Proteasome inhibition reprograms chromatin landscape in breast cancer (Start-Seq)

The 26S proteasome regulates general protein homeostasis and controls vital cellular processes, including cell division and transcriptional regulation. Cancer cells are dependent on the proper functioning of the proteasome to modulate gene expression networks that promote tumor growth. Proteasome inhibition has emerged as an effective therapeutic strategy, although mechanisms by which this approach achieves its outcomes remain unclear. We performed an integrative analysis of the transcriptome and chromatin landscape of MCF-7 breast cancer cells treated with a model proteasome inhibitor, MG132, to examine the consequences of proteasome inhibition on gene regulation. MG132 treatment initiated dynamic changes in chromatin accessibility at specific loci termed Differentially Open Chromatin Regions (DOCRs). DOCRs with increased accessibility were primarily distal to transcription start sites (TSS), while those with decreased accessibility were promoter proximal and distal to TSS. Promoter proximal DOCRs showed a unique chromatin architecture associated with distinct divergent transcription patterns. Conversely, DOCRs distal to TSS were enriched in oncogenic super enhancers that are predominantly accessible in non-basal compared to basal breast tumor subtypes. These data define distinct chromatin states and RNAPII transcription patterns, revealing molecular mechanisms by which the proteasome modulates the expression of gene networks intrinsic to breast cancer biology. Overall design: Start-seq was used to characterize transcription initiation in MCF-7 breast cancer cells treated with either vehicle (UNTR) or proteasome inhibitor MG132 (1 uM) for 4 and 24 hr

26S蛋白酶体（26S proteasome）可调控整体蛋白质稳态，并控制包括细胞分裂与转录调控在内的关键细胞过程。癌细胞依赖蛋白酶体的正常功能，以调控促进肿瘤生长的基因表达网络。蛋白酶体抑制已成为一种有效的治疗策略，但其发挥疗效的分子机制仍未明确。我们对经模型蛋白酶体抑制剂MG132处理的MCF-7乳腺癌细胞的转录组与染色质景观（chromatin landscape）开展了整合分析，以探究蛋白酶体抑制对基因调控的影响。MG132处理可在特定位点引发染色质可及性的动态变化，这些位点被命名为差异开放染色质区域（Differentially Open Chromatin Regions，缩写DOCRs）。可及性升高的DOCRs主要位于转录起始位点（transcription start sites，TSS）远端，而可及性降低的DOCRs则同时位于启动子近端与TSS远端。启动子近端的DOCRs呈现出独特的染色质结构，与特定的双向转录模式相关。反之，TSS远端的DOCRs富集于致癌超级增强子（oncogenic super enhancers）区域，这类增强子在非基底样乳腺癌亚型中的可及性显著高于基底样乳腺癌亚型。本研究明确了不同的染色质状态与RNA聚合酶II（RNAPII）转录模式，揭示了蛋白酶体调控乳腺癌生物学相关固有基因网络表达的分子机制。实验设计：本研究采用转录起始测序（Start-seq）技术，对经溶剂对照（UNTR，未处理组）或1 μM蛋白酶体抑制剂MG132处理4小时、24小时的MCF-7乳腺癌细胞的转录起始情况进行表征。