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.
Abbreviations
- scRNA-seq
- single-cell RNA sequencing
- ASE
- allele-specific expression
- SNP
- single-nucleotide polymorphism
- RNA-seq
- RNA sequencing
- ME
- monoallelic expression
- RME
- random monoallelic expression
- FISH
- fluorescence in situ hybridization
- EM
- expectation-maximization
- FDR
- false discovery rate
- RPKM
- reads per kilo base per million reads
- PCA
- principal component analysis
- QC
- quality control
- QTL
- quantitative trait loci
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Posted February 17, 2017.
