Anti-SMIM45-107aa Pull-down and mass spectrometry study

We acknowledge the commentary by Leushkin et al. on our work, which scrutinizes the status of the de novo genes and the coding potential of a specific case gene (ENSG00000205704) in our proof-of-concept study. While we recognize the evolving nature of defining de novo genes with ribosome profiling data, we respectfully disagree with their assertions for the definition of ages, de novo status, translation and functions of these genes. Notably, the field’s consensus definition of de novo gene is based on the age of the open reading frames (ORFs), rather than that of the locus. Moreover, ribosome profiles alone, although indicative for translation, should not be used as a groundtruth for stable translation and in vivo functions, especially when generated from samples with limited range of temporospatial conditions and analyzed with parameters better suited for highly-expressed, conserved genes, as described in Leushkin et al. Here we present additional data and analyses, especially the verification of the status of these de novo genes and the compelling evidence for in vivo translation of the case gene, to address their concerns. The data presented in our initial report, coupled with this study, robustly support our original conclusions.