Description

Single-Cell Gene Expression Analyses with Allelic Resolution

Rickard Sandberg

Karolinska Institutet, Stockholm, Sweden

Assessing gene expression in individual cells hold promise to reveal the extent, function and origins of cell-to-cell variability. To this end, my lab has been developing single-cell RNA-sequencing methods (e.g. Smart-seq2) that we applied to analyse gene expression across thousands of individual cells. Analysing single-cell gene expression with allelic resolution (using the full-length feature of Smart-seq2 and SNPs) revealed fundamental patterns of expression for genes on autosomes and sex chromosomes. In early embryonic development, female mouse and human embryos achieve dosage compensation of X-chromosome expression using surprisingly different strategies. In mouse, the paternal X-chromosome in inactivated from 4-cell stage embryos whereas dosage compensation in human embryos proceeds with dampening of expression from both X chromosomes. Single-cell analyses of allelic expression of autosomal genes revealed that for a substantial fraction of genes in a cell, the transcribed RNA is derived from only one parental allele. The expression of alleles in a cell was seemingly random, and dynamic over time, even within cells of clonal origins. Importantly, we found no support for widespread allele-level regulation of gene expression of autosomal genes. Finally, we have used our collections of allelic resolution single-cell RNA-seq data to investigate kinetic aspects of transcription. The stochastic allelic transcription increases heterogeneity among cells, and might even contribute to phenotypic variance among individuals of identical genotype.