West Jessica D, Smith Hannah J, Vu Luyen Tien, Fogarty Elizabeth A, Matreyek Kenneth A, Fowler Douglas M, Grimson Andrew
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States.
Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, United States.
Nucleic Acids Res. 2025 Jun 20;53(12). doi: 10.1093/nar/gkaf568.
Control of gene expression is fundamental to biology, and post-transcriptional regulation is an important component of this process. In mammals, the 3'UTR in particular serves as a major source of regulatory information within the transcript. Here we developed an accurate massively parallel reporter assay (MPRA) system to evaluate the impact of >1400 full-length human 3'UTRs on RNA abundance, stability, translational regulation, and total protein output. We demonstrated that our MPRA is consistent with regulation of the corresponding endogenous transcripts. We used the MPRA datasets to model the relative contributions of RNA abundance and translational efficiency toward total 3'UTR-mediated regulation, revealing an unexpectedly large role for 3'UTR-specified translational control, and providing additional evidence that much of 3'UTR-encoded regulation is mediated by concerted regulation of translation plus decay. We observed relationships between GC content and 3'UTR length and different modes of regulation, and identified sequence motifs corresponding to regulatory RNA-binding proteins associated with mediating 3'UTR-dependent gene expression. We compared regulation from >1400 3'UTRs under control of two dissimilar promoters, which revealed promoter-associated differences in post-transcriptional regulation for certain 3'UTRs. Together, this dataset represents a comprehensive characterization of 3'UTR-mediated quantitative regulation.
基因表达的调控是生物学的基础，而转录后调控是这一过程的重要组成部分。在哺乳动物中，3'非翻译区（3'UTR）尤其作为转录本中调控信息的主要来源。在此，我们开发了一种精确的大规模平行报告基因检测（MPRA）系统，以评估超过1400个人类全长3'UTR对RNA丰度、稳定性、翻译调控和总蛋白输出的影响。我们证明了我们的MPRA与相应内源性转录本的调控一致。我们使用MPRA数据集来模拟RNA丰度和翻译效率对3'UTR介导的总调控的相对贡献，揭示了3'UTR指定的翻译控制出乎意料的重要作用，并提供了额外的证据，表明许多3'UTR编码的调控是由翻译加降解的协同调控介导的。我们观察到GC含量、3'UTR长度与不同调控模式之间的关系，并鉴定出与介导3'UTR依赖性基因表达相关的调控性RNA结合蛋白对应的序列基序。我们比较了超过1400个3'UTR在两种不同启动子控制下的调控情况，这揭示了某些3'UTR在转录后调控中与启动子相关的差异。总之，这个数据集代表了对3'UTR介导的定量调控的全面表征。
