Rachel M. Petersen1,2, Christopher M. Vockley3 and Amanda J. Lea1,2,4 1Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232, USA; 2Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee 37232, USA; 3The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; 4Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA Corresponding author: amanda.j.leavanderbilt.edu Abstract

A major goal in evolutionary biology and biomedicine is to understand the complex interactions between genetic variants, the epigenome, and gene expression. However, the causal relationships between these factors remain poorly understood. mSTARR-seq, a methylation-sensitive massively parallel reporter assay, is capable of identifying methylation-dependent regulatory activity at many thousands of genomic regions simultaneously and allows for the testing of causal relationships between DNA methylation and gene expression on a region-by-region basis. Here, we develop a multiplexed mSTARR-seq protocol to assay naturally occurring human genetic variation from 25 individuals from 10 localities in Europe and Africa. We identify 6957 regulatory elements in either the unmethylated or methylated state, and this set was enriched for enhancer and promoter chromatin annotations, as expected. The expression of 58% of these regulatory elements is modulated by methylation, which is generally associated with decreased transcription. Within our set of regulatory elements, we use allele-specific expression analyses to identify 8020 sites with genetic effects on gene regulation; further, we find that 42.3% of these genetic effects vary in direction or magnitude between methylated and unmethylated states. Sites exhibiting methylation-dependent genetic effects are enriched for GWAS and EWAS annotations, implicating them in human disease. Compared with data sets that assay DNA from a single European ancestry individual, our multiplexed assay is able to uncover more genetic effects and methylation-dependent genetic effects, highlighting the importance of including diverse genomes in assays that aim to understand gene regulatory processes.

Footnotes

[Supplemental material is available for this article.]

Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.279957.124.

Freely available online through the Genome Research Open Access option.

Received August 23, 2024. Accepted June 17, 2025.