CUT&Tag for efficient epigenomic profiling of small samples and single cells (965 single cells)

Many chromatin features play critical roles in regulating gene expression. A complete understanding of gene regulation will require the mapping of specific chromatin features in small samples of cells at high resolution. Here we describe Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components. In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a proteinA-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background. All steps from live cells to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day. We demonstrate the utility of CUT&Tag by profiling histone modifications, RNA Polymerase II and transcription factors on low cell numbers and single cells. Overall design: Single-cell CUT&Tag using ICELL8 platform followed by Illumina sequencing. H3K27me3 in 486 H1 cells and 479 K562 cells.

众多染色质特征在基因表达调控中发挥关键作用。要全面解析基因调控机制，需在高分辨率下对少量细胞样本中的特定染色质特征进行图谱绘制。本研究介绍了靶标切割与标签化技术（Cleavage Under Targets and Tagmentation, CUT&Tag），这是一种酶锚定策略，可高效生成高分辨率测序文库，用于分析多种染色质组分。在CUT&Tag技术中，染色质蛋白会被特异性抗体原位结合，随后该抗体可锚定蛋白A-Tn5转座酶融合蛋白。转座酶激活后可高效生成高分辨率且背景信号极低的片段文库。从活细胞到可测序文库的所有实验步骤，均可在台式单管或高通量流程的微孔板中完成，且整个流程可在一天内完成。本研究通过在低细胞数样本及单细胞中分析组蛋白修饰、RNA聚合酶II与转录因子，验证了CUT&Tag技术的实用性。实验整体设计：采用ICELL8平台开展单细胞CUT&Tag实验，随后进行Illumina测序。涉及486个H1细胞与479个K562细胞中的H3K27me3修饰检测。