Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Radboud University & Oncode Institute, Utrecht, The Netherlands.
Methods Mol Biol. 2022;2532:215-241. doi: 10.1007/978-1-0716-2497-5_11.
Spatial genome organization is considered to play an important role in mammalian cells, by guiding gene expression programs and supporting lineage specification. Yet it is still an outstanding question in the field what the direct impact of spatial genome organization on gene expression is. To elucidate this relationship further, we have recently developed scDam&T-seq, a method that simultaneously quantifies protein-DNA interactions and transcriptomes in single cells. This method efficiently combines two preexisting methods: DamID for measuring protein-DNA contacts and CEL-Seq2 for quantification of the transcriptome in single cells. scDam&T-seq has been successfully applied to measure DNA contacts with the nuclear lamina, while at the same time revealing the effect of these contacts on gene expression. This method is applicable to many different proteins of interest and can thereby aid in studying the relationship between protein-DNA interactions and gene expression in single cells.
空间基因组组织被认为在哺乳动物细胞中发挥重要作用，通过指导基因表达程序和支持谱系特化。然而，空间基因组组织对基因表达的直接影响是什么，这在该领域仍然是一个悬而未决的问题。为了进一步阐明这种关系，我们最近开发了 scDam&T-seq 方法，该方法可在单细胞中同时定量蛋白质-DNA 相互作用和转录组。该方法有效地结合了两种已有的方法：DamID 用于测量蛋白质-DNA 接触，CEL-Seq2 用于单细胞中转录组的定量。scDam&T-seq 已成功应用于测量与核层的 DNA 接触，同时揭示了这些接触对基因表达的影响。该方法适用于许多不同的感兴趣的蛋白质，因此可以帮助研究单细胞中蛋白质-DNA 相互作用与基因表达之间的关系。
