Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq

Cellular heterogeneity can emerge from the expression of only one parental allele. However, it has remained controversial whether, or to what degree, random monoallelic expression of autosomal genes (aRME) is mitotically inherited (clonal) or stochastic (dynamic) in somatic cells, particularly in vivo. Here, researchers at the Karolinska Institutet used allele-sensitive single-cell RNA-seq on clonal primary mouse fibroblasts and freshly isolated human CD8+ T cells to dissect clonal and dynamic monoallelic expression patterns. Dynamic aRME affected a considerable portion of the cells’ transcriptomes, with levels dependent on the cells’ transcriptional activity. Notably, clonal aRME was detected, but it was surprisingly scarce (<1% of genes) and mainly affected the most weakly expressed genes. Consequently, the overwhelming majority of aRME occurs transiently within individual cells, and patterns of aRME are thus primarily scattered throughout somatic cell populations rather than, as previously hypothesized, confined to patches of clonally related cells.

Dynamic and clonal aRME in human T cells


(a) Schematic of the experimental design. (b) Box plots of the percentage of genes with aRME in HLA-B7–restricted T cells, isolated at day 15 or day 136 after vaccination, and in all T cells expanded in vivo and ex vivo. Expression threshold, RPKM > 20. (c) Top, percentage of aRME in 32 T cell clones expanded in vivo (circle, per-cell level; dot, median) and in all T cells expanded in vivo (box plot to the right). Bottom, blue box plots show the percentage of clone-consistent aRME (observed minus expected, from sampled in silico pooling). The pink box plot and red solid line show the median percentage of clonal aRME estimated over all clones. P value corresponds to clonal aRME above zero according to a one-sided Wilcoxon test. Expression threshold, RPKM > 1. (d) Example of gene-level testing in a T cell clone expanded ex vivo (clone C), showing highly significant clonal aRME for KLRB1

Reinius B, Mold JE, Ramsköld D, Deng Q, Johnsson P, Michaëlsson J, Frisén J, Sandberg R. (2016) Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq. Nat Genet [Epub ahead of print]. [abstract]

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