RNA and protein synthesis mechanisms

The paper identifies GC3 codons as a universal factor enhancing protein production across diverse plant species by improving translation efficiency and mRNA abundance.

RNA-X is a foundation model for designing RNA sequences that bind to multiple targets, including proteins, RNA, and DNA, and it outperforms existing methods in binding prediction and design.

The paper studies tRNA gene evolution in Drosophila, finding rapid duplication and loss, sexual dimorphism in expression, and implications for regulatory diversity.

CodonTranslator is a Transformer-based model for codon optimization across species, achieving better codon usage and stability than existing methods.

The paper identifies ZAKα as a sensor that detects mRNA stasis at the ribosomal exit channel through interactions with ribosomal proteins and rRNA.

This paper introduces PSP, a method to identify actively translated mRNAs in yeast without ribosome isolation, and shows it captures condition-specific translational programs and expands detectable genes.

The paper investigates how codon usage and context affect mRNA decay rates in Arabidopsis, finding that codon optimality explains 21% of decay rate variance and that codon context also influences stability.

The paper introduces NC-Bench, a benchmark for RNA non-canonical base pair prediction, and NCfold, a framework that achieves state-of-the-art results on this benchmark.

This paper develops synthetic cells that respond to pH changes by synthesizing and releasing proteins on demand.

This paper identifies eIF2 phosphorylation as a major barrier to translation in human cell-derived systems and presents strategies to overcome it through genome editing or expression-based rescue.

This study shows that eIF3d's RNA-binding domain is essential for stress granule assembly in human cells and C. elegans, rescuing granule formation when expressed exogenously.

This study investigates co-translational assembly of homomeric proteins, showing that PheA in E. coli primarily assembles via trans-assembly across neighboring mRNAs.

The paper identifies a doxycycline-binding aptamer with exceptional regulatory properties in yeast and human cells, revealing a unique structural mechanism and validating its effectiveness through experimental methods.

This study identifies mRNA stem-loops and their stability as key regulators of stop codon readthrough in Drosophila, refining computational predictions of this phenomenon.

The paper designs convergent overlapping genes using a transformer encoder and structural proxies, achieving high success rates across all phases with phase 1 being most effective.

This study shows that non-optimal codon usage affects cell cycle progression and apoptosis by altering mRNA and protein stability in CDK1 and NUF2 genes.

The paper analyzes 46,015 bacterial genomes to show hibernation factors evolved from large proteins, reduced in size, and were lost in over 10% of species, with some bacteria borrowing factors from others.

This paper introduces NUWA, an mRNA language model that enables unified sequence perception and generation across diverse species and tasks.

This study investigates translation initiation mechanisms on endogenous eukaryotic circular RNAs, showing that initiation depends on UTRs and specific initiation factors.

The paper identifies codon bias patterns and tRNA modification indices that influence translational programs in human tissues and cancers, revealing functional divergence and implications for mRNA therapeutics.

TOM is a Transformer model that optimizes mRNA secondary structure at the translation initiation region, significantly improving protein production by outperforming existing methods in MFE and other metrics.

The paper provides a comprehensive analysis of tRNA modifications in Staphylococcus aureus, revealing species-specific features and decoding dynamics.

This paper introduces a one-pot acetylation platform for site-specific protein acetylation in E. coli and mammalian cells using novel lysine acetyltransferases.

The paper identifies a cytoplasmic surveillance pathway that detects and degrades faulty ribosomes during biogenesis but allows defective ribosomes to escape into translation if they bypass the pathway.

This study shows that tRNA thiolation defects in humans cause proteostasis and tissue homeostasis issues, but mice with similar defects develop normally.

RiboWich improves ribosome profiling by eliminating ribosome purification and enabling high-throughput, low-input translatome analysis.

The paper designs and builds a partial synthetic genome that can be expressed in a cell-free system and replicated, demonstrating a proof-of-concept for a minimal synthetic cell.

The paper analyzes the structure of Mycoplasma penetrans MetRS, revealing it as an asymmetric dimer with N-terminal ancillary domains and a partially resolved MetRS domain.

The paper uses cryo-electron tomography to visualize bacterial translation processes in Mycoplasma pneumoniae, revealing structural coordination between transcription, translation, and membrane attachment.

This study identifies Hib, a new family of ribosome hibernation factors in Archaea, showing its role in preserving ribosomes during stress and revealing its structural and functional mechanisms.