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Background   Alu  elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some  Alu  exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important regulatory roles in modulating mRNA degradation or translational efficiency. However, the contribution of  Alu  exons to the human proteome remains unclear and controversial. The prevailing view is that exons derived from young repetitive elements, such as  Alu  elements, are restricted to regulatory functions and have not had adequate evolutionary time to be incorporated into stable, functional proteins.    Results  We adopt a proteotranscriptomics approach to systematically assess the contribution of  Alu  exons to the human proteome. Using RNA sequencing, ribosome profiling, and proteomics data from human tissues and cell lines, we provide evidence for the translational activities of  Alu  exons and the presence of  Alu  exon derived peptides in human proteins. These  Alu  exon peptides represent species-specific protein differences between primates and other mammals, and in certain instances between humans and closely related primates. In the case of the RNA editing enzyme ADARB1, which contains an  Alu  exon peptide in its catalytic domain, RNA sequencing analyses of A-to-I editing demonstrate that both the  Alu  exon skipping and inclusion isoforms encode active enzymes. The  Alu  exon derived peptide may fine tune the overall editing activity and, in limited cases, the site selectivity of ADARB1 protein products.    Conclusions  Our data indicate that  Alu  elements have contributed to the acquisition of novel protein sequences during primate and human evolution.    Electronic supplementary material  The online version of this article (doi:10.1186/s13059-016-0876-5) contains supplementary material, which is available to authorized users.

The contribution of Alu exons to the human proteome