RNA and protein synthesis mechanisms

Transfer Matrix and Tensor Approaches to Nucleic Acid Secondary Structure Thermodynamics

This paper introduces transfer matrix and tensor models for nucleic acid secondary structure thermodynamics, achieving higher accuracy with fewer parameters and improved computational efficiency.

fuzzyfold: a high-performance framework for stochastic RNA folding kinetics

The paper introduces fuzzyfold, a Rust-based software framework for stochastic RNA folding kinetics, enabling efficient simulation of long RNA molecules and flexible model integration.

RNA3D-Decoy: A Large-Scale Benchmark Dataset of AI-Generated RNA Structure Models for Quality Assessment

The paper introduces RNA3D-Decoy, a benchmark dataset of AI-generated RNA structure models, to evaluate quality assessment methods for RNA structure prediction.

Real-time single-molecule imaging in zebrafish embryos uncovers non-canonical translation

This study uses real-time single-molecule imaging in zebrafish embryos to reveal non-canonical translation mechanisms of bmp2b mRNA.

sORF-Trans2MS: a two-module deep learning framework for sORF translation and MS-supported microprotein prediction

sORF-Trans2MS is a two-module deep learning framework that predicts Ribo-supported sORFs and MS-supported microproteins, improving prediction and extending discovery to underrepresented candidates.

Monitoring the translation initiation process in prokaryotes via large-scale examination using optimized SSU-seq technique

The paper develops an optimized SSU-seq protocol for E. coli to study ribosome-mRNA interactions, revealing patterns of small subunit distribution linked to rRNA-mRNA hybridization.

Initiation codon context governs translation-coupled mRNA decay and coordinated expression in the human parasite Leishmania

This study shows that the Kozak sequence context influences mRNA stability and protein expression in Leishmania by modulating translation-coupled decay and polysome recruitment.

Joint protein, mRNA and DNA sequence design and optimization with nucleotide-level Potts models

A structure-conditioned nucleotide-level Potts model designs protein and coding sequences jointly, enabling tRNA adaptation and RNA motif embedding beyond synonymous codons with designability comparable to Caliby.

Structural basis of eIF4E recognition of synthetic mRNA 5' cap analogues links cap architecture to affinity and biological activity

This study investigates how synthetic 5' cap analogues interact with eIF4E, revealing structural features that influence mRNA translation efficiency and biological activity.

Quantitative profiling of basal and stress-induced ribosome collisions

The paper quantifies disome levels across the transcriptome in yeast and human cells under basal and stress conditions, showing stress-induced increases and context-dependent redistribution.

Long-form hibernation-promoting factor coordinates 100S assembly and translational repression

This study identifies modular contributions of HPF domains to 100S assembly and translational repression using cryo-EM and functional analyses.

Fluorescent proteins misreport ribosome abundance under translation inhibition

The paper shows that fluorescent proteins misreport ribosome abundance under translation inhibition, as fluorescence intensity does not track ribosome abundance during chloramphenicol treatment.

Spatial Uncoupling of Protein Synthesis from Viral Factories during Rabies Virus Infection

This study shows that during rabies virus infection, protein synthesis occurs outside viral factories (Negri bodies) and newly synthesized viral proteins are later targeted to these compartments.

Unexpected ribosome turnover during prolonged translation inhibition

This study shows that prolonged translation inhibition by cycloheximide causes proteasome-dependent degradation of ribosomal RNA and proteins, revealing a new quality control pathway called GRIP.

Rational design of intrinsic transcription terminators with programmable strength

The paper designs intrinsic transcription terminators with programmable strength using a sequence-to-function model and provides web tools for prediction and design.

Codon usage bias maps ocean microbiome adaptation to temperature-nutrients regimes

The paper shows that codon usage bias in metabolism-related genes reflects microbial adaptation to temperature and nutrient regimes in ocean communities.

A small molecule increases mycobacterial translation fidelity without a fitness cost by targeting ribosomal protein S5

This paper identifies a small molecule that enhances translational fidelity in mycobacteria without reducing translation speed, targeting ribosomal protein S5 to combat antibiotic tolerance.

Downstream mRNA Secondary Structure, Not Codon Elongation Supply, Coordinates Co-Translational Protein Folding Across the Human Ribosomal Exit Tunnel

A conserved archaeal ribosome-associated factor linking bacterial hibernation and eukaryotic energy sensing

This study identifies AHA, a conserved archaeal ribosome-associated factor involved in hibernation and energy sensing, linking prokaryotic translational silencing to eukaryotic energy sensing.

Population reweighting and reporter distortion obscure ribosome regulation during translation inhibition

The paper shows that population-level measurements of ribosome regulation during translation inhibition can be misleading due to growth-dependent reweighting and reporter distortion, highlighting the need for longitudinal sampling and validated reporter behavior.

eIF4E and Ezrin cooperate in pseudopods to drive a localized migratory translation program in acute myeloid leukemia

In acute myeloid leukemia, Ezrin binds eIF4E and anchors active ribosomes in pseudopods for local translation of CD44 and hyaluronan pathway proteins; eIF4E loss impairs mouse engraftment.

3D confinement reshapes RNA folding and enhances circularisation in the Zika virus

This study models how 3D confinement affects RNA folding and circularization in the Zika virus genome, showing increased circularization under confinement.

Ribosome remodeling drives translation adaptation during viral infection and cellular stress

The paper shows that ribosome remodeling enables enhanced viral protein synthesis during infection and cellular stress by altering ribosome composition and structure.

Protoribosomal condensate formation across cationic chemistries

This study compares how different cationic chemistries influence peptide-RNA coacervation, showing that statistical peptide ensembles can drive protoribosomal condensate formation without sequence-specific optimization.

Conserved Obg-type GTPases Sustain Protein Synthesis across Domains of Life

This study identifies conserved Obg-type GTPases that support protein synthesis during physiological ribosomal pauses across domains of life.

Bridging the gap between omics and structural data: A framework for interpreting protein-RNA interaction specificity

This paper evaluates AlphaFold3's ability to predict protein-RNA interaction specificity using omics data and structural information, highlighting both its potential and limitations.

DisenTE: Sparse Pattern-Context Modeling for Interpretable Translation-Efficiency Matrix Completion

DisenTE improves translation-efficiency matrix completion by modeling sparse sequence-context patterns, achieving higher accuracy than existing methods.

The mitoribosome-associated factor Mrx9 acts as a negative regulator of the prohibitin/m-AAA complex

The paper shows that Mrx9 negatively regulates the prohibitin/m-AAA complex by impairing Yta10 and Yta12 proteolytic functions, leading to splicing defects and aberrant polypeptide accumulation.

RNASeek: A Cross-Phyla Generative Foundation Model for Multipurpose RNA Modeling and Reinforcement Learning-Based Design

RNASeek is a generative foundation model for RNA sequence design and functional prediction, using reinforcement learning to optimize RNA properties like stability and cleavage activity.

RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols

RiboBA improves ncORF identification by accounting for protocol-induced biases in ribosome profiling data.