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

Massively parallel reporter assays (MPRAs) are useful tools to discover and characterize regulatory elements in human genomes. Partly because enhancer function is assumed to be orientation independent with respect to each strand of the DNA helix, most reported MPRA results ignore stranded information. However, we find pervasive strand asymmetry of MPRA signals in datasets from multiple reporter configurations and 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 biological function related to endogenous transcription is driving the phenomenon. Similarly, within Alu mobile element insertions, we find that strand asymmetry favors the transcribed strand of the ancestral retrotransposon. The effect is consistent across the multiplicity of Alu elements in human genomes, and is more pronounced in younger, less diverged Alu elements. We find sequence features driving MPRA strand asymmetry and demonstrate its prediction from sequence alone. We see some evidence for both RNA stabilization and transcriptional activation mechanisms, and hypothesize that the effect is driven by natural selection favoring efficient transcription. Our results indicate that strand asymmetry, as a pervasive and reproducible feature, should be accounted for in analysis of MRPA data. More importantly, the fact that MPRA asymmetry favors naturally transcribed strands suggests that it stems from preserved biological functions that have a substantial, global impact on gene and genome evolution.