Massively parallel reporter assay reveals promoter-, position-, and strand-specific effects in transcription start sites

Previous MPRA studies have screened thousands of functional SNPs associated with various complex traits and conditions. Most MPRA libraries utilize a single plasmid configuration, a single minimal promoter to drive expression, and a single-strand orientation, which may fail to capture the context-dependent activity of disease-associated cis-regulatory elements.

We interrogate the potential regulatory differences introduced by variable MPRA plasmid promoters and positions. We used an MPRA library to quantify the activity of 1,305 pancreatic islet-derived transcription start sites generated from Cap analysis of gene expression profiling. We cloned fragments upstream or downstream of a reporter gene along with either the human insulin (INS) promoter or a synthetic housekeeping promoter (SCP1).