Locus-Scale Massively Parallel Reporter Assays

Interactions among c is-regulatory elements (CREs) are central to mammalian gene regulation. Long @$$ massively parallel reporter assays (LAMPRAs) integrate combinatorial cloning, molecular barcoding and long- and short-read sequencing, to scalably measure how CRE identities, numbers, spacings, orders, orientations, and interactions shape regulatory output at multi-kilobase length scales. As a proof-of-concept, we assay 36,000 × 5-kb synthetic c is-regulatory loci (sCRLs), each a 5 × 1-kb random combination of enhancers, insulators and spacers, to model how locus composition drives gene expression.