Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands.

ABSTRACT: Massively parallel reporter assays (MPRAs) are useful tools to characterize regulatory elements in human genomes. An aspect of MPRAs that is not typically the focus of analysis is their intrinsic ability to differentiate activity levels for a given sequence element when placed in both of its possible orientations relative to the reporter construct. Here, we describe pervasive strand asymmetry of MPRA signals in data sets from multiple reporter configurations in both published and newly reported data. These effects are reproducible across different cell types and in different treatments within a cell type and are observed both within and outside of annotated regulatory elements. From elements in gene bodies, MPRA strand asymmetry favors the sense strand, suggesting that function related to

SUBMITTER: Roberts BS 

PROVIDER: S-EPMC8092006 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature