Yamada Keisuke, Suga Kanta, Abe Naoko, Hashimoto Koji, Tsutsumi Susumu, Inagaki Masahito, Hashiya Fumitaka, Abe Hiroshi, Hamada Michiaki
Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan.
Department of Bioengineering, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA 19104, United States.
Brief Bioinform. 2025 May 1;26(3). doi: 10.1093/bib/bbaf225.
The computational design of messenger RNA (mRNA) sequences is a critical technology for both scientific research and industrial applications. Recent advances in prediction and optimization models have enabled the automatic scoring and optimization of $5^\prime $ UTR sequences, key upstream elements of mRNA. However, fully automated design of $5^\prime $ UTR sequences with more than two objective scores has not yet been explored. In this study, we present a computational pipeline that optimizes human $5^\prime $ UTR sequences in a multi-objective framework, addressing up to four distinct and conflicting objectives. Our work represents an important advancement in the multi-objective computational design of mRNA sequences, paving the way for more sophisticated mRNA engineering.
信使核糖核酸（mRNA）序列的计算设计是科学研究和工业应用的一项关键技术。预测和优化模型的最新进展已实现对mRNA关键上游元件5′非翻译区（UTR）序列的自动评分和优化。然而，具有两个以上目标分数的5′UTR序列的全自动设计尚未得到探索。在本研究中，我们提出了一种计算流程，该流程在多目标框架下优化人类5′UTR序列，可处理多达四个不同且相互冲突的目标。我们的工作代表了mRNA序列多目标计算设计的一项重要进展，为更复杂的mRNA工程铺平了道路。
