Modeling allele-specific gene expression by single-cell RNA sequencing

Jiang, Y.; Zhang, N. R.; Li, M.

doi:10.1101/109629

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bioRxiv · 10.1101/109629

Modeling allele-specific gene expression by single-cell RNA sequencing

Jiang, Y.·Zhang, N. R.·Li, M.

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Abstract

Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing (scRNA-seq) allows the comparison of expression distribution between the two alleles of a diploid organism and thus the characterization of allele-specific bursting. We propose SCALE to analyze genome-wide allele-specific bursting, with adjustment of technical variability. SCALE detects genes exhibiting allelic differences in bursting parameters, and genes whose alleles burst non-independently. We apply SCALE to mouse blastocyst and human fibroblast cells and find that, globally, cis control in gene expression overwhelmingly manifests as differences in burst frequency.

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Jiang, Y., Zhang, N. R., Li, M.. 2017-02-17. Modeling allele-specific gene expression by single-cell RNA sequencing. https://doi.org/10.1101/109629

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