Genomic environments scale the activities of diverse core promoters

One model for how cells integrate cis-regulatory information is that housekeeping and developmental core promoters respond specifically to certain types of enhancers or chromatin features at different chromosomal locations. We tested this model using a genome-integrated massively parallel reporter assay (MPRA) to measure the activity of hundreds of diverse core promoters at four genomic locations While genomic locations had large effects on expression, the relative strengths of core promoters were preserved across locations regardless of promoter class, suggesting that their intrinsic activities are scaled at different genomic locations. We further show that core promoter scaling is a genome-wide phenomenon by testing six core promoters at thousands of locations across the genome. While the rank order of core promoters is preserved, the scaling of expression across the genome is non-linear and depends on the genomic location and the strength of the core promoter, but not on its class, suggesting that housekeeping and developmental promoters do not make different interactions with the surrounding genomic environment. Instead, our results support a modular genome in which genomic environments containing different enhancers and chromatin features scale the activities of core promoters in an independent, but non-linear manner. Overall design: patchMPRA: A library of 676 core promoters was integrated into 4 different genomic locations in K562 cells. DNA and RNA was harvested from the cell lines and the barcodes of the library were amplified and sequenced. Episomal MPRA: Library of core promoters was transiently transfected into K562 cells and RNA was harvested after 24 hours. The barcodes of the RNA and plasmid library were amplified and sequenced. TRIP: Six promoters were randomly barcoded and integrated into the K562 genome with piggyBac transposase. DNA and RNA was harvested from the cell lines and the barcodes were amplified and sequenced.