Single-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cells

In the diploid genome, genes come in two copies, which can have different DNA sequence and where one is maternal and one is paternal. In a particular cell, a gene could potentially be expressed from both copies (biallelic expression) or only one (monoallelic). We performed RNA-Sequencing on individual cells, from zygote to the cells of the late blastocyst, and also individual cells from the adult liver. Using first generation crosses between two distantly related mouse strains, CAST/Ei and C57BL/6, we determined the expression separately from the maternal and paternal alleles. We found that half of the genes were expressed by only one allele, randomly so that some cells would express the paternal allele, some the maternal and a few cell both alleles. We also observed the spread of the progressive inactivation of the paternal X chromosome. First generation mouse strain crosses were used to study monoallelic expression on the single cell level在二倍体基因组（diploid genome）中，基因以两份拷贝的形式存在，二者的DNA序列可存在差异，其中一份源自母本，另一份源自父本。在单个细胞中，基因可通过两份拷贝同时表达（双等位基因表达（biallelic expression）），也可仅通过其中一份拷贝表达（单等位基因表达（monoallelic expression））。我们对从合子（zygote）到晚期囊胚（late blastocyst）细胞的各发育阶段的单个细胞，以及成年肝脏的单个细胞开展了RNA测序（RNA-Sequencing）实验。本研究利用两个亲缘关系较远的小鼠品系CAST/Ei与C57BL/6之间的第一代杂交（first generation crosses），分别检测了母本与父本等位基因（alleles）的表达情况。研究发现，半数基因仅通过单一份等位基因表达，且该选择具有随机性：部分细胞表达父本等位基因，部分表达母本等位基因，仅有少数细胞同时表达两份等位基因。此外，我们还观测到了父本X染色体（paternal X chromosome）的渐进性失活（progressive inactivation）扩散过程。本研究通过小鼠品系第一代杂交技术，在单细胞层面开展了单等位基因表达的相关研究。