Figure 4.

De novo motif search in oxidative stress-responsive nucleosome-free ATAC-seq peaks. (A) Previously identified Cap1 motif [45] used for enrichment analysis in nucleosome-free ATAC-seq peaks with increased signal in H₂O₂-treated cells. (B) Cap1 binding sites are enriched for nucleosome-free ATAC-seq fragments in response to H₂O₂. Published Cap1 binding sites [45] were used for enrichment analysis within nucleosome-free ATAC-seq peaks. Read coverage in H₂O₂-treated and untreated cells around the Cap1 binding sites is shown. (C) Logos of position weight matrices from de novo identified motifs occurring in nucleosome-free ATAC-seq peaks in H₂O₂-treated cells (see Material and Methods for details). The number of positive matches among the input sequences and the e-value from the MEME suite DREME tool are indicated above each logo. The top four logos are presented.