Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes

Area of Science:

• Evolutionary biology
• Genomics
• Epigenetics

Background:

• Understanding gene regulation requires dissecting interactions between genetic variants, epigenome, and gene expression.
• Causal relationships between DNA methylation and gene expression are not well understood.

Purpose of the Study:

• To develop a multiplexed mSTARR-seq protocol for assaying human genetic variation.
• To investigate methylation-dependent gene regulation across diverse populations.

Main Methods:

• Developed a multiplexed methylation-sensitive massively parallel reporter assay (mSTARR-seq).
• Assayed genetic variation from 25 individuals across Europe and Africa.
• Utilized allele-specific expression analyses.

Main Results:

• Identified 6,957 regulatory elements, enriched for promoters and enhancers.
• Found that 58% of regulatory elements were modulated by methylation, usually decreasing RNA expression.
• Discovered 8,020 sites with genetic effects on gene regulation, with 42.3% varying by methylation state.
• Identified sites with methylation-dependent genetic effects enriched for GWAS and EWAS annotations.

Conclusions:

• Multiplexed mSTARR-seq effectively identifies regulatory elements and their responses to methylation and genetic variation.
• Methylation-dependent genetic effects are prevalent and linked to human diseases.
• Incorporating diverse individuals in assays significantly enhances the discovery of genetic and regulatory effects.