RNA and protein synthesis mechanisms

The paper shows ELP3 modifies tRNA at U34 and regulates proteome composition through specific di-codon pairs, affecting cancer cell proliferation.

The paper proposes a theoretical framework to understand ribozyme ecology and evolution by mapping ribozyme structures to animal body plans and analyzing their interactions.

CDS-BART is a foundation model for mRNA sequence analysis that can handle sequences up to 4kb, pre-trained on nine taxonomic groups and available under MIT License.

The paper identifies molecules that selectively bind the prfA thermosensor RNA in Listeria monocytogenes without inhibiting translation.

This study identifies Def1 as a cytoplasmic regulator of mRNA translation and decay by linking ribosome status to mRNA degradation through ubiquitylation.

This paper introduces an AI framework to improve mRNA therapeutic manufacturing by predicting and optimizing sequence design for in vitro transcription efficiency.

This paper identifies BisRoc, a dimeric rocaglate ligand that suppresses translation more potently and specifically than monomeric RocA by promoting multivalent eIF4A-RNA assembly.

The paper shows that molecularly aged ribosomes alter translational dynamics by impairing elongation and increasing ribosome collisions during organismal aging.

This study shows pancreatic cancer cells use tunnelling nanotubes to transfer ribosomes and mRNAs, restoring protein synthesis in cells with impaired translation.

The paper shows directional co-transcriptional folding and pausing enable selective riboswitch function by stabilizing ligand binding and promoting RNA polymerase readthrough.

The paper identifies conserved microproteins from upstream ORFs in yeast using Ribo-Seq and Nanopore data, showing they are subject to purifying selection.

This paper optimizes low-cost reagent formulations for cell-free gene expression, achieving high yields and cost reductions across multiple scales and protein types.

This paper introduces FY-RNA origami structures that are serum-stable and capable of molecular sensing and targeting, revealing structural insights through cryo-EM and simulations.

The paper introduces tRIBO-seq, a nanopore-based method to profile ribosome-associated tRNAs, revealing stress-induced changes in tRNA abundance, modification, and fragmentation.

The paper determines the structure of the human KEOPS/tRNA complex and characterizes pathogenic variants in the t6A pathway linked to Galloway-Mowat syndrome.

This study elucidates the mechanism of human tRNA 3'CCA maturation by determining TRNT1 structures and showing a continuous polymerization and translocation mechanism.

The paper determines the Cryo-EM structure of Cfr, revealing its mechanism of C8 methylation on 23S rRNA and its role in antibiotic resistance.

This paper evaluates three RNA 3D structure prediction tools on a dataset of ssDNA structures to assess their applicability to ssDNA and identify limitations in predicting complex motifs.

The paper examines allelic variation in tRNA genes across three nematode species, finding high mutation rates and purifying selection, with functional mismatches between tRNA anticodons and amino acids.

The paper improves a cell-free system for DNA replication and gene expression by optimizing energy mixes to enhance efficiency and consistency.

The paper analyzes tRNA allelic variation in C. elegans to model how transcription-associated mutagenesis (TAM) influences tRNA microevolution and structural stability.

This study maps allosteric rewiring in viral RNA by analyzing how sequence changes affect protein binding mechanisms through molecular dynamics and graph-network analysis.

The paper investigates how EF-Tu D81 mutation affects tRNA release and ribosome dynamics using GTPase assays, AlphaFold modeling, and SURFS.

The paper determines the structure and catalytic mechanism of two new HDV ribozymes from a nematode and a virus, revealing a unique Lewis acid mechanism distinct from other ribozymes.

This study quantifies tRNA supply and codon demand in human blood cells, revealing large inter-codon variation and codon-specific interindividual differences.

The paper identifies a direct interaction between postsynaptic proteins and ribosomes, revealing a localized synaptic translatome that preferentially translates PSD-related mRNAs.

This study shows that deoptimizing serine codons in multispecific biologics reduces mispairing and increases protein purity during transient mammalian expression.

The paper analyzes translational buffering across human and mouse datasets, finding conserved patterns and highlighting the role of cellular context in gene expression regulation.

This paper shows that KSHV uses eIF5B to mimic hypoxia and support viral replication and oncogenesis by altering translation initiation.

This study uses machine learning potentials to explore RNA dimer conformations, showing improved accuracy over classical models.