Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity

Abstract Cis regulatory elements (CREs) interact with their target promoters over long genomic distances and can be identified using chromatin conformation capture (3C) assays. Their regulatory activity can be functionally characterized in a high-throughput manner using massively parallel reporter assays (MPRAs) that generally test an enhancer alongside a minimal promoter. Here, we developed a novel technology called Capture-C MPRA (ccMPRA) that combines both technologies and can simultaneously obtain chromatin interactions and measure CRE activity alongside their target promoters. We utilized ccMPRA to analyze the regulatory activity of 650 promoters interacting with 42,719 sequences. As C-based techniques also capture isolated promoters, we were able to obtain promoter baseline activity, enabling the identification of both enhancers and silencers. Analysis of CREs interacting with more than one promoter showed significant activity differences depending on the promoter. In summary, ccMPRA can simultaneously characterize chromatin interactions and regulatory activity, allowing to further dissect regulatory grammar. Competing Interest Statement N.A. is a cofounder and on the scientific advisory board of Regel Therapeutics. N.A. receives funding from BioMarin Pharmaceutical Incorporate. J.S. is a scientific advisory board member, consultant and/or co-founder of Adaptive Biotechnologies, Camp4 Therapeutics, Guardant Health, Pacific Biosciences, Phase Genomics, Prime Medicine, Scale Biosciences, Sixth Street Capital and Somite Therapeutics. The other authors declare no competing interests.