Jia-Ying Su, Yun-Lin Wang, Yu-Tung Hsieh, Yu-Chi Chang, Cheng-Han Yang et al.
Untranslated regions (UTRs) contain crucial regulatory elements for RNA stability, translation and localization, so their integrity is indispensable for gene expression. Approximately 3.7% of genetic variants associated with diseases occur in UTRs, yet a comprehensive understanding of UTR variant functions remains limited due to inefficient experimental and computational assessment methods. To systematically evaluate the effects of UTR variants on RNA stability, we established a massively parallel reporter assay on 6555 UTR variants reported in human disease databases. We examined the RNA degradation patterns mediated by the UTR library in two cell lines, and then applied LASSO regression to model the influential regulators of RNA stability. We found that UA dinucleotides and UA-rich motifs are the most prominent destabilizing element. Gain of UA dinucleotide outlined mutant UTRs with reduced stability. Studies on endogenous transcripts indicate that high UA-dinucleotide ratios in UTRs promote RNA degradation. Conversely, elevated GC content and protein binding on UA dinucleotides protect high-UA RNA from degradation. Further analysis reveals polarized roles of UA-dinucleotide-binding proteins in RNA protection and degradation. Furthermore, the UA-dinucleotide ratio of both UTRs is a common characteristic of genes in innate immune response pathways, implying a coordinated stability regulation through UTRs at the transcriptomic level. We also demonstrate that stability-altering UTRs are associated with changes in biobank-based health indices, underscoring the importance of precise UTR regulation for wellness. Our study highlights the importance of RNA stability regulation through UTR primary sequences, paving the way for further exploration of their implications in gene networks and precision medicine.
Jia-Ying Su, Yun-Lin Wang, Yu-Tung Hsieh, Yu-Chi Chang, Cheng-Han Yang, YoonSoon Kang, Yen-Tsung Huang, Chien-Ling Lin. Multiplexed assays of human disease-relevant mutations reveal UTR dinucleotide composition as a major determinant of RNA stability. 2025-02-18. https://doi.org/10.7554/eLife.97682.3
A library of 155-nt reference and disease-relevant mutant human 3' UTR fragments fused downstream of EGFP was in vitro transcribed, capped, polyadenylated, and transfected into SH-SY5Y neuroblastoma cells. Amplicon sequencing at 20, 40, and 60 minutes quantified RNA decay and mutant/reference half-life differences.
A library of 155-nt reference and disease-relevant mutant human 3' UTR fragments fused downstream of EGFP was in vitro transcribed, capped, polyadenylated, and transfected into HEK293T cells. Amplicon sequencing at 30, 75, and 120 minutes quantified RNA decay and mutant/reference half-life differences.
A library of 155-nt reference and disease-relevant mutant human 5' UTR fragments fused upstream of EGFP was in vitro transcribed, capped, polyadenylated, and transfected into SH-SY5Y neuroblastoma cells. Amplicon sequencing at 20, 40, and 60 minutes quantified RNA decay and mutant/reference half-life differences.
A library of 155-nt reference and disease-relevant mutant human 5' UTR fragments fused upstream of EGFP was in vitro transcribed, capped, polyadenylated, and transfected into HEK293T cells. Amplicon sequencing at 30, 75, and 120 minutes quantified RNA decay and mutant/reference half-life differences.
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 9 files (ZIP)elife-97682-supp1-v1.xlsxelife-97682-supp9-v1.xlsxGSE217518_family.soft.gzGSE217518_HEK_U3_Raw.csv.gzGSE217518_HEK_U5_Raw.csv.gzGSE217518_series_matrix.txt.gzGSE217518_SH_U3_Raw.csv.gzGSE217518_SH_U5_Raw.csv.gzSOURCES.txt