近日，美国加州大学伯克利分校Aaron Streets、斯坦福大学Aaron F. Straight等研究人员合作开发出一种长读、单分子方法用于绘制全基因组的蛋白质-DNA相互作用。相关论文于2022年4月8日在线发表于国际学术期刊《自然—方法学》。

研究人员表示，对基因组调控的研究通常使用高通量DNA测序方法来确定特定蛋白质与DNA的相互作用，它们依赖于DNA扩增和短读测序，这限制了它们在复杂基因组区域的定量应用。

为了解决这些限制，研究人员开发了定向甲基化长读测序（DiMeLo-seq），它使用抗体拴住的酶在原位对目标蛋白的结合位点附近的DNA进行甲基化。然后利用长读单分子测序技术，将这些外源性甲基化标记与未扩增DNA上的内源性CpG甲基化同时检测。研究人员通过绘制整个人类基因组的染色质结合蛋白和组蛋白修饰图对DiMeLo-seq进行了优化和基准测试。

此外，研究人员确定了中心粒蛋白A在高重复性区域内的定位，这些区域无法用短测序读数进行测量，研究人员还估计了中心粒蛋白A分子沿单个染色质纤维的密度。DiMeLo-seq是一种多功能的方法，可以为研究蛋白质-DNA相互作用提供多模式的全基因组信息。

附：英文原文

Title: DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide

Author: Altemose, Nicolas, Maslan, Annie, Smith, Owen K., Sundararajan, Kousik, Brown, Rachel R., Mishra, Reet, Detweiler, Angela M., Neff, Norma, Miga, Karen H., Straight, Aaron F., Streets, Aaron

Issue&Volume: 2022-04-08

Abstract: Studies of genome regulation routinely use high-throughput DNA sequencing approaches to determine where specific proteins interact with DNA, and they rely on DNA amplification and short-read sequencing, limiting their quantitative application in complex genomic regions. To address these limitations, we developed directed methylation with long-read sequencing (DiMeLo-seq), which uses antibody-tethered enzymes to methylate DNA near a target protein’s binding sites in situ. These exogenous methylation marks are then detected simultaneously with endogenous CpG methylation on unamplified DNA using long-read, single-molecule sequencing technologies. We optimized and benchmarked DiMeLo-seq by mapping chromatin-binding proteins and histone modifications across the human genome. Furthermore, we identified where centromere protein A localizes within highly repetitive regions that were unmappable with short sequencing reads, and we estimated the density of centromere protein A molecules along single chromatin fibers. DiMeLo-seq is a versatile method that provides multimodal, genome-wide information for investigating protein–DNA interactions.

DOI: 10.1038/s41592-022-01475-6

Source: https://www.nature.com/articles/s41592-022-01475-6