Fig 2: H3K9ac and chromatin accessibility are decreased at ATAC- and SAGA-dependent genes(A) Representative images of western blot analyses of H3K9ac levels in extracts prepared from WT, Yeats2AID/AID, Tada2a-/-+Tada2b-/-, Tada3AID/AID, and Supt7l-/- cells. AID cells were treated for 24 h with IAA. Tbp serves as loading control.(B) Quantification of H3K9ac levels normalized to Ponceau staining. Error bars show mean ± SD of at least 6 biological replicates using at least two independent clones.(C) Heatmap representation of H3K9ac ChIP-seq coverage in WT, Yeats2AID/AID, Tada2a-/-+Tada2b-/-, Tada3AID/AID, and Supt7l-/- cells over promoter regions of 8,201 genes considered as expressed based on 4sU-seq. TSS, transcription start site.(D) Violin plots showing log2 FC of H3K9ac ChIP-seq coverage at promoters between Yeats2AID/AID (top panels) or Supt7l-/- cells (bottom panels) and WT cells for either genes found significantly downregulated (red) or unchanged (gray, absolute log2 FC < 0.2 and an adjusted p value > 0.2) by 4sU-seq in either Yeats2AID/AID (left panels) or Supt7l-/- cells (right panels). Numbers of genes per category are indicated below each violin graphs.(E) Violin plots showing log2 FC of ATAC-seq coverage at promoters for genes which were found either downregulated (red) or unchanged (gray) in the respective 4sU-seq experiments. Statistical test performed in (B) is Wilcoxon rank-sum test with Benjamini-Hochberg correction for multiple testing and in (D) and (E) is two-sided Welch t test. Only statistically significant results (p < 0.05) are indicated. See also Figure S5.

Fig 3: ATAC is required for the expression of translation-related genes(A) Volcano plots representation of differential expression between Supt7l-/-, Yeats2AID/AID, Zzz3AID/AID, Tada3AID/AID, and WT cells. Numbers of significantly misregulated genes are indicated. Ribosome protein genes (RPGs) are highlighted as blue dots.(B) Heatmap showing log2 FCs observed for all RPGs in Supt7l-/-, Yeats2AID/AID, Zzz3AID/AID, and Tada3AID/AID cell lines.(C) Intron-containing mRNA levels of three RPGs (Rps24, Rpl29, and Rps5) in Yeats2AID/AID, Zzz3AID/AID, and WT cells upon 2–24 h of IAA treatment were normalized as in Figure 1G. Error bars show SD of 4 biological replicates, using two independent clones. Statistical test performed is Wilcoxon rank-sum test with Benjamini-Hochberg correction for multiple testing.(D) Heatmap showing log2 FCs observed for four transcription factors involved in the regulation of RPG expression in the indicated cell lines.(E and F) Western blot analysis of Rpl29 protein levels in two independent Yeats2AID/AID and Zzz3AID/AID cell lines (E) or Supt7l-/- cell lines (F) compared with WT cells. ?Tubulin serves as loading control.

Fig 4: SAGA and ATAC regulate the expression of different sets of genes(A) Genome browser view showing newly synthesized mRNA sequencing coverage of Sf3b3 and Cog4 in Supt7l-/-, Yeats2AID/AID, and Zzz3AID/AID cell lines compared with WT cells. The top panel shows total RNA-seq coverage in WT cells. Blue arrows indicate transcription direction.(B) MA plots showing log2 fold changes (log2 FCs) of newly synthesized mRNA levels in Supt7l-/-, Yeats2AID/AID, and Zzz3AID/AID cell lines relative to WT cells against the mean of normalized reads. For each cell line, two independent clones were treated for 24 h with IAA. Numbers of significantly up- and downregulated genes are indicated. An adjusted p value of 0.05 and absolute log2 FC of 0.5 were used as thresholds for significantly affected genes.(C) Correlation analyses of log2 FCs of newly synthesized mRNA between Supt7l-/-, Yeats2AID/AID, and Zzz3AID/AID lines.(D) Venn diagrams comparing overlaps of significantly downregulated genes between Supt7l-/-, Yeats2AID/AID, and Zzz3AID/AID cells.(E) Left, genome browser view showing newly synthesized mRNA sequencing coverage of Sf3b3 and Cog4 in WT and Tada3AID/AID cells treated with IAA for 24 h. Right, MA plot showing log2 FCs of newly synthesized mRNA levels in Tada3AID/AID cells relative to WT cells treated with IAA. See also Figure S4.

Fig 5: XPC interacts directly with KAT2A. a Immunoprecipitation performed on nuclear extract of untreated XP-CWT or XP-CDEL fibroblasts with antibody against GFP, KAT2A, or IgG. b Blue staining of recombinant Flag-KAT2A and duplex strep-XPC/His-HR23B (left panel). In vitro co-immunoprecipitation assay performed by antibodies against Flag tag and IgG with the recombinant protein Flag-KAT2A and the duplex strep-XPC/His-HR23B. c Immunoprecipitation performed on nuclear extract of untreated XP-CWT fibroblasts with antibody against TRRAP, ZZZ3, GFP, or IgG. Western blot was revealed with antibodies directed against GFP, KAT2A, KAT2B, ZZZ3, WDR5 (ATAC), TRRAP, and SPT7L (SAGA). d ChIP experiment monitoring the recruitment of KAT2B, KAT2A, ZZZ3, and TRRAP at CCND1 and DAPK1 promoters, before and after ATRA treatment. Error bars represent the standard deviation of three independent experiments