Fig. 5: ATAC-seq reveals the divergence of chromatin modifications between microglial aging and reactivity to LPS challenge.
From: Transcriptional and epigenetic decoding of the microglial aging process
a, Scheme of LPS and PBS administration and timepoints for ATAC-seq. b, ATAC peaks around the TSSs (−1 kb to 1 kb) of LPS-challenged microglia at three ages. Data are presented as mean ± s.d., heat map showing enrichment of normalized ATAC-seq reads within ±1 kb of TSSs in microglia at different stages. c, PCA plot showing that microglia of different ages exhibit distinct chromatin modifications in response to LPS challenge. d, Volcano plots of differentially accessible peaks upon LPS challenge (3 MO LPS versus 3 MO PBS) and age-related change (24 MO PBS versus 3 MO PBS), revealing divergent chromatin modifications between LPS challenge and the aging process (P < 0.05, log2FC ≥ 1, QL F-tests). e, Bar plots showing the distribution of differential peaks in gene encoding and regulatory element regions. f, Representative genome browser views showing ATAC peaks of Il1rn, Vmp1, Aff1, Bach1 and Map2k3os. The numbers in brackets indicate the minimum and maximum values of the y axis. Ref, reference genome view, mm10. g, Volcano plots of differential accessible peaks of LPS-challenged microglia across different ages reveal conserved epigenetic modifications across different ages. n = 2 ATAC-seq tests for each group. Microglia from 2–3 mice were pooled together for each ATAC-seq test (P < 0.05, log2FC ≥ 1, QL F-tests). BW, body weight; MO, months old; UTR, untranslated region; Dim, dimension.
