Supplementary Figure 3: ChIP-seq analysis of NFI, PPARγ and other transcription factors.

(a) Genomic location of PPARγ binding sites in brown adipocytes at day 0 and day 6 of differentiation. (b) Enriched known motifs within NFIA binding sites in NFIA-expressing myoblasts at day 7. (c) Enriched de novo motifs within NFIA binding sites in NFIA-expressing myoblasts at day 7. (d) Enriched known motifs within PPARγ binding sites in brown adipocytes at day 6. (e) Venn diagram showing the overlap of NFI binding sites in brown adipocytes and NFIA binding sites in NFIA-expressing C2C12 myoblasts within BAT FAIRE peaks. (f–j) Venn diagram showing the overlap of indicated transcription factors at day0 and day 6 of differentiation. (k) Venn diagram showing the overlap of NFI and PPARγ ChIP-seq peaks in 3T3-F442A white adipocytes at day 6. (l) Bar graph showing the number of co-localizing sites per gene within ±50 kb of BAT- and WAT-selective genes stratified by the fold changes of gene expression. (m) To the left, NF-1 motif density around the NFI binding sites near BAT genes, WAT genes and control genes (genes with invariant expression between BAT and WAT, N = 2000 genes). The definition of BAT- and WAT- selective genes (N = 549 and N = 849, respectively) are shown in the methods. To the right, distance from NFI binding sites to the nearest DR1 motif is shown for binding sites near BAT genes, WAT genes and control genes. Statistical significance was determined by Mann–Whitney U test. The analyses were performed once based on the ChIP-seq dataset.