Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA.
Nat Biotechnol. 2021 Jul;39(7):819-824. doi: 10.1038/s41587-021-00865-z. Epub 2021 Apr 12.
Methods for quantifying gene expression and chromatin accessibility in single cells are well established, but single-cell analysis of chromatin regions with specific histone modifications has been technically challenging. In this study, we adapted the CUT&Tag method to scalable nanowell and droplet-based single-cell platforms to profile chromatin landscapes in single cells (scCUT&Tag) from complex tissues and during the differentiation of human embryonic stem cells. We focused on profiling polycomb group (PcG) silenced regions marked by histone H3 Lys27 trimethylation (H3K27me3) in single cells as an orthogonal approach to chromatin accessibility for identifying cell states. We show that scCUT&Tag profiling of H3K27me3 distinguishes cell types in human blood and allows the generation of cell-type-specific PcG landscapes from heterogeneous tissues. Furthermore, we used scCUT&Tag to profile H3K27me3 in a patient with a brain tumor before and after treatment, identifying cell types in the tumor microenvironment and heterogeneity in PcG activity in the primary sample and after treatment.
单细胞中基因表达和染色质可及性的定量方法已经很成熟，但具有特定组蛋白修饰的染色质区域的单细胞分析在技术上具有挑战性。在这项研究中，我们将 CUT&Tag 方法改编为可扩展的纳米孔和液滴单细胞平台，以对来自复杂组织的单细胞（scCUT&Tag）和人类胚胎干细胞分化过程中的染色质景观进行分析。我们专注于对单细胞中由组蛋白 H3 赖氨酸 27 三甲基化（H3K27me3）标记的多梳抑制复合物（PcG）沉默区域进行分析，作为一种鉴定细胞状态的染色质可及性的正交方法。我们表明，scCUT&Tag 对 H3K27me3 的分析可区分人类血液中的细胞类型，并允许从异质组织中生成细胞类型特异性的 PcG 图谱。此外，我们使用 scCUT&Tag 在一名脑肿瘤患者治疗前后对 H3K27me3 进行了分析，鉴定了肿瘤微环境中的细胞类型以及原发性样本和治疗后的 PcG 活性异质性。
