upstream promoter-transcription factor II regulates nuclear receptor, myogenic, and metabolic gene expression in skeletal muscle cells. Physiol Genomics 43: 213-227, 2011. First published November 30, 2010 doi:10.1152/physiolgenomics.00195.2010.-We demonstrate that chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII) mRNA is more abundantly expressed (than COUP-TFI mRNA) in skeletal muscle C2C12 cells and in (type I and II) skeletal muscle tissue from C57BL/10 mice. Consequently, we have utilized the ABI TaqMan Low Density Array (TLDA) platform to analyze gene expression changes specifically attributable to ectopic COUP-TFII (relative to vector only) expression in muscle cells. Utilizing a TLDA-based platform and 5 internal controls, we analyze the entire NR superfamily, 96 critical metabolic genes, and 48 important myogenic regulatory genes on the TLDA platform utilizing 5 internal controls. The low density arrays were analyzed by rigorous statistical analysis (with Genorm normalization, Bioconductor R, and the Empirical Bayes statistic) using the (integromics) statminer software. In addition, we validated the differentially expressed pathophysiologically relevant gene (identified on the TLDA platform) glucose transporter type 4 (Glut4). We demonstrated that COUP-TFII expression increased the steady state levels of Glut4 mRNA and protein, while ectopic expression of truncated COUP-TFII lacking helix 12 (COUP-TF⌬H12) reduced Glut4 mRNA expression in C2C12 cells. Moreover, COUP-TFII expression trans-activated the Glut4 promoter (Ϫ997/ϩ3), and ChIP analysis identified selective recruitment of COUP-TFII to a region encompassing a highly conserved SP1 binding site (in mouse, rat, and human) at nt positions Ϫ131/Ϫ118. Mutation of the SpI site ablated COUP-TFII mediated trans-activation of the Glut4 promoter. In conclusion, this study demonstrates that in skeletal muscle cells, COUP-TFII regulates several nuclear hormone receptors, and critical metabolic and muscle specific genes. glucose metabolism; differentiation; TaqMan low density array; myogenesis CHICKEN OVALBUMIN UPSTREAM PROMOTER TRANSCRIPTION FACTORS (COUP-TFs) I and II are orphan members of the nuclear hormone receptor (NR) superfamily. NRs are ligand modulated transcription factors that regulate expression of genes involved in reproduction, development, cell differentiation, and metabolism (22).It is known that COUP-TFI and COUP-TFII can act as transcriptional repressors or activators, and the role of COUPTFs in metabolism has been examined in tissues such as liver and adipose tissue.In liver cells, COUP-TFII stimulates CYP7A (33, 37, 73) and CETP transcription (20), and represses apolipoprotein AI expression (38), demonstrating a role for COUP-TFII in the regulation of cholesterol homeostasis in liver. Also in HepG2 cells, COUP-TFI inhibits transactivation of the CPT-II promoter by PPAR␣/RXR␣, and is required for stimulation of phosphoenolpyruvate ca...