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. Author manuscript; available in PMC: 2021 Sep 10.
Published in final edited form as: Cell Rep. 2021 Aug 24;36(8):109598. doi: 10.1016/j.celrep.2021.109598

Figure 4. SAGA and ATAC regulate the expression of different sets of genes.

Figure 4.

(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.