Cited by 120Single-cell and spatial transcriptomicsRNA Research and SplicingGenetic Associations and Epidemiology

Biased Allelic Expression in Human Primary Fibroblast Single Cells

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Borel, Christelle, Ferreira, Pedro G., Santoni, Federico, Delaneau, Olivier, Fort, Alexandre, Popadin, Konstantin Y., Garieri, Marco, Falconnet, Emilie +6 more·2015·The American Journal of Human Genetics

Abstract

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

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Crossref · 10.1016/j.ajhg.2014.12.001

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Authors
Borel, C., Ferreira, P. G., Santoni, F., Delaneau, O., Fort, A., Popadin, K. Y., Garieri, M., Falconnet, E., Ribaux, P., Guipponi, M., Padioleau, I., Carninci, P., Dermitzakis, E. T., & Antonarakis, S. E.
Affiliations
  • University of Geneva (CH)
  • RIKEN (JP)
Corresponding author
  • Dermitzakis, Emmanouil T.
  • Antonarakis, Stylianos E.
Venue
The American Journal of Human Genetics
Publisher
Elsevier BV
Published
2015-01
Volume
96
Issue
1
Pages
70-80
ISSN
0002-9297 (ISSN-L)
OpenAlex
W1982998729
Cited by
120
References
49
Citations by year
2026: 2 · 2025: 9 · 2024: 3 · 2023: 6 · 2022: 7 · 2021: 9 · 2020: 15 · 2019: 12 · 2018: 11 · 2017: 18 · 2016: 17 · 2015: 10 · 2014: 1
FWCI
6.28
Type
journal article
Language
en
Open access
Locations
  • The American Journal of Human Genetics (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • Archive ouverte UNIGE (University of Geneva) (publishedVersion)
  • IRIS (submittedVersion)
  • SERVAL (Université de Lausanne) (submittedVersion)
  • Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
Funders
  • Louis-Jeantet Foundation
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (249968, 144082)
  • Hôpitaux Universitaires de Genève
  • Nature
  • Institute of Genetics and Genomics of Geneva
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords
allelic expression, monoallelic expression, allele-specific expression, single-cell RNA sequencing, gene expression variation
MeSH terms
Alleles, Fibroblasts, Haplotypes, Heterozygote, Humans, Phenotype, RNA, Messenger, Genome, Human, Sequence Analysis, RNA, DNA, Complementary, Single-Cell Analysis

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