Binary outcomes of enhancer activity underlie stable random monoallelic expression

Area of Science:

• Genetics
• Epigenetics
• Molecular Biology

Background:

• Mitotically stable random monoallelic gene expression (RME) is observed in a small subset of autosomal genes.
• The precise regulatory mechanisms, particularly the role of enhancers, in RME are not fully understood.

Purpose of the Study:

• To investigate the role of enhancers in random monoallelic gene expression (RME) using an in vivo genetic model.
• To analyze natural killer (NK) cell receptor gene expression and enhancer function at a single-cell level.

Main Methods:

• Developed an in vivo genetic model in mice.
• Utilized high-resolution single-cell analysis of NK cell receptor gene expression.
• Performed enhancer deletions in the mouse germline and analyzed H3K27ac enrichment.

Main Results:

• Enhancers of RME NK receptor genes were accessible and marked by H3K27ac on both silent and active alleles.
• Enhancer deletion reduced gene expression frequency, converting a universally expressed gene (NKG2D) into an RME gene.
• Analysis of hematopoietic lineage genes (NKG2D, CD45, CD8α, Thy-1) revealed probabilistic expression patterns.

Conclusions:

• Enhancer activation and gene expression status can be decoupled, supporting a binary model of enhancer action.
• RME appears to be a general consequence of enhancer-driven gene regulation, not an RME-specific epigenetic program.
• Intrinsically probabilistic gene allele regulation is likely a general property of enhancer-controlled gene expression.