Fig. 3: Beige-specific transcription factor activity and chromatin interaction networks.
From: Remodeling of gene regulatory networks underlying thermogenic stimuli-induced adipose beiging
a Biological function of beige-specific peaks by GREAT analysis. b Genome tracks showing the aggregated snATAC-seq profiles near the Ucp1 locus in adipocytes. H3K27ac ChIP-seq signal tracks (n = 2 for each)27 show the aggregated H3K27ac signals in white and beige adipocytes. snATAC-seq signal tracks show the aggregated snATAC-seq signals in white and beige adipocytes. Red boxes indicate beige-specific regions overlapping with PGC-1α binding sites39. Fragment coverage show the single cell profile (each row) of randomly selected 100 single cells from white and beige adipocytes respectively. Links show cis-coaccessibility network with multiple connections between peaks around Ucp1. c Motif enrichment for white and beige adipocytes. Positive and negative log2-fold changes respectively indicate enrichment in white and beige adipocytes. Motifs with adjusted p-value < 10−30 & Abs(log2 fold-change) > 2.0 are colored and labeled. d Most variable TF motifs are ranked. Motif sequence logos for the top variable motifs are shown. e, f TF footprints for PPARG e and ESRRA f from (white) adipocytes and beige adipocytes. Tn5 DNA sequence bias was normalized by subtracting the Tn5 bias from the footprinting signal. X-axis is distance to motif center (bp). g Venn diagram showing the number of overlaps between white-specific or beige-specific peaks and PGC-1α binding sites39. h–j The number of overlapping beige-specific peaks with PGC-1α binding sites39 h, ESRRs i, and MEFs j motifs from cisbp database41. The genes closest to the overlapping peaks are sorted by the number of peaks. k Genome tracks showing the aggregate snATAC-seq profiles near the Pdk4 locus in adipocytes. H3K27ac ChIP-seq signal tracks (n = 2 merged)27 show the aggregated H3K27ac signals from white and beige adipocytes. snATAC-seq signal tracks show the aggregated snATAC-seq signals in white and beige adipocytes. Red boxes indicate beige-specific regions overlapping with PGC-1α39, ESRRα42, and MEF2α43 ChIP-seq binding sites. Links show cis-coaccessibility network with multiple connections between peaks around Pdk4.
