Fig. 4: NPAS4–NuA4-bound sites undergo DNA repair as inducible transcription subsides.

a, PCA of paired RNA-seq prepared from the same tissue used to generate the sBLISS-seq time course in hippocampus. Samples clustered according to the stimulation state, with 10 h stimulation samples separating into groups with either dampening or sustained transcriptional induction. DeSeq2-normalized counts of inducible genes Bdnf and Nptx2 shown for each sample (0 h, n = 8; 2 h, n = 8; 10 h, n = 10). One mouse per replicate. b, Boxplots of average sBLISS-seq-normalized counts in 0 h (n = 8), 2 h (n = 8), 10 h less active (n = 4), and 10 h still active (n = 6) samples at activity-inducible regulatory elements, subset by quartiles of NPAS4 binding. One mouse per replicate. Boxplots show the median (line), IQR (box) and 1.5× IQR (whiskers), and notches indicate the median ± 1.58× IQR/sqrt(n). Q1 = 1,017 sites, Q4 = 764 sites. Q1, *P = 0.03435, **P = 2.049 × 10^–8, ***P = 3.057 × 10^–13; Q4, ***P < 2.2 × 10^–16, not significant (NS) = 0.1742. P values were calculated using unpaired, two-tailed Wilcoxon rank-sum tests. c, IGV tracks of sBLISS-seq, γH2AX ChIP–seq, NPAS4, EP400, MRE11 and RAD50 CUT&RUN signals. Data plotted show the aggregate signals from all replicates per factor. The y axis displays normalized coverage scaled for each factor at the chosen locus. CUT&RUN and γH2AX ChIP–seq, n = 3–5 mice pooled per replicate. sBLISS-seq, n = 1 mouse per replicate. Replicate numbers provided in Supplementary Table 2. d, Boxplots of average MRE11 and RAD50 normalized counts at activity-inducible regulatory elements, subset by quartiles of NPAS4 CUT&RUN signals. Q1 = 1,017 sites, Q4 = 764 sites. Boxplots show the median (line), IQR (box) and 1.5× IQR (whiskers), and notches indicate the median ± 1.58× IQR/sqrt(n). n = 3–5 mice pooled per replicate. Replicate numbers provided in Supplementary Table 2. ***P < 2.2 × 10⁻¹⁶. P values were calculated using unpaired, two-tailed Wilcoxon rank-sum tests.

Source Data