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. 2019 Aug 23;10:3807. doi: 10.1038/s41467-019-11791-9

Fig. 6.

Fig. 6

Pax7 binding on closed chromatin is only productive in Tpit-expressing cells. a Read density heatmaps of assay for transposase-accessible chromatin using sequencing (ATACseq) signal density in a 4 kb window centered on binding sites for the indicated factors. The heatmaps are ranked by their decreasing ATACseq central (200 bp) read densities. b, c Genome browser views of ATACseq profiles in AtT-20 and αT3 cells at the Tpit (b) and SF1 (c) loci. d Dispersion plots of central (200 bp) ATACseq read densities in Neo (x-axis) versus Pax7 (y-axis) expressing AtT-20 (left) and αT3 cells (right) at all Pax7 binding sites in the indicated cell lines. Colored dots represent sites with significantly stronger signals after Pax7 expression. e Dispersion plots of ATACseq read densities in Pax7-expressing cells (x-axis) over Pax7 chromatin immunoprecipitation sequencing (ChIPseq) read densities (y-axis) in AtT-20 (left) and αT3 cells (right) at Pax7 binding sites with no ATACseq signal (<1 reads per kilobase of transcript, per million mapped reads (RPKM) in Neo cells) before Pax7 expression. f, g Boxplots of Tpit ChIPseq (f) and ATACseq (g) read densities in Neo- and Pax7-expressing AtT-20 cells at Pax7 sites without ATACseq signal (<1 RPKM in Neo cells) before Pax7 expression subdivided into Tpit-bound (>1 RPKM in Pax7-expressing cells, blue) and not bound by Tpit (<1 RPKM in Pax7-expressing cells, gray). Right panels: in light blue, Tpit binding and ATACseq signals are shown at sites bound by Tpit before Pax7 expression, that is, at open chromatin sites (without filtering the initial ATAC signal). Center lines show medians; box limits indicate the 25th and 75th percentiles; whiskers extend to 1.5 times the interquartile range from the 25th to 75th percentiles. h Tpit motif density at Pax7 sites without ATACseq signal before Pax7 expression subdivided into Tpit-bound (>1 RPKM in Pax7-expressing cells, blue) and not bound by Tpit (<1 RPKM in Pax7-expressing cells, gray). i Pull-down assay of in vitro translated Tpit interaction with MBP-Pax7, but not with MBP-βGal