Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts
Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts
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DOI：
10.1073/pnas.1806811115
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发表时间：
2018-12-18
影响因子：
11.1
通讯作者：
Antonarakis, Stylianos E.
中科院分区：
文献类型：
--
作者：
Garieri, Marco;Stamoulis, Georgios;Antonarakis, Stylianos E.
X染色体灭活（XCI）提供了一种剂量补偿机制，在每个雌性细胞中，两个X染色体之一被随机沉默。然而，在非活性X染色体和假体区域外的某些基因从XCI中逃脱，并从两个等位基因（逃生）中表达。我们研究了单细胞分辨率的XCI，将深层单细胞RNA测序与全基因组测序结合在一起，以检查935个原发性成纤维细胞和48个女性个体的48个淋巴母细胞单细胞中的等位基因特异性表达。在此框架中，我们集成了一种原始方法，以识别和排除单元格的双重双线。在成纤维细胞中，我们已经确定了55个基因为逃生基因，包括5个未描述的Escape基因。此外，我们观察到，所有基因在每个细胞和细胞类型中都表现出可变的倾向，并且每个细胞都显示出Escapee基因的独特表达曲线。指标，即灭活得分定义为每个细胞可逃避者的等位基因表达曲线的平均值，以发现具有“无效”细胞代表的极端的异质性和连续程度来自活性X染色体的基因和表达来自两个等位基因的逃生的细胞。我们发现这种作用与细胞周期相以及独立的XIST表达水平有关，在静态相（G0）中较高。单细胞等位基因特异性表达是一种强大的工具，可以识别不同组织中的新型逃生并提供XCI的意外细胞异质性的证据。
X-chromosome inactivation (XCI) provides a dosage compensation mechanism where, in each female cell, one of the two X chromosomes is randomly silenced. However, some genes on the inactive X chromosome and outside the pseudoautosomal regions escape from XCI and are expressed from both alleles (escapees). We investigated XCI at single-cell resolution combining deep single-cell RNA sequencing with whole-genome sequencing to examine allelic-specific expression in 935 primary fibroblast and 48 lymphoblastoid single cells from five female individuals. In this framework we integrated an original method to identify and exclude doublets of cells. In fibroblast cells, we have identified 55 genes as escapees including five undescribed escapee genes. Moreover, we observed that all genes exhibit a variable propensity to escape XCI in each cell and cell type and that each cell displays a distinct expression profile of the escapee genes. A metric, the Inactivation Score-defined as the mean of the allelic expression profiles of the escapees per cell-enables us to discover a heterogeneous and continuous degree of cellular XCI with extremes represented by "inactive" cells, i.e., cells exclusively expressing the escaping genes from the active X chromosome and "escaping" cells expressing the escapees from both alleles. We found that this effect is associated with cell-cycle phases and, independently, with the XIST expression level, which is higher in the quiescent phase (G0). Single-cell allele-specific expression is a powerful tool to identify novel escapees in different tissues and provide evidence of an unexpected cellular heterogeneity of XCI.