Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity
Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity
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DOI：
10.1074/jbc.ra119.011174
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发表时间：
2020-01-31
影响因子：
4.8
通讯作者：
Archer, Trevor K.
中科院分区：
文献类型：
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作者：
Kinyamu, H. Karimi;Bennett, Brian D.;Archer, Trevor K.
蛋白酶体活性是多种细胞过程所必需的，包括转录和表观遗传调节。然而，抑制蛋白酶体活性可导致转录输出增加，这与启动子和基因体处的三甲基H3K4和磷酸化形式的RNA聚合酶（Pol）II的富集水平相关。在这里，我们在用蛋白酶体抑制剂MG 132处理的MCF-7乳腺癌细胞中进行基因表达分析和ChIP测序（ChIP-seq），我们进一步探索蛋白酶体抑制对染色质状态和RNA Pol II转录的全基因组影响。基因表达程序和染色质结构的分析表明，化学抑制蛋白酶体活性产生了一个独特的染色质状态，定义为扩散的H3K4me3标记到差异表达基因的基因体。不同的H3K4me3染色质谱和转录起始位点的超乙酰化核小体建立了一个染色质景观，促进了Ser-5-和Ser-2-磷酸化RNA Pol II的募集。随后的转录事件导致不同的基因表达变化。基因体中H3K36me3水平的改变反映了被诱导的基因转录物的生产性RNA Pol II延伸，强调了在转录周期的多个阶段对蛋白酶体活性的需求。最后，通过整合基因组学数据和途径分析，我们发现蛋白酶体抑制对染色质状态的差异影响调节了对癌细胞存活至关重要的基因。总之，我们的研究结果揭示了蛋白酶体抑制剂的未被充分认识的下游作用，这些作用可能是靶向不同染色质状态和癌细胞中RNA Pol II介导的转录的关键步骤的基础。
Proteasome activity is required for diverse cellular processes, including transcriptional and epigenetic regulation. However, inhibiting proteasome activity can lead to an increase in transcriptional output that is correlated with enriched levels of trimethyl H3K4 and phosphorylated forms of RNA polymerase (Pol) II at the promoter and gene body. Here, we perform gene expression analysis and ChIP followed by sequencing (ChIP-seq) in MCF-7 breast cancer cells treated with the proteasome inhibitor MG132, and we further explore genome-wide effects of proteasome inhibition on the chromatin state and RNA Pol II transcription. Analysis of gene expression programs and chromatin architecture reveals that chemically inhibiting proteasome activity creates a distinct chromatin state, defined by spreading of the H3K4me3 mark into the gene bodies of differentially-expressed genes. The distinct H3K4me3 chromatin profile and hyperacetylated nucleosomes at transcription start sites establish a chromatin landscape that facilitates recruitment of Ser-5- and Ser-2-phosphorylated RNA Pol II. Subsequent transcriptional events result in diverse gene expression changes. Alterations of H3K36me3 levels in the gene body reflect productive RNA Pol II elongation of transcripts of genes that are induced, underscoring the requirement for proteasome activity at multiple phases of the transcriptional cycle. Finally, by integrating genomics data and pathway analysis, we find that the differential effects of proteasome inhibition on the chromatin state modulate genes that are fundamental for cancer cell survival. Together, our results uncover underappreciated downstream effects of proteasome inhibitors that may underlie targeting of distinct chromatin states and key steps of RNA Pol II-mediated transcription in cancer cells.