Most of our current knowledge about gene regulation is based on studies of mRNA levels, despite both the greater functional importance of protein abundance, and evidence that post-transcriptional regulation is pervasive. However, understanding the molecular basis of regulatory variation within and between species may prove very useful. Indeed, the majority of identified human disease-risk alleles lie in non-coding regions of the genome, suggesting that they affect gene regulation. Until recently, the lack of performant high-throughput methods for detecting protein abundance hampered the in-depth study of gene regulation. However, a new method known as ribosome profiling has enabled us to study divergence in the regulation of translation.