Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
Commun Biol. 2022 Jul 8;5(1):678. doi: 10.1038/s42003-022-03584-6.
Cell-to-cell variation in gene expression is a widespread phenomenon, which may play important roles in cellular differentiation, function, and disease development. Chromatin is implicated in contributing to the cellular heterogeneity in gene expression. Fully understanding the mechanisms of cellular heterogeneity requires simultaneous measurement of RNA and occupancy of histone modifications and transcription factors on chromatin due to their critical roles in transcriptional regulation. We generally term the occupancy of histone modifications and transcription factors as Chromatin occupancy. Here, we report a technique, termed scPCOR-seq (single-cell Profiling of Chromatin Occupancy and RNAs Sequencing), for simultaneously profiling genome-wide chromatin protein binding or histone modification marks and RNA expression in the same cell. We demonstrated that scPCOR-seq can profile either H3K4me3 or RNAPII and RNAs in a mixture of human H1, GM12878 and 293 T cells at a single-cell resolution and either H3K4me3, RNAPII, or RNA profile can correctly separate the cells. Application of scPCOR-seq to the in vitro differentiation of the erythrocyte precursor CD36 cells from human CD34 stem or progenitor cells revealed that H3K4me3 and RNA exhibit distinct properties in clustering cells during differentiation. Overall, our work provides a promising approach to understand the relationships among different omics layers.
细胞间基因表达的变化是一种普遍现象，它可能在细胞分化、功能和疾病发展中发挥重要作用。染色质被认为有助于基因表达的细胞异质性。由于其在转录调控中的关键作用，要充分了解细胞异质性的机制，需要同时测量 RNA 和组蛋白修饰及转录因子在染色质上的占有率。我们通常将组蛋白修饰和转录因子的占有率称为染色质占有率。在这里，我们报告了一种技术，称为 scPCOR-seq（单细胞染色质蛋白结合或 RNA 测序分析），用于在同一细胞中同时分析全基因组染色质蛋白结合或组蛋白修饰标记和 RNA 表达。我们证明，scPCOR-seq 可以以单细胞分辨率在人 H1、GM12878 和 293T 细胞的混合物中分析 H3K4me3 或 RNAPII 和 RNA，并且 H3K4me3、RNAPII 或 RNA 图谱可以正确地区分细胞。将 scPCOR-seq 应用于人类 CD34 干细胞或祖细胞来源的红细胞前体 CD36 细胞的体外分化，表明 H3K4me3 和 RNA 在分化过程中聚类细胞时具有不同的特性。总的来说，我们的工作为理解不同组学层面之间的关系提供了一种有前途的方法。
