bims-protra 2025-10-12 papers

Issue of 2025–10–12
four papers selected by
Marius d’Hervé, McGill University

iScience. 2025 Oct 17. 28(10): 113544

Enhancing mRNA translation efficiency with discriminative and generative artificial intelligence by optimizing 5' UTR sequences.

Yu Liu, Chunmei Cui, Limei Liu, Qinghua Cui.

The mRNA-based therapeutics, notably mRNA vaccines, represent a new era of powerful tools to combat various diseases. However, the relatively low translation efficiency of exogenous mRNA often limits its wide application. Here, we propose a computational framework called UTailoR (UTR tailor), which significantly improves the challenge by optimizing 5' UTR sequences based on a two-step artificial intelligence strategy. We first develop a deep-learning-based discriminative model for predicting mRNA translation efficiency with 5' UTR sequences and then present a generative model to generate optimized 5' UTR sequences, which are designed to be highly close to the original sequences but predicted to result in high translation efficiency. The experimental results show that the UTailoR-optimized sequences outstrip the corresponding original sequences by ∼200%. This work provides an efficient and convenient method for mRNA 5' UTR optimization, which can be easily accessed online.

Keywords: Biochemistry; artificial intelligence

DOI: https://doi.org/10.1016/j.isci.2025.113544

Nucleic Acids Res. 2025 Sep 23. pii: gkaf994. [Epub ahead of print]53(18):

Canonical translation factors eIF1A and eIF5B modulate the initiation step of repeat-associated non-AUG translation.

Hayato Ito, Kodai Machida, Yuzo Fujino, Mayuka Hasumi, Soyoka Sakamoto, Yoshitaka Nagai, Hiroaki Imataka, Hideki Taguchi.

Nucleotide repeat expansions, such as the GGGGCC repeats in C9orf72, associated with C9-ALS, are linked to neurodegenerative diseases. These repeat sequences undergo a noncanonical translation known as repeat-associated non-AUG (RAN) translation. Unlike canonical translation, RAN translation initiates from non-AUG codons and occurs in all reading frames. To identify potential regulators of RAN translation, we employed a bottom-up approach using a human factor-based reconstituted cell-free translation system to recapitulate RAN translation. This approach revealed that omission of either eIF1A or eIF5B enhanced the translation in all reading frames of C9orf72-mediated RAN translation (C9-RAN), suggesting that eIF1A and eIF5B act as repressors of RAN translation. eIF1A and eIF5B are known to contribute to the fidelity of translation initiation. In HEK293T cells, double knockdown of eIF1A and eIF5B further promoted C9-RAN compared to single knockdowns, indicating that these factors regulate C9-RAN through distinct initiation steps. Furthermore, under eIF1A knockdown conditions, the enhancement of RAN translation via the integrated stress response (ISR) was not observed in HEK293T cells, indicating that eIF1A is involved in the ISR-mediated non-AUG translation.

DOI: https://doi.org/10.1093/nar/gkaf994

Science. 2025 Oct 09. 390(6769): eado8279

mRNA initiation and termination are spatially coordinated.

Ezequiel Calvo-Roitberg, Christine L Carroll, GyeungYun Kim, Valeria Sanabria, Sergey V Venev, Steven T Mick, Joseph D Paquette, Maritere Uriostegui-Arcos, Job Dekker, Ana Fiszbein, Athma A Pai.

Transcriptional initiation and termination decisions drive messenger RNA (mRNA) isoform diversity but the relationship between them remains poorly understood. By systematically profiling joint usage of transcription start and end sites, we observed that mRNA using upstream starts preferentially use upstream end sites and that the usage of downstream sites is similarly coupled. Our results suggest a positional initiation termination axis (PITA), in which usage of alternative terminal sites are coupled based on their genomic order. PITA is enriched in longer genes with distinct chromatin features. We find that mRNA 5' start choice directly influences 3' ends depending on RNA polymerase II trafficking speed. Our results indicate that spatial organization and transcriptional dynamics couple transcription initiation and mRNA 3' end decisions to define mRNA isoform expression.

DOI: https://doi.org/10.1126/science.ado8279

Proc Natl Acad Sci U S A. 2025 Oct 14. 122(41): e2519788122

5'-terminal glycosylation of protein-coding transcripts: An epitranscriptomic modification that prolongs mRNA lifetimes.

Tithi Banerjee, Daniel J Luciano, Joel G Belasco.

Glycosylation is among the most common molecular modifications in living organisms, one that affects the function of myriad macromolecules: mostly proteins, lipids, and polysaccharides of various kinds but also a few specific noncoding RNAs that undergo glycosylation at an internal site. Here we expand the glycome by showing that protein-coding transcripts can also be glycosylated, but in the form of a 5'-terminal glucose cap. These caps are present on up to 30 to 40% of the 5' ends of U-initiated mRNAs in Escherichia coli, a remarkably high level of noncanonical capping that requires no transcript or promoter characteristic other than a 5'-terminal U. By contrast, no N-acetylglucosamine caps are evident. Due to their resistance to enzymatic removal, glucose caps can greatly prolong the cellular lifetime of mRNA by impeding its degradation via a 5'-end-dependent mechanism. The prevalence and protective impact of glucose caps set them apart from other bacterial RNA caps. This epitranscriptomic modification has the potential to selectively increase the synthesis of bacterial proteins encoded by U-initiated transcripts, especially after transcription is downregulated.

Keywords: GalU; RNA decay; RppH; UDP-glucose; noncanonical initiating nucleotide

DOI: https://doi.org/10.1073/pnas.2519788122