Genome-wide ChIP analysis of ERRγ

ChIP assays were performed using a Pierce Agarose ChIP Kit (Thermo Scientific)^{35 (link)}, as described by the manufacturer. Briefly, 70% confluent mouse articular chondrocytes were infected with Ad-Esrrg at an MOI of 800 for 36 h. The primers for ChIP assays were designed to amplify two different ERRE-containing regions of the Mmp3 promoter and three regions of the Mmp13 promoter (Supplementary Table 3). DNA and proteins were cross-linked by incubating cells with 1% formaldehyde for 10 minutes at room temperature. Excess formaldehyde was quenched by incubating with glycine for 5 minutes. Cells were lysed and nuclei were digested using micrococcal nuclease. Sheared chromatin was diluted and immunoprecipitated with 2 μg of anti-ERRγ or control IgG antibody. DNA–protein complexes were eluted from protein A/G agarose beads using a spin column, and then reverse cross-linked by incubation with NaCl at 65 °C. The relative binding of ERRγ to the ERRE regions of Mmp3 and Mmp13 promoters was analyzed by PCR amplification using a Mastercycler thermal cycler. For quantitative ChIP assays, qRT-PCR was performed using an iCycler thermal cycler (Bio-Rad) and SYBR premixExTaq reagents (TaKaRa Bio). The data represent fold-changes relative to each input.