Journal
GENOME BIOLOGY
Volume 18, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/s13059-017-1200-8
Keywords
Single-cell RNA sequencing; Expression stochasticity; Allele-specific expression; Transcriptional bursting; cis and trans transcriptional control; Technical variability
Funding
- National Institutes of Health (NIH) [R01HG006137, R01GM108600, R01HL113147]
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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.
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