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. 2020 Feb 6;77(3):475–487.e11. doi: 10.1016/j.molcel.2019.10.020

Figure 3.

Figure 3

TFIIIC-Associated HAT Activity Acetylates H3K18 at Nucleosomes over AEs in Response to Serum Depletion

(A) ATAC-seq signal enrichment in T47D grown in the presence (+S) or in the absence of serum (–S) across TFIIIC-bound AEs detected in the absence of serum (–S) (–log10 of the Poisson p value). p value, two-tailed t test comparing each condition to its random control.

(B) Average profile of H3K18ac enrichment in T47D grown in the presence (+S,) or absence of serum (–S) across all TFIIIC-bound AEs (–log10 of the Poisson p value). p value, two-tailed paired t test.

(C) Sitepro average plot of nucleosome signals derived from ATAC-seq by selecting sequenced fragments of 180–250 bp (Buenrostro et al., 2013) spanning a 1 kb region over all the AEs bound by TFIIIC in T47D grown in the presence (+S) or absence (–S) of serum. Note the presence of a peak in the center of the region representing the AE (gray rectangle). SS causes a decrease in the nucleosome signal for both the AE-nucleosome and the surrounding ones (two-tailed unpaired t test).

(D) Genome browser view of representative cell-cycle-related TFIIIC-associated promoters with normalized counts of ATAC-derived nucleosome signal for T47D grown in the presence (+S) or absence (–S) of serum. The position of the AE bound by TFIIIC positive for H3K18ac is indicated by a yellow rectangle. AE nucleosomes reduced upon SS are highlighted by a gray rectangle.

(E) Venn diagram showing the total number of AEs bound by TFIIIC and those acetylated in H3K18 in serum-starved T47D.

(F) Venn diagram showing the total number of TFIIIC-associated Pol II promoters and those enriched in H3K18ac in T47D grown in the absence of serum.

(G) Plot for p300 occupancy across all TFIIIC-bound AEs spanning a 6 kb region in T47D grown in the presence (+S) or absence (–S) of serum.

(H) H3K18ac immunostaining (red) in serum-starved T47D cells knocked down for GTF3C1 (siGTF3C1) or control (siCTRL). DAPI was used to stain nuclei (blue). Two different fields are shown. Scale bar, 100 μm. GTF3C1 depletion levels are shown in Figure S3H and quantification in Figure S3I.