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

Area of Science:

• Genomics
• Epigenetics
• Evolutionary Biology

Background:

• Understanding gene regulation involves complex interactions between genetic variants, epigenome, and gene expression.
• Causal relationships between DNA methylation and gene expression are poorly understood.
• Methylation-sensitive massively parallel reporter assay (mSTARR-seq) identifies methylation-dependent regulatory activity.

Purpose of the Study:

• Develop a multiplexed mSTARR-seq protocol to assay naturally occurring human genetic variation.
• Test causal relationships between DNA methylation, genetic variation, and gene expression.
• Investigate the role of methylation-dependent genetic effects in human disease.

Main Methods:

• Developed a multiplexed mSTARR-seq protocol.
• Assayed genetic variation from 25 individuals across diverse geographic locations.
• Utilized allele-specific expression analyses.

Main Results:

• Identified 6957 regulatory elements, enriched for enhancers and promoters.
• Found that 58% of regulatory elements are modulated by methylation, typically decreasing transcription.
• Discovered 8020 sites with genetic effects on gene regulation, with 42.3% showing methylation-dependent effects.
• Identified sites with methylation-dependent genetic effects enriched for GWAS and EWAS annotations.

Conclusions:

• Multiplexed mSTARR-seq effectively uncovers more genetic and methylation-dependent genetic effects than single-ancestry assays.
• Including diverse genomes is crucial for comprehensive gene regulatory process understanding.
• Methylation-dependent genetic effects are implicated in human disease, highlighting their biomedical relevance.