Paul J. Sample, Ban Wang, David W. Reid, Vlad Presnyak, Iain McFadyen et al.
The ability to predict the impact of cis-regulatory sequence on gene expression would facilitate discovery in fundamental and applied biology. Here, we combine polysome profiling of a library of 280,000 randomized 5′ UTRs with deep learning to build a predictive model that relates human 5′ UTR sequence to translation. Together with a genetic algorithm, we use the model to engineer new 5′ UTRs that accurately direct specified levels of ribosome loading, providing the ability to tune sequences for optimal protein expression. We show that the same approach can be extended to chemically modified RNA, an important feature for applications in mRNA therapeutics and synthetic biology. We test 35,000 truncated human 5′ UTRs and 3,577 naturally occurring variants and show that the model predicts ribosome loading of these sequences. Finally, we provide evidence of 45 SNVs associated with human diseases that substantially change ribosome loading and thus may represent a molecular basis for disease.
Paul J. Sample, Ban Wang, David W. Reid, Vlad Presnyak, Iain McFadyen, David R. Morris, Georg Seelig. Human 5′ UTR design and variant effect prediction from a massively parallel translation assay. 2019-07-01. https://doi.org/10.1038/s41587-019-0164-5
A single polysome-profiling experiment measured 50-nt eGFP-context sequences spanning human transcript UTRs, ClinVar/SNV/indel constructs, engineered target-MRL sequences, and controls. The table retains observed MRLs and author-supplied variant-effect annotations where they can be matched.
A single polysome-profiling experiment tested synthetic random, human, control, and uAUG/no-uAUG sequence subsets with 5′-UTR lengths from 25 to 100 nt in a constant eGFP context. Rows with at least 10 total reads and valid sequence/MRL measurements are retained.
Duplicate polysome-profiling measurements of a 280,000-member random 50-nt 5′-UTR library in a constant eGFP reporter context using pseudouridine-substituted IVT mRNA in HEK293T cells. The processed table contains sequence-supported replicate MRLs and a derived two-replicate mean.
Duplicate polysome-profiling measurements of a random 50-nt 5′-UTR library in a constant mCherry reporter context using unmodified IVT mRNA in HEK293T cells. The processed table contains sequence-supported replicate MRLs and a derived two-replicate mean.
Duplicate polysome-profiling measurements of a 280,000-member random 50-nt 5′-UTR library in a constant eGFP reporter context using N1-methylpseudouridine-substituted IVT mRNA in HEK293T cells. The processed table contains sequence-supported replicate MRLs and a derived two-replicate mean.
Duplicate polysome-profiling measurements of a 280,000-member random 50-nt 5′-UTR library in a constant eGFP reporter context using unmodified IVT mRNA in HEK293T cells. The processed table contains sequence-supported replicate MRLs and a derived two-replicate mean.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 4 files (ZIP)GSE114002_family.soft.gzGSE114002_filelist.txtGSE114002_RAW.tarsnv_phenotype_log_diff.csv