Allele-resolved monosome and polysome sequencing identifies cis-variants affecting mRNA translation

To prioritize germline genetic variants affecting mRNA fate at the translational level, we used sucrose gradient-based isolation of 80S monosomes and polysomes, followed by RNA sequencing in RPE-1 cells, under mock and nutlin treatment conditions. Differential gene expression analysis confirmed a canonical p53 response. Heterozygous SNPs and SNVs were identified from the RNA-sequencing data, and allelic fractions were calculated for total, monosomal, and polysomal mRNAs. Variants showing reproducible allelic fraction differences across fractions beyond experimental variability were defined as tranSNPs. Among over 7,000 heterozygous variants analyzable in polysomal RNA and over 5,000 in mRNAs associated with monosome-enriched fractions, 1,247 in 1,015 genes displayed a significant imbalance. Reporter assays performed in RPE-1 and HCT116 cells validated allelic or haplotype effects for 17 selected variants in UTRs and coding regions, confirming differences in 15 cases, with evidence of cell line-specific responses. Proteomic analysis supported allelic imbalance for a few selected missense variants. Monosome-enriched fractions improved sensitivity in measuring allelic imbalances without introducing a tranSNP positional bias, suggesting that 80S profiling enhances detection of allele-specific translational regulation in RPE-1 cells.