Nucleotide variants that modify upstream ORFs can alter ribosome occupancy of the main coding region. (A) We identified single nucleotide polymorphisms that generate, delete, or otherwise modify an upstream open reading frame (uORF). We tested whether changes to uORFs affected ribosome occupancy of the main coding region using a linear regression framework. The absolute value of the effect size from the regression was plotted against the P-value of association. For 17 uORF changes shown with red circles, the association was solely with ribosome occupancy (nominal P-value > 0.05 or opposite signed regression coefficients for RNA expression). Supplemental Table S5 shows the robustness to population stratification and linear mixed model. (B) A SNP in the 5′ UTR of the LENG8 gene introduces a premature in-frame stop codon that shortens an existing uORF. This event results in lower ribosome occupancy of the main coding region, as shown in the boxplot (pRibo = 0.002). The horizontal bar reflects the median of the distribution, and the box depicts the interquartile range. The whiskers are drawn to 1.5 times the interquartile range. (C) In another example, SRRM1, a SNP completely eliminates an existing uORF by removing its start codon. The loss of this uORF is associated with reduced ribosome occupancy of the main coding region (pRibo = 0.0004; pRNA = 0.19). (D) The reference sequence of ZNF215 gene has two short uORFs. Two different genetic variants eliminate the stop codon of the first uORF (UGA to UAC or UGA to CAA), resulting in merging of the two short uORFs into a single long uORF. The merging of the uORF significantly modulates both ribosome occupancy and RNA expression (pRibo = 0.0001 and pRNA = 10−9, respectively).
