Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA.
Institute of Immunology of PLA, Third Military Medical University, Chongqing 400038, PR China.
Nucleic Acids Res. 2021 Jun 4;49(10):e56. doi: 10.1093/nar/gkab102.
Single cell chromatin accessibility assays reveal epigenomic variability at cis-regulatory elements among individual cells. We previously developed a single-cell DNase-seq assay (scDNase-seq) to profile accessible chromatin in a limited number of single cells. Here, we report a novel indexing strategy to resolve single-cell DNase hypersensitivity profiles based on bulk cell analysis. This new technique, termed indexing single-cell DNase sequencing (iscDNase-seq), employs the activities of terminal DNA transferase (TdT) and T4 DNA ligase to add unique cell barcodes to DNase-digested chromatin ends. By a three-layer indexing strategy, it allows profiling genome-wide DHSs for >15 000 single-cells in a single experiment. Application of iscDNase-seq to human white blood cells accurately revealed specific cell types and inferred regulatory transcription factors (TF) specific to each cell type. We found that iscDNase-seq detected DHSs with specific properties related to gene expression and conservation missed by scATAC-seq for the same cell type. Also, we found that the cell-to-cell variation in accessibility computed using iscDNase-seq data is significantly correlated with the cell-to-cell variation in gene expression. Importantly, this correlation is significantly higher than that between scATAC-seq and scRNA-seq, suggesting that iscDNase-seq data can better predict the cellular heterogeneity in gene expression compared to scATAC-seq. Thus, iscDNase-seq is an attractive alternative method for single-cell epigenomics studies.
单细胞染色质可及性分析揭示了单个细胞中顺式调控元件的表观基因组变异性。我们之前开发了一种单细胞 DNase-seq 分析方法（scDNase-seq），用于对有限数量的单细胞进行可及性染色质分析。在这里，我们报告了一种新的索引策略，基于批量细胞分析来解析单细胞 DNase 敏感性谱。这项新技术被称为索引单细胞 DNase 测序（iscDNase-seq），它利用末端 DNA 转移酶（TdT）和 T4 DNA 连接酶的活性将独特的细胞条形码添加到 DNase 消化的染色质末端。通过三层索引策略，它可以在单个实验中为 >15000 个单细胞进行全基因组 DHS 分析。将 iscDNase-seq 应用于人类白细胞，可以准确地揭示特定的细胞类型，并推断出每个细胞类型特有的调节转录因子（TF）。我们发现，iscDNase-seq 检测到的 DHSs 具有与 scATAC-seq 相同的细胞类型相关的特定基因表达和保守性特征。此外，我们发现使用 iscDNase-seq 数据计算的可及性细胞间变异与基因表达的细胞间变异显著相关。重要的是，这种相关性明显高于 scATAC-seq 和 scRNA-seq 之间的相关性，这表明与 scATAC-seq 相比，iscDNase-seq 数据可以更好地预测基因表达的细胞异质性。因此，iscDNase-seq 是单细胞表观基因组学研究的一种有吸引力的替代方法。
