Mapping of Open Chromatin in Adipocytes/Fibroblasts by FAIRE-seq. Mus musculus

Genome-wide maps of open chromatin sites in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation) and NIH-3T3 fibroblasts using formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq). We generated genome-wide maps of open chromatin sites in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation) and NIH-3T3 fibroblasts using formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq). FAIRE peaks at the promoter were associated with active transcription and histone modifications of H3K4me3 and H3K27ac. Non-promoter FAIRE peaks were characterized by H3K4me1+/me3-, the signature of enhancers, and were largely located in distal regions. The non-promoter FAIRE peaks showed dynamic change during differentiation while the promoter FAIRE peaks were relatively constant. Functionally, the adipocyte- and preadipocyte-specific non-promoter FAIRE peaks were, respectively, associated with genes up-regulated and down-regulated by differentiation. Among the adipocyte-specific FAIRE peaks, 45.3% and 11.7% overlapped binding sites for, respectively, PPARg and C/EBP??, the master regulators of adipocyte differentiation. The adipocyte-specific FAIRE peaks were not evenly distributed in the genome but tended to form clusters. Genes highly up-regulated during differentiation were associated with multiple clustered adipocyte-specific FAIRE peaks. Neighboring genes were often co-regulated during differentiation. Our study demonstrates the utility of FAIRE-seq in providing a global view of cell-type-specific cis-regulatory elements in the genome and in identifying transcriptional regulators of adipocyte differentiation.