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Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects

Author

Listed:
  • Guanghao Qi

    (Johns Hopkins University
    University of Washington)

  • Benjamin J. Strober

    (Harvard T.H. Chan School of Public Health)

  • Joshua M. Popp

    (Johns Hopkins University)

  • Rebecca Keener

    (Johns Hopkins University)

  • Hongkai Ji

    (Johns Hopkins Bloomberg School of Public Health)

  • Alexis Battle

    (Johns Hopkins University
    Johns Hopkins University
    Johns Hopkins University)

Abstract

Differential allele-specific expression (ASE) is a powerful tool to study context-specific cis-regulation of gene expression. Such effects can reflect the interaction between genetic or epigenetic factors and a measured context or condition. Single-cell RNA sequencing (scRNA-seq) allows the measurement of ASE at individual-cell resolution, but there is a lack of statistical methods to analyze such data. We present Differential Allelic Expression using Single-Cell data (DAESC), a powerful method for differential ASE analysis using scRNA-seq from multiple individuals, with statistical behavior confirmed through simulation. DAESC accounts for non-independence between cells from the same individual and incorporates implicit haplotype phasing. Application to data from 105 induced pluripotent stem cell (iPSC) lines identifies 657 genes dynamically regulated during endoderm differentiation, with enrichment for changes in chromatin state. Application to a type-2 diabetes dataset identifies several differentially regulated genes between patients and controls in pancreatic endocrine cells. DAESC is a powerful method for single-cell ASE analysis and can uncover novel insights on gene regulation.

Suggested Citation

  • Guanghao Qi & Benjamin J. Strober & Joshua M. Popp & Rebecca Keener & Hongkai Ji & Alexis Battle, 2023. "Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42016-9
    DOI: 10.1038/s41467-023-42016-9
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