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Biased allelic expression in human primary fibroblast single cells.

The study of gene expression in mammalian single cells using genomic technologies now provides the possibility to investigate the patterns of allelic gene expression. We have used single-cell RNA sequencing to detect the allele-specific mRNA level in 203 single human primary fibroblast cells over 133,633 unique heterozygous single nucleotide variants (hetSNVs). We have observed that at the snapshot of analyses each cell contains mostly transcripts from one allele from the majority of genes; indeed 76.4% of the hetSNVs display stochastic monoallelic expression in single cells. Remarkably, adjacent hetSNVs exhibit haplotype consistent allelic ratio; in contrast distant sites located in two different genes are independent of the haplotype structure. Moreover, the allele-specific expression in single cells correlated with the abundance of the cellular transcript. We observed that genes expressing both alleles in majority of the single cells at a given time point are rare and enriched in highly expressed genes. The relative abundance of each allele in a cell is controlled by some regulatory mechanisms since we observed related single-cell allelic profiles according to genes. Overall, these results have direct implications in cellular phenotypic variability.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001001083 Illumina HiSeq 2000 2
EGAD00001001084 Illumina HiSeq 2000 209
Publications Citations
Biased allelic expression in human primary fibroblast single cells.
Am J Hum Genet 96: 2015 70-80
Early X chromosome inactivation during human preimplantation development revealed by single-cell RNA-sequencing.
Sci Rep 7: 2017 10794
Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts.
Proc Natl Acad Sci U S A 115: 2018 13015-13020
Human genes escaping X-inactivation revealed by single cell expression data.
BMC Genomics 20: 2019 201
BIRD: identifying cell doublets via biallelic expression from single cells.
Bioinformatics 36: 2020 i251-i257