RNA and protein synthesis mechanisms

LIMBER: A Hybrid RNA Foundation Model for Predicting and Understanding RNA Structure and Function

LIMBER is a hybrid RNA foundation model that predicts RNA structure and function, showing strong performance in secondary-structure prediction and classification, along with transferability to related tasks.

ScanFold3: a robust and rapid approach for identifying structured RNA targets in genomes and transcriptomes

ScanFold3 improves RNA structure prediction speed and accuracy, outperforming previous versions in benchmarking and validation.

DUET: a sequence-only ensemble for RNA-small molecule binding-site prediction

DUET is a sequence-only ensemble model for RNA-small molecule binding-site prediction that outperforms existing methods on benchmark datasets.

Live-cell, single-molecule imaging resolves the dual nature of mRNA silencing by SARS-CoV-2 Nsp1

This study uses live-cell imaging to show SARS-CoV-2 Nsp1 silences mRNAs by reducing their numbers through two cap-dependent mechanisms, while viral UTRs enhance translation but do not protect from Nsp1.

Viral tRNA-like structure hijacks host ribosomes for poly(A)-independent translation

This study shows how a viral tRNA-like structure recruits host ribosomes for poly(A)-independent translation by binding to ribosomal subunits and substituting for poly(A) tails.

Glioblastoma Hijacks Astrocyte Ribosomes to Feul Malignancy through Translatome Reprogramming

This study shows glioblastoma hijacks astrocyte ribosomes via tunneling nanotubes, reprograms the tumor translatome to promote malignancy, and identifies INTS12 as a therapeutic target.

Selective tRNA charging defects reshape ribosomal pausing and stress adaptation

The paper investigates how selective tRNA charging defects affect translation and stress responses using inhibitors in different cell types.

Structural basis for repeat-associated non-AUG translation initiation on C9orf72 mRNA

The paper determines the structure of C9orf72 RAN translation initiation complexes and identifies a key RNA-RNA interaction that drives DPR production, suggesting a therapeutic target.

Comparative analysis identifies a shared topological organisation among divergent intergenic RNAs

The paper identifies a shared topological organisation in divergent arenavirus intergenic RNAs using graph theory and structural analysis.

Pyrrolocytosine as a Fluorescent Sensor of RNA-Small Molecule Interactions

This study uses pyrrolocytosine (pC) as a fluorescent sensor to detect RNA-small molecule interactions, showing it can distinguish between similar ligands based on hydrogen bonding.

Widespread Presence of Catalytic RNAs in All Domains of Life

The paper identifies millions of self-cleaving ribozymes in humans and other species, revealing a much larger ribozyme-ome than previously thought and their potential roles in gene regulation and biotechnology.

The LudP arrest peptide stalls translation by remodeling the ribosomal A-site

The paper identifies LudP, an arrest peptide that stalls translation by remodeling the ribosomal A-site, revealing its mechanism and evolutionary conservation.

Pervasive short hairpin folding in non-encapsidated RNA viruses

The paper identifies pervasive short hairpin RNA structures in non-encapsidated viruses and shows their association with structural constraints and evolutionary origins.

SMARTFlexDB: a paired apo-holo RNA structure database and analysis platform for RNA conformational flexibility and small-molecule recognition

SMARTFlexDB links ligand-bound and ligand-free RNA structures to study conformational flexibility and small-molecule recognition, providing a resource for RNA-targeted drug discovery.

A ribosome exit tunnel component is required for robust expression of the Drosophila hox gene, abdominal A

This study shows that a mutation in the Drosophila ribosomal protein RpL39 causes embryonic patterning defects by impairing hox gene expression.

RiboCouple links RNA backbone generation to sequence design through a learned interaction topology

The paper introduces RiboCouple, a method that links RNA backbone geometry to sequence design using learned interaction topologies, improving refolding validity in RNA structure prediction.

Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells

This paper introduces a method to measure RNA structure and protein binding in human cells, showing how RNA folding and sequence determine protein occupancy and function.

Structural basis for start codon selection by eIF5-mimic proteins

This study reveals how eIF5-mimic proteins regulate start codon selection through structural insights from cryo-EM and biochemical assays.

RNASTOP: A Deep Learning Framework for mRNA Chemical Stability Prediction and Optimization

RNASTOP predicts and optimizes mRNA chemical stability using deep learning, improving accuracy by 13% and reducing free energy in a vaccine sequence.

Alignment-free discovery of conserved RNA structures in the human genome

This paper introduces RLMHelix, an alignment-free method to discover conserved RNA structures in the human genome, identifying new candidates that correlate with RNA-binding protein interactions.

RiboDFM: Robust RNA sequence design using backbone-conditioned discrete flow matching

RiboDFM designs RNA sequences that fold into target 3D structures using a backbone-conditioned discrete flow-matching framework, achieving high sequence recovery and tertiary-structure consistency.

A mitochondrion-like ribosome in an insect endosymbiont

This study shows that features of mitochondrial ribosomes, such as host protein acquisition and structural changes, are also present in an ancient insect endosymbiont, suggesting these traits arise from endosymbiont ancestry rather than mitochondrial specificity.

NuFold RNA Structure Database: Large-Scale RNA Tertiary Structure Prediction with Confidence Metrics

The paper introduces NuFold, a tool for large-scale RNA tertiary structure prediction, and provides a database with precomputed structures and confidence metrics.

Systematic mapping of the prokaryotic noncoding sequence space with a genomic language model

The paper uses a genomic language model to cluster and annotate noncoding sequences in prokaryotic genomes, identifying structured RNAs and their potential functions.

RiboTxAlign maps and quantifies ribosome footprints using sample-specific transcript references

RiboTxAlign maps and quantifies ribosome footprints using sample-specific transcript references, achieving high accuracy in genomic placement and transcript-level abundance estimation.

Adaptation of fluorescence rescue reporters of mistranslation for use in Saccharomyces cerevisiae

This paper adapts a fluorescence-based method to detect mistranslation in yeast and shows it detects mistranslation events differently than mass spectrometry.

PhyloScore: Improved covariation score for RNA alignments using phylogeny

PhyloScore improves RNA alignment covariation scores by incorporating phylogenetic trees, enhancing accuracy in predicting RNA secondary structures.

Mechanism-Based Discovery of New TRIDs Targeting Ribosome Pockets

This paper identifies new TRIDs that target ribosome pockets to increase PTC readthrough, showing some are more potent than ataluren in vitro.

The ABC-F protein Uup, Rescues Stalled Ribosomal Termination Complexes to Modulate DNA Maintenance

This study shows Uup rescues stalled ribosomal termination complexes, indirectly affecting DNA maintenance genes like ssb and dnaX.

RAPPL-Seq Enables Rapid, High-Sensitivity Ribosome Profiling of Scarce Samples

RAPPL-Seq enables rapid, high-sensitivity ribosome profiling of scarce samples by improving RPF recovery efficiency and reducing processing time.