Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden.
Nat Biotechnol. 2021 Jul;39(7):825-835. doi: 10.1038/s41587-021-00869-9. Epub 2021 Apr 12.
In contrast to single-cell approaches for measuring gene expression and DNA accessibility, single-cell methods for analyzing histone modifications are limited by low sensitivity and throughput. Here, we combine the CUT&Tag technology, developed to measure bulk histone modifications, with droplet-based single-cell library preparation to produce high-quality single-cell data on chromatin modifications. We apply single-cell CUT&Tag (scCUT&Tag) to tens of thousands of cells of the mouse central nervous system and probe histone modifications characteristic of active promoters, enhancers and gene bodies (H3K4me3, H3K27ac and H3K36me3) and inactive regions (H3K27me3). These scCUT&Tag profiles were sufficient to determine cell identity and deconvolute regulatory principles such as promoter bivalency, spreading of H3K4me3 and promoter-enhancer connectivity. We also used scCUT&Tag to investigate the single-cell chromatin occupancy of transcription factor OLIG2 and the cohesin complex component RAD21. Our results indicate that analysis of histone modifications and transcription factor occupancy at single-cell resolution provides unique insights into epigenomic landscapes in the central nervous system.
与测量基因表达和 DNA 可及性的单细胞方法相比，分析组蛋白修饰的单细胞方法受到灵敏度和通量的限制。在这里，我们将 CUT&Tag 技术（开发用于测量批量组蛋白修饰）与基于液滴的单细胞文库制备相结合，以产生染色质修饰的高质量单细胞数据。我们将单细胞 CUT&Tag（scCUT&Tag）应用于数万只小鼠中枢神经系统细胞，并探测到活跃启动子、增强子和基因体（H3K4me3、H3K27ac 和 H3K36me3）和非活性区域（H3K27me3）的特征组蛋白修饰。这些 scCUT&Tag 图谱足以确定细胞身份，并阐明调节原则，如启动子二价性、H3K4me3 的扩散和启动子-增强子连接性。我们还使用 scCUT&Tag 研究了转录因子 OLIG2 和黏连蛋白复合物成分 RAD21 的单细胞染色质占据情况。我们的结果表明，单细胞分辨率下组蛋白修饰和转录因子占据的分析为中枢神经系统中的表观基因组景观提供了独特的见解。
