RNA Research and Splicing

Enzymes can activate and mobilize the cytoplasmic environment across scales

This study shows that enzymes in biomolecular condensates enhance catalytic activity through crowding-induced conformational changes and enable increased mobility despite environmental viscosity.

Neuronal late endosomes serve as selective RNA hubs disrupted by ALS-linked FUS mutation

The paper identifies late endosomes as selective RNA carriers in motor neurons and shows that ALS-linked FUS mutations disrupt this process.

The nonsense-mediated decay RNA-surveillance pathway facilitates the hypoxia response by C. elegans

This study identifies a functional interaction between the HIF-1 hypoxia response pathway and the NMD RNA surveillance pathway in C. elegans, showing NMD enhances specific aspects of the HIF-1 response.

Dosage-sensitive RBFOX2 autoregulation promotes cardiomyocyte differentiation by maturing the transcriptome

This study shows that RBFOX2 autoregulation is critical for cardiomyocyte differentiation by maturing the transcriptome, and its disruption leads to congenital heart disease.

Brr2p-mediated unwinding of U4/U6 is promoted by a mutually exclusive intra-molecular stem loop in U4 and involves destabilization of the 5' stem-loop of U4

The paper investigates how Brr2p unwinds U4/U6 base pairs in yeast by disrupting U4 secondary structures and shows that an intramolecular stem loop in U4 antagonizes U4/U6 reannealing.

Targeting CLK1 by CRISPR tools and pharmacological inhibition modulates the innate immune response and dengue virus replication

The paper shows that CLK1 inhibition enhances antiviral defenses against dengue virus by boosting IFN-stimulated gene expression and reducing viral replication.

RNA synthesis and degradation regulate biomolecular condensates through non-equilibrium feedback

This study shows RNA synthesis and degradation dynamically regulate transcriptional condensates through non-equilibrium feedback, affecting their composition and stability.

nHOTAIRM1 scaffolds ANXA11-dependent assemblies to drive axonal mRNA localization in human motor neurons

This study identifies nHOTAIRM1's role in axonal mRNA localization by scaffolding ANXA11-dependent transport assemblies in human motor neurons.

S. cerevisiae Cwc15p Tunes the Spliceosome Active Site for Remodeling and Catalysis

This study investigates the role of Cwc15p in S. cerevisiae splicing, finding it stabilizes and facilitates structural transitions of the spliceosome active site, important for splicing under nonoptimal conditions.

Phosphorylation tunes electrostatically driven protein-RNA interactions

This study quantifies how phosphorylation modulates electrostatic interactions between charged IDPs and RNA, showing that phosphorylation reduces binding affinity linearly with net charge.

Temporal gating dictates stress-induced transcript export from the nucleus

The paper shows that transcription timing, not sequence features, determines nuclear export of stress-induced mRNAs in human cells.

A systematic delineation of 3' UTR regulatory elements and their contextual associations

The paper identifies 3'UTR regulatory elements using synthetic inserts and a deep learning model, revealing their effects on gene expression and nuclear-cytoplasmic partitioning, and highlights disease-relevant variants.

Stepwise Ligand Capture Primes PKR for Activation and RNA Discrimination

This study reveals how PKR's dsRBDs work together to enable selective RNA recognition and activation through a two-step ligand sampling mechanism.

Pumilio and Brain tumor regulate the expression of Smaug during the Drosophila maternal-to-zygotic transition

This study shows that Pumilio and Brain tumor regulate Smaug mRNA degradation during the Drosophila maternal-to-zygotic transition, preventing ectopic Smaug protein expression and ensuring proper mRNA clearance.

ZNF121 recruits YTHDF2 to modulate mRNA stability

The paper identifies ZNF121 as a cofactor that enhances YTHDF2-mediated mRNA decay by facilitating its binding to target transcripts, thereby modulating mRNA stability and cell-cycle regulation.

PQBP1-dependent alternative RNA splicing underlies high calorie diet-induced cognitive impairment

This study identifies PQBP1-dependent alternative RNA splicing as a mechanism underlying HFD-induced cognitive impairment through effects on synaptic vesicle release.

Proteome profiling of plant Cajal bodies uncovers kingdom-specific components

The paper profiles the proteome of plant Cajal bodies, revealing a distinct kingdom-specific composition compared to animal CBs.

Deadenylation and Decapping Factors Cooperatively Stimulate Biochemical Activities of DEAD-Box ATPase Dhh1

This study shows that Dhh1's ATPase activity is cooperatively enhanced by deadenylation and decapping factors through distinct mechanisms.

The moonlighting functions of SEC13 in nonsense-mediated mRNA decay and the regulation of ER stress

This study identifies SEC13 as a novel NMD factor in mammalian cells and shows its role in regulating ER stress through the UPR pathway.

Perplexity as a Metric for Isoform Diversity in the Human Transcriptome

The paper introduces perplexity as a metric to quantify isoform diversity in the human transcriptome using long-read RNA-sequencing data, showing it provides interpretable and reproducible measurements.

PRMT1-SFPQ regulates intron retention to control matrix gene expression during craniofacial development

This study identifies PRMT1-SFPQ as a regulator of intron retention in craniofacial development, leading to reduced matrix gene expression through NMD.

RBP-Driven RNA Sorting and Local Translation Establish the Molecular Identities of Individual Sensory Axons

The paper identifies compartment-specific translational programs in sensory neuron axons using spatial translatomics and shows that RNA-binding proteins guide mRNA sorting to establish molecular identities.

Functional characterization of RNA profiles in processing bodies of human embryonic stem cells and mesodermal cells

The paper characterizes RNA profiles in P-bodies of human embryonic stem cells and mesodermal cells, revealing cell type-specific RNA composition and roles in differentiation.

Bacterial Ribonucleoprotein bodies maintain an acidic pH environment as a mechanism of enzyme regulation

The paper shows bacterial ribonucleoprotein bodies (BR-bodies) maintain an acidic pH environment, enhancing enzyme activity and suggesting pH regulation as a mechanism for RNA processing.

HS-AFM Reveals Hierarchical RNA Folding Driving Condensate Assembly and Material States

This study uses HS-AFM to show how RNA folding leads to condensate assembly and distinct material states at the nanoscale.

RNA degradation by DIS3 is a necessary step in the resolution of backtracked transcription complexes

This paper shows that DIS3's 3-5 exoribonuclease activity degrades backtracked RNA, resolving stalled RNAPII complexes and enabling transcription elongation.

Chronic stress disrupts the network among stress granules, P-bodies, and motor proteins

This study shows chronic stress disrupts the myosin-SG-PB network and inhibits SG maturation through reduced MYH9 and UBAP2L levels.

Primer- and template-independent RNA polymerization by terminal nucleotidyltransferase TENT4B

This study demonstrates that human TENT4B can synthesize RNA from free nucleotides without a primer or template, showing high processivity for adenosine nucleotides.

Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms

The paper generates a high-resolution proteogenomic atlas of human neuronal development using long-read RNA sequencing and proteomics, revealing novel isoforms and their role in neurodevelopmental risk mechanisms.

Interactions Underlying Stress Granule Structure and Therapeutic Dissolution

This study develops a minimal stress-granule model and uses simulations to identify small molecules that dissolve stress granules, aligning with experimental results.