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SCALE: modeling allele-specific gene expression by single-cell RNA sequencing.

ABSTRACT: Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, 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 cis control in gene expression overwhelmingly manifests as differences in burst frequency.

SUBMITTER: Jiang Y

PROVIDER: S-EPMC5407026 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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SCALE: modeling allele-specific gene expression by single-cell RNA sequencing.

Jiang Yuchao Y Zhang Nancy R NR Li Mingyao M

Genome biology 20170426 1

Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, 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 wh ...[more]

PMID: 28446220

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