Massively parallel reporter assay for mapping gene-specific regulatory regions at single nucleotide resolution.

ABSTRACT: Precise gene regulation is essential for the development and function of complex tissues, yet comprehensive mapping of cis-regulatory modules (CRMs) remains challenging due to limitations in throughput, resolution, and the ability to assay within specific cell types. Here, we introduce two complementary approaches-a locus-specific massively parallel reporter assay (LS-MPRA) and a degenerate MPRA (d-MPRA)-specifically designed to address some of these shortcomings. LS-MPRA leverages bacterial artificial chromosomes (BACs) to generate high-complexity libraries spanning large genomic regions, enabling unbiased interrogation of millions of DNA fragments potentially relevant for the regulation of a specific gene or set of genes. The d-MPRA employs systematic mutagenesis to resolve the fu

SUBMITTER: Tulloch AJ 

PROVIDER: S-EPMC12132421 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature