Systematic evaluation of the impact of promoter proximal short tandem repeats on gene expression

ABSTRACT: This study uses a massively parallel reporter assay (MPRA) to investigate how short tandem repeats (STRs) within promoter regions influence gene regulation. A custom DNA library encoding promoter variants with different STR configurations was linked to a GFP reporter and unique barcodes for expression tracking. We transfected this MPRA to HEK293T cells in triplicate which showed highly reproducible reporter expression across replicates (R=0.98). We identified 1,366 out of 19,818 loci with significant associations between repeat copy number and expression, with a strong bias toward positive effect sizes (p<1.04e-110, binomial distribution testing). We designed a second array to perform more detailed study of top regulatory STRs by modifying the repeat unit, orientation, and length, for a total of 200-300 perturbations per locus. This second array identified repeat unit sequence as the key driver of differences in expression associations across loci, whereas strand and sequence context had far weaker effects. Overall, in this work we identified optimal conditions for studying STRs using MPRAs, allowing us to perform the first in depth interrogation of the impact of STR characteristics on transcriptional regulation and study the critical roles STRs play in genome function.

ORGANISM(S): Homo sapiens

PROVIDER: GSE306816 | GEO | 2026/02/26

REPOSITORIES: GEO