Protein-DNA interactions are essential for establishing cell type-specific chromatin architecture and gene expression. We recently developed scDam&T-seq, a multi-omics method that can simultaneously quantify protein-DNA interactions and the transcriptome in single cells. The method effectively combines two existing methods: DNA adenine methyltransferase identification (DamID) and CEL-Seq2. DamID works through the tethering of a protein of interest (POI) to the Escherichia coli DNA adenine methyltransferase (Dam). Upon expression of this fusion protein, DNA in proximity to the POI is methylated by Dam and can be selectively digested and amplified. CEL-Seq2, in contrast, makes use of poly-dT primers to reverse transcribe mRNA, followed by linear amplification through in vitro transcription. scDam&T-seq is the first technique capable of providing a combined readout of protein-DNA contact and transcription from single-cell samples. Once suitable cell lines have been established, the protocol can be completed in 5 d, with a throughput of hundreds to thousands of cells. The processing of raw sequencing data takes an additional 1-2 d. Our method can be used to understand the transcriptional changes a cell undergoes upon the DNA binding of a POI. It can be performed in any laboratory with access to FACS, robotic and high-throughput-sequencing facilities.

中文翻译：

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使用 scDam&T-seq 同时定量单细胞中的蛋白质-DNA 相互作用和转录组。


蛋白质-DNA 相互作用对于建立细胞类型特异性染色质结构和基因表达至关重要。我们最近开发了 scDam&T-seq，这是一种多组学方法，可以同时量化单细胞中蛋白质-DNA 相互作用和转录组。该方法有效结合了两种现有方法：DNA腺嘌呤甲基转移酶鉴定（DamID）和CEL-Seq2。 DamID 通过将目标蛋白 (POI) 与大肠杆菌 DNA 腺嘌呤甲基转移酶 (Dam) 结合来发挥作用。该融合蛋白表达后，POI 附近的 DNA 会被 Dam 甲基化，并可被选择性消化和扩增。相比之下，CEL-Seq2 使用聚 dT 引物来反转录 mRNA，然后通过体外转录进行线性扩增。 scDam&T-seq 是第一种能够提供单细胞样本中蛋白质-DNA 接触和转录的组合读数的技术。一旦建立了合适的细胞系，该方案可在 5 天内完成，吞吐量可达数百至数千个细胞。原始测序数据的处理还需要 1-2 天。我们的方法可用于了解细胞在 POI 与 DNA 结合后发生的转录变化。它可以在任何能够使用 FACS、机器人和高通量测序设施的实验室中进行。