Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
Mol Cell. 2017 Feb 16;65(4):604-617.e6. doi: 10.1016/j.molcel.2017.01.007.
Precise gene expression patterns are established by transcription factor (TFs) binding to regulatory sequences. While these events occur in the context of chromatin, our understanding of how TF-nucleosome interplay affects gene expression is highly limited. Here, we present an assay for high-resolution measurements of both DNA occupancy and gene expression on large-scale libraries of systematically designed regulatory sequences. Our assay reveals occupancy patterns at the single-cell level. It provides an accurate quantification of the fraction of the population bound by a nucleosome and captures distinct, even adjacent, TF binding events. By applying this assay to over 1,500 promoter variants in yeast, we reveal pronounced differences in the dependency of TF activity on chromatin and classify TFs by their differential capacity to alter chromatin and promote expression. We further demonstrate how different regulatory sequences give rise to nucleosome-mediated TF collaborations that quantitatively account for the resulting expression.
精确的基因表达模式是通过转录因子（TFs）与调控序列结合来建立的。虽然这些事件发生在染色质的背景下，但我们对 TF-核小体相互作用如何影响基因表达的理解还非常有限。在这里，我们提出了一种用于在系统设计的调控序列的大规模文库中进行高分辨率 DNA 占有率和基因表达测量的测定方法。我们的测定方法在单细胞水平上提供了占有率模式。它可以准确地定量被核小体结合的群体的分数，并捕获独特的，甚至相邻的，TF 结合事件。通过将这种测定方法应用于酵母中超过 1500 个启动子变体，我们揭示了 TF 活性对染色质的依赖性的显著差异，并根据它们改变染色质和促进表达的不同能力对 TF 进行分类。我们进一步证明了不同的调控序列如何产生核小体介导的 TF 协作，这些协作可以定量解释所产生的表达。
