RNA and protein synthesis mechanisms

This study determines the structure of the hibernating ribosome in Borrelia burgdorferi using cryo-EM, revealing new structural features and insights into antibiotic binding.

This study develops a method to produce circular mRNA in cells, enhancing protein expression duration and enabling its use in virus-like particle delivery systems.

This paper evaluates RNA 3D structure prediction methods in CASP15, finding that non-deep learning groups outperformed deep learning models, with challenges in fine details and model ranking.

This paper introduces an RNA language model based on multiple sequence alignment, showing it can accurately predict RNA structure from sequence data.

This study investigates the role of opal stop codon translational readthrough in CHIKV replication by replacing stop codons and analyzing structural and functional effects.

The paper models the evolution of the Standard Genetic Code through computational simulations of code division and fusion, identifying the most efficient pathways for its emergence.

This study identifies a repressing and novel activating corrinoid riboswitch, enabling the engineering of synthetic riboswitches with robust gene induction.

This paper engineers a bacterial gene regulation system using the mammalian RNA-binding protein Musashi-1 to repress translation through an allosteric mechanism.

DeepRaccess predicts RNA accessibility using deep learning, achieving high correlation with Raccess and significant speed improvements.

The paper identifies a non-canonical genetic code in a ciliate where UAA and UAG codons specify different amino acids, challenging the universality of the genetic code.

This study shows that the tRNA methyltransferase Trm1 can promote tRNA functionality without catalytic activity and interacts with La to influence tRNA modification.

The paper analyzes RNA backbone conformations using pseudo-torsional angles, showing that combining data from different sources provides a more complete picture and that protein interactions alter the {eta}-{theta} space.

The paper identifies dsRNA structures in uORFs that regulate translation and shows ASO targeting can modulate mORF translation and reduce cardiac hypertrophy.

The paper shows that synonymous mutations in mycobacteria can create new transcription start sites within genes, leading to smaller protein isoforms.

The paper quantifies elongation stalls in yeast and shows how different codons affect protein and mRNA levels through distinct rescue pathways.

The paper introduces a streamlined ribosome profiling method using P1 nuclease and Ordered Two-Template Relay, improving sensitivity and reducing bias in yeast and human cells.

This study uses atomistic simulations to investigate how RNA duplex thermal denaturation depends on sequence and forcefield, showing sequence-specific deviations from the two-state model and forcefield limitations.

This study investigates Nsp1-mediated translational shutdown in three Betacoronaviruses, revealing a conserved mechanism and identifying how Nsp1 allows viral mRNA translation.

The paper investigates how anticodon mutations in tRNAAla affect yeast growth and mistranslation, finding that anticodon sequence influences mistranslation extent and growth impact.

The paper presents a 1.9 Å cryo-EM structure of the human 80S ribosome, revealing new rRNA modifications and ions, and their roles in RNA architecture and function.

This paper reveals RNA structures and dynamics at near-atomic resolution using x-ray free electron lasers, showing how RNA folds through intermediate states and forms triplexes.

The paper shows that translational regulation, particularly through 5' leader uORFs, enhances cell-type distinction in the Drosophila nervous system by preferentially translating neuronal proteins in neurons.

This study identifies BOLA3 and NFU1 as critical for mitoribosome iron-sulfur cluster assembly, linking their dysfunction to mitochondrial and metabolic disorders.

The paper quantifies tRNA expression in human and mouse RNA-Seq data, revealing conserved spatiotemporal patterns and disease-related associations.

The paper shows that the 5' UTRs of Insr and Igf1r transcripts support translation initiation independently of eIF4G1 in both in vitro and cellular settings.

This paper identifies KKL-55, a tetrazole-based antibiotic that specifically inhibits EF-Tu binding to tmRNA without affecting tRNA binding, suggesting a new target for antibiotic development.

This paper improves DNA structure design by introducing a new base pair alphabet with P-Z pairs and thermodynamic parameters, enhancing design accuracy and reducing off-target folding.

The paper evaluates four methods for detecting translated non-canonical ORFs from Ribo-Seq data and finds they have low precision and accuracy, especially for ORFs with near-cognate start codons.

The paper evaluates how machine learning models handle RNA secondary structure prediction and complementary strand recognition, finding that model capacity and data quality significantly impact performance.