RNA and protein synthesis mechanisms

Failure to release from the ER translocon induces 60S ribosome degradation

The paper identifies a cell-state-dependent pathway for degrading ER-retained 60S ribosomal subunits through UFMylation loss and the action of TLSD1.

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

The paper uses Nanopore and Illumina sequencing to study age-related changes in yeast tRNA modifications and CCA-tail dynamics.

DSSNA: Automated Nucleic Acid Structure Analysis in Molecular Dynamics

DSSNA v2026 analyzes nucleic acid structures in MD simulations, identifying base pairs, hydrogen bonds, and stacking interactions, showing that canonical pairs are stable while non-canonical ones are transient.

Not all TOP RNAs are created equal: 3'UTR length and TSS selection predict the translational regulation of LARP1-bound mRNAs in CD4+ T cells

The paper investigates how 3'UTR length and TSS selection influence the translational regulation of LARP1-bound TOP RNAs in CD4+ T cells, revealing differential dependencies on LARP1 and MTORC1.

De novo design of functional RNAs through higher-order interactions

This paper introduces DS3dRNA, a framework for de novo RNA design that uses higher-order interactions, achieving better performance than existing methods in structure prediction and function recovery.

Engineering a ribozyme with aminoacyl-tRNA synthetase activity

This paper engineers a ribozyme that can aminoacylate tRNA and discriminate between cognate and non-cognate tRNAs, enabling non-canonical amino acid incorporation.

Translation fidelity mechanisms and their changes in aging

This study measures proteome-wide translation errors in yeast and mouse, finding that fidelity varies by organism and tissue, increases with age in post-mitotic cells, and is regulated by tRNA pool remodeling.

Strong correlation between amino acid frequency and codon degeneracy in genetic codes across all domains of life

The paper analyzes the correlation between codon degeneracy and amino acid frequencies across genetic codes, revealing consistent patterns of over- and underrepresentation of amino acids across domains of life.

Evaluating the reliability of tools for mRNA annotation and IRES studies

A back-splicing circRNA reporter yields linear trans-spliced artifacts; in orthogonal assays three reported cellular IRESes are inactive, and Iso-Seq 5' ends agree with nAnT-iCAGE start sites.

Structural characterization of hibernating ribosomes in four Gram-negative pathogenic bacteria

This study reports cryo-EM structures of hibernating ribosomes from four Gram-negative bacteria, revealing how hibernation factors inhibit translation.

Mapping the Functional Landscape and Viral Diversity of 2A Peptides

The paper develops a FRET-based system to analyze 2A peptides' activity, identifies key residues, and discovers a novel subclass with high StopGo efficiency.

An RNA Language Model trained on sequence alone reveals the structural logic of Internal Ribosome Entry Sites

Continued pretraining of an RNA language model on picornaviral 5′ UTRs alone predicts IRES base pairs with median precision 0.80 versus 0.47 for Infernal, and reveals a Type II subclass.

Collided ribosomes are rescued by the endonuclease Rae1 and trans-translation

The paper identifies a bacterial mechanism, CART, where Rae1 endonuclease cleaves mRNA from collided ribosomes to enable trans-translation and rescue stalled ribosomes.

A human cell-free translation screen identifies the NT-2 mycotoxin as a ribosomal inhibitor that binds the peptidyl transferase center

FAST-MaP: Chemical Mapping of RNA Structures Using Primer-less Sequencing

FAST-MaP provides a protocol for per-nucleotide RNA structure characterization using chemical modification and primer-less sequencing without requiring sequencing infrastructure or bioinformatics expertise.

Enterovirus RNase L inhibiting RNAs are highly conserved with limited phylogenetic distribution

The paper identifies conserved structural features of PV1 ciRNA that inhibit RNase L and shows limited phylogenetic distribution of functional ciRNAs within Enterovirus coxsackiepol.

FRET-guided integrative modeling resolves Mg2+-dependent RNA tertiary-contact formation

This study uses smFRET-guided integrative modeling to show that Mg2+ influences RNA tertiary contact formation, revealing coexistence of bound and unbound conformations at intermediate concentrations.

Molecular Architecture of the Human GCN1-ABCF3 Ribosome Collision Sensor

This study identifies ABCF3 as the mammalian ortholog of yeast Gcn20, which is recruited to ribosomes during amino acid starvation and interacts with GCN1 to activate Gcn2.

Topology, Energy Landscapes and Folding Kinetics of RNA Hairpins

This study develops a computational framework to model RNA conformational ensembles and their dynamics, showing temperature's effect on folding landscapes and agreement with experimental data.

Local translation couples synaptic activity to mitochondrial adaptation in dendrites

This study identifies eIF4G2-dependent local translation as a mechanism linking synaptic activity to mitochondrial adaptation in dendrites.

An RNase Toxin Hijacks Elongation Factor-Tu to Cleave the Ribosomal Sarcin-Ricin Loop

This paper characterizes SRLase1, an RNase toxin that cleaves the sarcin-ricin loop of 23S rRNA by repurposing EF-Tu, revealing a new mechanism of ribosome inhibition.

Conditional Generation And Inpainting Of Non-coding RNA Sequences With Masked Discrete Diffusion

This paper introduces RNA-MDLM, a model for generating and inpainting non-coding RNA sequences, showing it produces sequences with natural composition and folding statistics.

The Shewanella oneidensis Fic enzyme SoFic targets the switch-Iregion of EF-Tu for AMPylation

This study identifies EF-Tu as a target of the Fic enzyme SoFic, showing AMPylation disrupts EF-Tu's switch-I region and inhibits translation, while SoFic also binds DNA, suggesting dual regulatory roles.

A bacterial nucleolus for cold adaptation

The paper identifies a nucleolus-like condensate in E. coli that forms during cold adaptation to enhance ribosome biogenesis.

A B1 SINE element within the mouse Malat1 long noncoding RNA acts as an internal ribosome entry site mediating micropeptide translation

Structural and biophysical insights into the unique RNase YicC

This study reveals the structural and biophysical mechanisms of YicC, a novel bacterial RNase, showing its RNA binding and cleavage mechanism involving Mg2+ ions and dimeric conformations.

Structural framework for the assembly of the human tRNA ligase complex

This study determines the atomic structure of the human tRNA-ligase complex and reveals its assembly mechanism and functional implications.

Engineered mRNA nanostructures expand the design space of mRNA therapeutics through programmable protein expression and immune stimulation

This paper introduces mRNA-OG, a programmable mRNA nanostructure that affects protein expression, delivery, and immune response through its architecture.

FORGE audits residue-level information encoded in RNA tertiary structure geometry

FORGE converts RNA geometry into interpretable descriptors to identify native nucleotides and predict base-pair states, showing high accuracy and separable properties in RNA structure analysis.

RNAbridge: a database of extended and non-canonical helices

RNAbridge is a database that identifies and visualizes non-canonical RNA helices and junctions using structural data from the Protein Data Bank.