Serum-based culture conditions provoke gene expression variability in mouse embryonic stem cells as revealed by single cell analysis. Mus musculus

Variation in gene expression is an important feature of mouse embryonic stem cells (ESCs). However, the mechanisms responsible for global gene expression variation in ESCs are not fully understood. We performed single cell mRNA-seq analysis of mouse ESCs and uncovered significant heterogeneity in ESCs cultured in serum. Using novel computational approaches we define highly variable gene clusters; and reveal their distinct epigenetic characteristics. We show that bivalent genes are prone to expression variation. At the same time, we identify an ESC priming pathway that initiates the exit from the naïve ESC state. Finally, we provide evidence that a large proportion of intracellular network variability is due to the extracellular culture environment. Serum free culture reduces cellular heterogeneity and transcriptome variation in ESCs. Overall design: Single cell mRNA-seq analysis of ES cells cultured with serum

基因表达变异是小鼠胚胎干细胞（Embryonic Stem Cells，ESCs）的重要特征。然而，目前尚未完全阐明介导小鼠胚胎干细胞全局性基因表达变异的分子机制。本研究对小鼠胚胎干细胞开展单细胞mRNA测序（mRNA-seq）分析，发现血清培养条件下的胚胎干细胞存在显著的细胞异质性。借助全新的计算生物学方法，我们鉴定出高度可变的基因簇，并揭示了其独特的表观遗传特征。研究证实二价基因易于发生表达变异；与此同时，我们还识别出一条可启动初始态小鼠胚胎干细胞退出的预启动通路。最后，本研究提供证据表明，细胞内调控网络的大量变异源于细胞外培养环境。无血清培养可降低小鼠胚胎干细胞的细胞异质性与转录组变异水平。整体实验设计：对血清培养条件下的胚胎干细胞开展单细胞mRNA测序分析。