Dissecting the clonal nature of allelic expression in somatic cells by single-cell RNA-seq

Cellular heterogeneity can emerge from the expression of only one parental allele, however it has remained unknown to what degree patterns of random monoallelic expression of autosomal genes (aRME) are mitotically inherited (clonal) or stochastic (dynamic) in somatic cells. Here, we resolved this by applying allele-sensitive single-cell RNA-seq on primary mouse fibroblasts and in vivo human T-cells to simultaneously investigate clonal and dynamic aRME. Dynamic aRME affected a considerable portion of the transcriptome, with levels dependent on the cell’s transcriptional activity, but clonal aRME was surprisingly scarce (<1% of genes) and affected mainly lowly expressed genes. Consequently, the overwhelming portion of aRME occurs transiently and is scattered throughout somatic populations rather than, as previously hypothesized, confined to spatially restricted patches of clonally related cells.

仅单个亲本等位基因的表达即可引发细胞异质性，但目前学界仍不清楚，体细胞中常染色体基因的随机单等位基因表达（random monoallelic expression of autosomal genes, aRME）模式，在有丝分裂过程中究竟以多大程度通过克隆遗传方式或是随机动态方式维持。本研究通过对原代小鼠成纤维细胞与体内人T细胞开展等位基因敏感的单细胞RNA测序，同时探究克隆型与动态型aRME的特征，从而解决了这一科学问题。研究显示，动态型aRME可影响转录组中相当大的一部分基因，其表达水平与细胞的转录活性密切相关；而克隆型aRME却意外地极为稀少（仅占基因总数的<1%），且主要影响低表达基因。综上，绝大多数aRME均以瞬时形式存在，并分散于整个体细胞群体中——而非如此前假说所推测的那样，局限于克隆相关细胞形成的空间受限区域内。