Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-1674, USA.
Genome Res. 2021 Oct;31(10):1831-1842. doi: 10.1101/gr.260893.120. Epub 2021 Apr 14.
Recently, multiple single-cell assays were developed for detecting histone marks at the single-cell level. These techniques are either limited by the low cell throughput or sparse reads which limit their applications. To address these problems, we introduce indexing single-cell immunocleavage sequencing (iscChIC-seq), a multiplex indexing method based on TdT terminal transferase and T4 DNA ligase-mediated barcoding strategy and single-cell ChIC-seq, which is capable of readily analyzing histone modifications across tens of thousands of single cells in one experiment. Application of iscChIC-seq to profiling H3K4me3 and H3K27me3 in human white blood cells (WBCs) enabled successful detection of more than 10,000 single cells for each histone modification with 11 K and 45 K nonredundant reads per cell, respectively. Cluster analysis of these data allowed identification of monocytes, T cells, B cells, and NK cells from WBCs. The cell types annotated from H3K4me3 single-cell data are specifically correlated with the cell types annotated from H3K27me3 single-cell data. Our data indicate that iscChIC-seq is a reliable technique for profiling histone modifications in a large number of single cells, which may find broad applications in studying cellular heterogeneity and differentiation status in complex developmental and disease systems.
最近，已经开发出了多种用于在单细胞水平检测组蛋白标记的单细胞分析技术。这些技术要么受到低细胞通量的限制，要么受到稀疏读取的限制，限制了它们的应用。为了解决这些问题，我们引入了索引单细胞免疫切割测序（iscChIC-seq），这是一种基于末端转移酶（TdT）和 T4 DNA 连接酶介导的条形码策略的多重索引方法，以及单细胞 ChIC-seq，它能够在一次实验中轻松分析数万单个细胞中的组蛋白修饰。将 iscChIC-seq 应用于人白细胞（WBC）中 H3K4me3 和 H3K27me3 的分析，能够成功检测到每个组蛋白修饰超过 10000 个单细胞，每个细胞的非冗余读取数分别为 11 K 和 45 K。对这些数据进行聚类分析，能够从 WBC 中鉴定出单核细胞、T 细胞、B 细胞和 NK 细胞。从 H3K4me3 单细胞数据注释的细胞类型与从 H3K27me3 单细胞数据注释的细胞类型特异性相关。我们的数据表明，iscChIC-seq 是一种在大量单细胞中分析组蛋白修饰的可靠技术，它可能在研究复杂发育和疾病系统中的细胞异质性和分化状态方面有广泛的应用。
