Dataset integration identifies transcriptional regulation of microRNA genes by PPARγ in differentiating mouse 3T3-L1 adipocytes

Peroxisome proliferator-activated receptor c (PPARc) is a key transcription factor in mammalian adipogenesis. Genome-wide approaches have identified thousands of PPARc binding sites in mouse adipocytes and PPARc upregulates hundreds of protein-coding genes during adipogenesis. However, no microRNA (miRNA) genes have been identified as primary PPARc-targets. By integration of four separate datasets of genomewide PPARc binding sites in 3T3-L1 adipocytes we identified 98 miRNA clusters with PPARc binding within 50kb from miRNA transcription start sites. Nineteen mature miRNAs were upregulated 2-fold during adipogenesis and for six of these miRNA loci the PPARc binding sites were confirmed by at least three datasets. The upregulation of five miRNA genes miR-103-1 (host gene Pank3), miR-148b (Copz1), miR-182/96/183, miR-205 and miR-378 (Ppargc1b) followed that of Pparg. The PPARcdependence of four of these miRNA loci was demonstrated by PPARc knock-down and the loci of miR-103-1 (Pank3), miR-205 and miR-378 (Ppargc1b) were also responsive to the PPARc ligand rosiglitazone. Finally, chromatin immunoprecipitation analysis validated in silico predicted PPARc binding sites at all three loci and H3K27 acetylation was analyzed to confirm the activity of these enhancers. In conclusion, we identified 22 putative PPARc target miRNA genes, showed the PPARc dependence of four of these genes and demonstrated three as direct PPARc target genes in mouse adipogenesis.