FIGURE 3 from Proteasome Inhibition Reprograms Chromatin Landscape in Breast Cancer

Proteasome inhibition exhibits specific effects on divergent transcription. A, Heat maps showing differential signal for start RNA, DNA accessibility (ATAC), RNAPII (Ser5P), and active histone marks (K27ac, K122ac, K4me1, K4me3) at genic TSSs with divergent transcription that overlap GAIN DOCRs. B, Heat maps as in A, overlap LOST DOCRs. Signal spans ±500 bases from the TSSs and is ranked by distance between sense and antisense TSS pairs, where TSSs at the top have the shortest distance between pairs. TSSs are split by category into Promoter Upstream Transcripts (PROMPT) and Bidirectional (head-to-head) TSS pairs. N is the number of TSS pairs in each category. C, Scatter plot showing gene expression changes of bidirectional (head-to-head) TSS pairs. TSS pairs are colored by gene class, where each TSS in the pair is either protein coding (PC) or non-coding (NC). D, Violin plot showing gene expression changes of genic TSSs associated with promoter upstream transcript (PROMPT) category. Significantly different genes (FDR ≤ 0.05, log₂FC±1) are colored red (upregulated) and blue (downregulated). Gold labeled are non-coding genes. E, Heat maps showing differential signal of features in A at non-genic TSSs that overlap GAIN DOCRs. F, Heat maps showing differential signal of features in A at non-genic TSSs that overlap LOST DOCRs. TSSs are split by genomic category into gene body and intergenic. G, Violin plot showing gene expression changes of genes closest to non-genic TSSs, which are split by genomic category into gene body and intergenic. N is the number of TSS pairs in each category.