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

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