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Figure 1 | Epigenetics & Chromatin

Figure 1

From: STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer

Figure 1

Open chromatin regions identified by FAIRE before and during transformation. (A) The pie chart represents the approximately 100,000 non-redundant FAIRE sites identified throughout transformation. A minority (17%) changed during transformation and is shown as the rows of the heatmap on the right. The columns of the heatmap display the replicates for FAIRE-seq at each of the indicated time points. For each FAIRE site, the normalized read count was calculated and the data in the heatmap was median centered by rows (yellow = increased and blue = decreased signal). (B) Distribution of FAIRE sites relative to RefSeq gene transcription start site (TSS) annotations. (C) A select set of TF motifs are enriched at FAIRE sites associated with genes whose RNA levels are differentially regulated during transformation. HOMER identified TF binding site motifs enriched at FAIRE sites within ±500 kb of the transcription start site of genes differentially expressed at the indicated time points (rows). Gray indicates an enriched motif (*P < 0.005).

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