Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs
Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs
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DOI：
10.1186/s13072-018-0243-8
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发表时间：
2018-12-21
影响因子：
3.9
通讯作者：
Henikoff, Steven
中科院分区：
文献类型：
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作者：
Janssens, Derek H.;Wu, Steven J.;Henikoff, Steven
背景我们对真核生物基因调控的理解受到蛋白质-DNA相互作用的复杂性和表征这些相互作用的低效方法的限制。我们最近推出了CUT&RUN，一种抗体靶向核酸酶切割方法，配置文件DNA结合蛋白，组蛋白和染色质修饰蛋白在原位具有特殊的灵敏度和resolution.ResultsHere，我们描述了一个自动化的CUT&RUN平台，并将其应用于表征人类细胞的染色质景观。我们发现，组蛋白修饰的自动化CUT&RUN配置文件严格划分活性和抑制染色质区域，我们开发了一个连续的度量，以确定细胞类型特异性启动子和增强子的活动。我们测试的能力，自动化切割和运行配置文件冷冻肿瘤样本，并发现我们的方法很容易区分两个小儿胶质瘤异种移植物的亚型特异性基因expression programmes.ConclusionsThe简单，成本效益高的工作流程，使自动化切割和运行一个有吸引力的工具，高通量表征细胞类型和患者样本。
BackgroundOur understanding of eukaryotic gene regulation is limited by the complexity of protein-DNA interactions that comprise the chromatin landscape and by inefficient methods for characterizing these interactions. We recently introduced CUT&RUN, an antibody-targeted nuclease cleavage method that profiles DNA-binding proteins, histones and chromatin-modifying proteins in situ with exceptional sensitivity and resolution.ResultsHere, we describe an automated CUT&RUN platform and apply it to characterize the chromatin landscapes of human cells. We find that automated CUT&RUN profiles of histone modifications crisply demarcate active and repressed chromatin regions, and we develop a continuous metric to identify cell-type-specific promoter and enhancer activities. We test the ability of automated CUT&RUN to profile frozen tumor samples and find that our method readily distinguishes two pediatric glioma xenografts by their subtype-specific gene expression programs.ConclusionsThe easy, cost-effective workflow makes automated CUT&RUN an attractive tool for high-throughput characterization of cell types and patient samples.