RNA and protein synthesis mechanisms

This paper introduces codonGPT, a generative language model for mRNA sequences, and a reinforcement learning framework for optimizing mRNA design under biological constraints.

The paper shows that mitochondrial SAM is essential for processing mitochondrial ribosomal RNA precursors and ribosome assembly.

This study uses ribosome profiling to analyze translational regulation during Arabidopsis seed germination, identifying codon usage patterns and uORFs involved in translational control.

This study measures EF-G power stroke and its effect on ribosome translocation fidelity using quantum sensing, showing that mutations alter translocation steps and fidelity.

The paper evaluates 53 Pepper RNA variants to show that HBC530 binding affinity and fluorescence intensity are only modestly correlated, with distal structural elements influencing both and Mg2+ binding being strongly correlated with HBC530 binding thermodynamics.

This study benchmarks RNA 3D structure prediction models using varying accuracy 2D structures, finding that 3D models modify input base-pairing interactions and are more sensitive to false positives in 2D structures.

This study maps ribosomal protein (RP) gene expression across human tissues using single-cell RNA sequencing, revealing tissue-specific patterns and linking RP heterogeneity to reproductive health and anaemia.

This paper introduces RISoTTo, a geometric deep learning method for RNA sequence design that incorporates molecular context, showing improved accuracy and binding affinity in in silico tests.

This study shows ZCCHC4 promotes translation of replication-dependent histone mRNAs by interacting with the cytoplasmic eIF3 complex, leading to genomic instability and tumor suppression upon its depletion.

This paper presents an efficient RNA 3D folding model using Transformer and equivariant techniques, achieving lower RMSD than baselines on a single GPU.

The paper identifies a pre-tRNA decay pathway mediated by EXOSC10 that is critical for neuron survival and linked to neurodevelopmental disorders.

The paper identifies a molecular switch at the yeast mitoribosomal tunnel exit that regulates cytochrome b synthesis by mediating interactions between translational activators and assembly factors.

This study identifies CtdA, a tRNA deacetylase that removes canavanine from mischarged tRNAArg, and reveals its structural and evolutionary relationships to B3/B4 domains.

This paper introduces a framework for model-informed mRNA design using integrated gradients and an agentic hypothesis engine, achieving improved in vivo expression.

The paper investigates the evolutionary diversity of drug-binding residues in bacterial ribosomes to determine if divergence from E. coli is common or rare.

RNAGym provides a benchmarking framework for RNA fitness, secondary structure, and tertiary structure prediction using diverse datasets and standardized assays.

The paper reanalyzes data from Rosenberg et al. to show that codon usage has no significant effect on dihedral angles in protein structures.

RWKV-IF generates RNA sequences from structures using an attention-free language model, achieving higher accuracy and lower edit distance than existing methods.

This paper introduces RIdiffusion, a hyperbolic diffusion model for 3D RNA inverse folding, which outperforms baselines in generating RNA sequences for target structures.

The paper introduces local stability compensation (LSC) as a principle governing RNA folding, showing it is prevalent in RNA structures and validated through chemical mapping experiments.

This study uses Massively Parallel Ribosome Profiling to identify thousands of viral ORFs, including non-canonical ones, and shows their impact on HLA-I peptides and protein synthesis regulation.

This study shows that methanogenic archaea use an ambiguous genetic code where the stop codon UAG can encode pyrrolysine, and that Pyl biosynthesis is regulated to manage this ambiguity.

The paper determines the cryo-EM structure of 48S initiation complexes on EMCV IRESs and identifies key interactions essential for ribosomal recruitment.

This study develops a method to measure ligand-binding events in structured RNAs by integrating a hammerhead ribozyme with a multi-base pair bridge, demonstrating its effectiveness with riboswitch candidates.

This study examines how low-protein and high-fat diets affect tRNA abundance and modifications in multiple mouse tissues using RNA mass spectrometry and OTTR-seq.

The paper characterizes somatic mutations in human tRNA genes, showing they are mutagenesis hotspots with tumor-specific loads and can generate altered tRNA variants affecting the genetic code.

The paper identifies and characterizes shifted GU wobble pairs in RNA through cheminformatics and experimental validation, showing alternative protonation states may enhance RNA function.

The paper shows that yeast rapidly adapts to glucose depletion by using metabolic changes to control translation, prioritizing stress-response genes.

This study shows uORFs reduce translational variability in Drosophila across development and evolution, with buffering effects observed in gene expression and phenotypes.