Biased allelic expression in human primary fibroblast single cells

Area of Science:

• Genomics
• Molecular Biology
• Cell Biology

Background:

• Gene expression analysis in mammalian single cells is crucial for understanding cellular function.
• Genomic technologies enable the investigation of allelic gene expression patterns.
• Allelic expression variability contributes to cellular phenotypic differences.

Purpose of the Study:

• To investigate allele-specific messenger RNA (mRNA) levels in single human primary fibroblasts.
• To analyze patterns of stochastic monoallelic expression across numerous heterozygous single-nucleotide variants (hetSNVs).
• To understand the regulatory mechanisms controlling allele-specific gene expression in single cells.

Main Methods:

• Single-cell RNA sequencing (scRNA-seq) was employed.
• Analysis of 133,633 unique heterozygous single-nucleotide variants (hetSNVs) in 203 single human primary fibroblasts.
• Assessment of allele-specific mRNA levels and haplotype consistency.

Main Results:

• 76.4% of hetSNVs showed stochastic monoallelic expression in single cells.
• Adjacent hetSNVs displayed haplotype-consistent allelic ratios, while distant sites were independent.
• Allele-specific expression correlated with transcript abundance and showed gene-specific regulatory patterns.
• Genes expressing both alleles were rare and enriched among highly expressed genes.

Conclusions:

• Stochastic monoallelic expression is a predominant mode of gene expression in single human fibroblasts.
• Haplotype structure influences allelic expression for linked sites but not for distant genes.
• Regulatory mechanisms control allele-specific expression, impacting cellular phenotypic variability.
• Understanding allelic expression is key to explaining cell-to-cell variation in gene activity.