RNA and protein synthesis mechanisms

The paper analyzes frameshifts in tandem repeats across proteomes, showing they significantly alter protein physicochemical properties and function.

The paper shows that IRES/Cap translation increases during hematopoietic and epithelial differentiation under normal conditions, correlating with lower stemness.

DOTSeq provides a framework to detect differential ORF usage in ribosome profiling data, offering improved sensitivity and FDR control for translational regulation analysis.

This study demonstrates genetically encoded RNA strand exchange circuits in living cells, showing that in vitro TMSE design principles apply to E. coli but with cellular-specific caveats.

This paper uses large language models and active learning to optimize cell-free protein synthesis, achieving significant yield improvements for antimicrobial proteins.

The paper reveals a cross-regulation between translation and NAD+ metabolism through the interaction of SerRS and SIRT2, mediated by ADP-ribose.

This study investigates mRNA translation dynamics during mouse pre-implantation development, revealing novel mechanisms of translational selectivity and the role of Eif1ad3 in ribosome biogenesis.

The paper identifies eIF1A and eIF5B as repressors of C9orf72-mediated RAN translation by showing their omission enhances RAN translation in all reading frames.

This paper develops a system for controlling in vitro DNA replication using genetically encoded circuits and demonstrates its replication and repression capabilities.

The paper investigates how the human ribosome modulates multidomain protein folding by delaying domain docking, contrasting with bacterial ribosomes.

This study uses computer simulations to reveal the conformational pathways of a T-box riboswitch in recognizing tRNA, showing three thermodynamic states and their dependence on Mg2+ concentration, with implications for antibiotic development.

This study investigates the RNA-binding mechanism of ProQ using molecular dynamics simulations, revealing electrostatic interactions and structural changes upon raiZ RNA binding.

This study investigates how auxiliary information improves RNA secondary structure prediction accuracy by analyzing suboptimal structures and using topological data analysis features.

The paper identifies and characterizes non-canonical ORFs in mammals, showing their evolutionary conservation and functional integration into the proteome.

The paper proposes a mechanism called droplet-assisted RNA folding, where RNA-binding protein condensates guide the folding of long regulatory RNAs by preventing premature interactions and enabling long-range contacts.

This paper introduces RLAgent, an LLM-based framework for RNA-ligand interaction modeling that enables interactive, code-free prediction at the RNA region level.

This study maps oxidative and nitrosative damage to ribosomal RNA in human cells under stress, revealing distinct damage patterns in cytosolic and mitochondrial ribosomes.

The paper introduces MoRNiNG, a database of RNA modification sites associated with RNA secondary structure dynamics, and validates the impact of modifications on G-quadruplex formation.

This study identifies EDN/RNase 2 as an endoribonuclease that cleaves tRNA anticodon loops to generate immunostimulatory RNA halves in asthma.

This study screens eukaryotic release factor 1 variants in yeast to enhance noncanonical amino acid incorporation, identifying mutations that improve efficiency and showing complementary effects with other genetic code expansion strategies.

The paper identifies a ribosomal mutation conferring cycloheximide resistance in C. elegans and shows it alters translation efficiency and developmental timing without activating stress pathways.

IRIS predicts protein-RNA binding affinities and motifs using sequence, structural, and AI-predicted data without requiring large-scale affinity measurements.

This study shows that excluding RARS1 from the multi-tRNA synthetase complex in mice causes behavioral and anatomical brain defects due to reduced oligodendrocyte myelination.

This study uses RNA-seq and Ribo-seq in Haloferax volcanii to identify genes and small RNAs with altered translation during oxidative stress, revealing new regulatory mechanisms.

This paper introduces a new ribosome profiling protocol that is faster, cheaper, and more sensitive, enabling use with minimal RNA input.

This study computationally predicts and experimentally validates a vectorial hierarchy of cotranslational protein folding intermediates stabilized by non-native hydrophobic interactions.

PhyloAug improves GLM performance by generating biologically plausible RNA sequence augmentations using evolutionary signals and RNA structure.

The paper shows that ribosome biogenesis affects translational regulation of non-optimal codon transcripts during IFN stimulation.

Structure providers for 18 CASP16 nucleic acid targets find blind predictions capture secondary structure but miss non-canonical interactions, backbone kinks, ligand sites, and intermolecular interfaces.