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. 2024 Apr 24;629(8012):688–696. doi: 10.1038/s41586-024-07328-w

Fig. 4. Chromatin accessibility changes underlie reversible and irreversible transcriptional changes.

Fig. 4

a, Clustering of ATAC-Seq peaks showing significant changes after constant or transient ph-KD. b, Over-representation of genes associated with irreversible (top), reversible (middle) or decreased (bottom) ATAC-Seq peaks, for each of the six RNA-seq clusters defined in Fig. 2b. One-sided Fisher’s exact test P values were corrected for multiple testing using FDR: *FDR < 5 × 10−2, ***FDR < 1 × 10−3, ****FDR < 1 × 10−5, NS, P > 0.05. Exact FDR values: 2 × 10−1, 4 × 10−23, 1 × 10−1, 1 × 100, 1 × 100, 1 × 100 (irreversible); 4 × 10−1, 2 × 10−5, 2 × 10−34, 1 × 100, 1 × 100, 3 × 10−1 (reversible), 8 × 10−2, 1 × 100, 1 × 100, 2 × 10−21, 5 × 10−32, 1 × 10−2 (decreased). c, Fraction of TSS-distal peaks per cluster (greater than 1 kb). d, Screenshot of ATAC-Seq tracks after no ph-KD (control, top), constant (middle) or transient (bottom) ph-KD, at the irreversibly upregulated upd3 gene (left) and the reversibly upregulated Ubx gene (right). e, Normalized enrichment scores of DNA binding motifs found at each cluster of ATAC-Seq peaks (±250 bp, x axis). f, Linear model t values of DNA binding motifs associated with increased (positive t values) or decreased (negative t values) accessibility after transient (x axis) or constant ph-KD (y axis). Only motifs with a significant P < 1 × 10−5 in at least one of the two linear models are shown. g, Fold changes at ATAC-Seq peaks (y axis) on transient ph-KD, as a function of the number of Stat92E (left, in orange) or zfh1 (right, in blue) motifs that they contain (x axis). Two-sided Wilcoxon test: **P < 1 × 10−2, ****P < 1 × 10−5. Box plots show the median (line), upper and lower quartiles (box) ±1.5× interquartile range (whiskers), outliers are not shown.