Extended Data Fig. 11: NPAS4-NuA4 recruits repair factors to chromatin in stimulated neurons.

a. Boxplots of average IgG-normalized MRE11 and RAD50 CUT&RUN signal (left) or ATAC-seq normalized counts (right) at activity-inducible elements plotted, subset by quartiles of NPAS4 CUT&RUN signal. The sites displayed were selected to have equivalent or higher inducible ATAC-seq signal in low quartiles (Q1) compared to top NPAS4-binding sites (Q4). Q1 = 111 sites, Q4 = 200 sites. Boxplot shows median (line), IQR (box), 1.5x IQR (whiskers), notches indicate median ± 1.58× IQR/sqrt(n). MRE11(0 h and 2 h, n = 2), RAD50 (0 h, n = 3), RAD50 (2 h, n = 4), ATAC-seq (0 and 2 h, n = 3). 3-5 mice pooled per replicate. MRE11 2 h Q1 vs Q4: ***P < 2.2e-16; RAD50 2 h Q1 vs Q4: ***P < 2.2e-16; ATAC 2 h NPAS4 Q1 vs NPAS4 Q4: P = 0.105. P values by unpaired, two-tailed Wilcoxon rank-sum tests. b. Boxplots of average IgG-normalized MRE11 and RAD50 CUT&RUN signal (left) or H3K27ac normalized counts (right) at activity-inducible elements plotted, subset by quartiles of NPAS4 CUT&RUN signal. The sites displayed were selected to have equivalent or higher inducible H3K27ac signal in low quartiles (Q1) compared to top NPAS4-binding sites (Q4). Q1 = 79 sites, Q4 = 88 sites. Boxplot shows median (line), IQR (box), 1.5x IQR (whiskers), notches indicate median ± 1.58× IQR/sqrt(n). MRE11(0 h and 2 h, n = 2), RAD50 (0 h, n = 3), RAD50 (2 h, n = 4), ATAC-seq (0 and 2 h, n = 3). 3-5 mice pooled per replicate. MRE11 2 h Q1 vs Q4: ***P < 2.2e-16; RAD50 2 h Q1 vs Q4: **P = 2.603e-12; H3K27ac 2 h Q1 vs Q4: P = 0.0567. P values by unpaired, two-tailed Wilcoxon rank-sum tests. c. Experimental design used to isolate Cre-mCherry- and ΔCre-GFP-infected nuclei using florescence-activated cell sorting (FACS). Nuclei are subsequently used for CUT&RUN of EP400, MRE11. d. FACS of Cre-mCherry-positive nuclei (gated from DRAQ5, a fluorescent DNA dye used to identify nuclei). Left panel shows the histogram distribution of Cre-mCherry signal in infected tissue relative to an uninfected control tissue sample. Middle panel shows the sorting scheme, with negative events defined by a DRAQ5-stained, uninfected tissue sample run in parallel on the day of sorting. Right panel shows the FITC vs mCherry signal for all DRAQ5+ nuclei and demonstrates no doubly-infected cells in the samples. See Supplementary Fig. 2 for gating scheme. e. FACS of ΔCre-GFP nuclei (gated from DRAQ5+ nuclei). Left panel shows the histogram distribution of ΔCre-GFP signal in infected tissue relative to an uninfected control tissue sample. Middle panel shows the sorting scheme, with negative events defined by a DRAQ5-stained, uninfected tissue sample run in parallel on the day of sorting. Right panel shows the FITC vs mCherry signal for all DRAQ5+ nuclei and demonstrates no doubly-infected cells in the samples. See Supplementary Fig. 2 for gating scheme. f. Boxplots of average MRE11 CUT&RUN normalized counts in Cre or ΔCre-infected hippocampi of Npas4^fl/fl mice at activity-inducible sites, subset by quartiles of NPAS4 binding. Q1 = 44,864 sites, Q4 = 7,378 sites. Boxplot shows median (line), IQR (box), 1.5x IQR (whiskers), notches indicate median ± 1.58× IQR/sqrt(n). MRE11 CRE (n = 3), MRE11 ΔCre (n = 3). 2-3 mice pooled per replicate. MRE11 Q1: P = 1, Q4: ***P < 2.2e-16. P values by unpaired, one-tailed Wilcoxon rank-sum tests (ΔCre > Cre). g. Boxplots of average EP400 CUT&RUN normalized counts in Cre or ΔCre-infected hippocampi of Npas4^fl/fl mice at activity-inducible sites, subset by quartiles of NPAS4 binding. Q1 = 44,864 sites, Q4 = 7,378 sites. Boxplot shows median (line), IQR (box), 1.5x IQR (whiskers), notches indicate median ± 1.58× IQR/sqrt(n). EP400 ΔCre (n = 3), EP400 Cre (n = 4). 2-3 mice pooled per replicate. EP400 Q1: P = 1, Q4: ***P < 2.2e-16. P values by unpaired, one-tailed Wilcoxon rank-sum tests (ΔCre > Cre). h. Integrative Genomics Viewer browser image displaying CUT&RUN signal for MRE11 and EP400 in Npas4-cKO (Cre) or Control (ΔCre) in 2 h KA-stimulated nuclei at the Rgs7bp gene. MRE11 CRE (n = 3), MRE11 ΔCre (n = 3), EP400 ΔCre (n = 3), EP400 Cre (n = 4). 2-3 mice pooled per replicate.