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Fig. 4 | Epigenetics & Chromatin

Fig. 4

From: Changes in chromatin accessibility landscape and histone H3 core acetylation during valproic acid-induced differentiation of embryonic stem cells

Fig. 4

VPA induces changes in chromatin accessibility at key genomic loci and alters TF occupancy in mESCs. A UCSC browser views of ATAC-seq peak patterns at the transcription start site of pluripotency genes Oct4 (Pou5f1) and Nanog suggesting reduced chromatin accessibility in response to VPA treatment (shaded boxes). Analysis of protein expression levels of POU5F1 (OCT4) by immunochemistry and western blotting in control and VPA-treated mESCs. Tubulin expression was used as housekeeping control. Immunochemical UCSC browser views of Tnnt2 and Hopx loci in control and VPA-treated mESCs. VPA treatment induces changes in chromatin accessibility (shaded boxes). B Comparison of transcription factor occupancy between control and VPA-treated cells. The Volcano plot shows the differential binding activity against the −log10(p-value). Each dot represents an individual motif. The top 5th percentile of enriched TFs in control samples are labeled blue, while the top 5th percentile of TFs with enriched activity in VPA-treated cells are marked in red. Aggregated footprint plots and binding motifs for representative TFs are shown. The number of TFs motifs with differential occupancy is classified by TF family and shown in the bar graph

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