Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands.
Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
Genome Res. 2020 Apr;30(4):635-646. doi: 10.1101/gr.256255.119. Epub 2020 Mar 18.
Transcription of a chromatin template involves the concerted interaction of many different proteins and protein complexes. Analyses of specific factors showed that these interactions change during stress and upon developmental switches. However, how the binding of multiple factors at any given locus is coordinated has been technically challenging to investigate. Here we used Epi-Decoder in yeast to systematically decode, at one transcribed locus, the chromatin binding changes of hundreds of proteins in parallel upon perturbation of transcription. By taking advantage of improved Epi-Decoder libraries, we observed broad rewiring of local chromatin proteomes following chemical inhibition of RNA polymerase. Rapid reduction of RNA polymerase II binding was accompanied by reduced binding of many other core transcription proteins and gain of chromatin remodelers. In quiescent cells, where strong transcriptional repression is induced by physiological signals, eviction of the core transcriptional machinery was accompanied by the appearance of quiescent cell-specific repressors and rewiring of the interactions of protein-folding factors and metabolic enzymes. These results show that Epi-Decoder provides a powerful strategy for capturing the temporal binding dynamics of multiple chromatin proteins under varying conditions and cell states. The systematic and comprehensive delineation of dynamic local chromatin proteomes will greatly aid in uncovering protein-protein relationships and protein functions at the chromatin template.
染色质模板的转录涉及许多不同蛋白质和蛋白质复合物的协同相互作用。对特定因子的分析表明，这些相互作用在应激和发育开关期间发生变化。然而，如何协调在任何给定基因座处的多个因子的结合一直是技术上具有挑战性的研究课题。在这里，我们在酵母中使用 Epi-Decoder 系统地解析了一个转录基因座，在转录受到干扰时，数百种蛋白质在染色质上的结合变化可以同时被平行解析。通过利用改进的 Epi-Decoder 文库，我们观察到化学抑制 RNA 聚合酶后，局部染色质蛋白质组发生了广泛的重新布线。RNA 聚合酶 II 结合的快速减少伴随着许多其他核心转录蛋白的结合减少和染色质重塑因子的获得。在静止细胞中，生理信号诱导强烈的转录抑制，核心转录机制的驱逐伴随着静止细胞特异性抑制剂的出现和蛋白质折叠因子和代谢酶相互作用的重新布线。这些结果表明，Epi-Decoder 提供了一种强大的策略，可以在不同条件和细胞状态下捕获多个染色质蛋白的瞬时结合动态。对动态局部染色质蛋白质组的系统和全面描绘将极大地有助于揭示染色质模板上的蛋白质-蛋白质关系和蛋白质功能。
