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Background  Gene expression differences between species are driven by both  cis  and  trans  effects. Whereas  cis  effects are caused by genetic variants located on the same DNA molecule as the target gene,  trans  effects are due to genetic variants that affect diffusible elements. Previous studies have mostly assessed the impact of  cis  and  trans  effects at the gene level. However, how  cis  and  trans  effects differentially impact regulatory elements such as enhancers and promoters remains poorly understood. Here, we use massively parallel reporter assays to directly measure the transcriptional outputs of thousands of individual regulatory elements in embryonic stem cells and measure  cis  and  trans  effects between human and mouse.    Results  Our approach reveals that  cis  effects are widespread across transcribed regulatory elements, and the strongest  cis  effects are associated with the disruption of motifs recognized by strong transcriptional activators. Conversely, we find that  trans  effects are rare but stronger in enhancers than promoters and are associated with a subset of transcription factors that are differentially expressed between human and mouse. While we find that  cis - trans  compensation is common within promoters, we do not see evidence of widespread  cis - trans  compensation at enhancers.  Cis - trans  compensation is inversely correlated with enhancer redundancy, suggesting that such compensation may often occur across multiple enhancers.    Conclusions  Our results highlight differences in the mode of evolution between promoters and enhancers in complex mammalian genomes and indicate that studying the evolution of individual regulatory elements is pivotal to understand the tempo and mode of gene expression evolution.

Cis and trans effects differentially contribute to the evolution of promoters and enhancers