RNA Research and Splicing

Protein-RNA condensation kinetics via filamentous nanoclusters

This study investigates protein-RNA condensation kinetics using a viral model, revealing the sequence of events leading to nanocluster formation and coacervate structures.

Formation of polyphasic RNP granules by intrinsically disordered Qβ coat proteins and hairpin-containing RNA

The paper shows that synthetic RNA with hairpin binding sites and disordered coat proteins form programmable polyphasic RNP granules with tunable phase behavior.

RNA Alternative Splicing and Polyadenylation and Regulation of the Glomerular Filtration Barrier

This study identifies altered alternative splicing and polyadenylation in glomerular genes during kidney disease models and demonstrates potential therapeutic modulation using antisense oligonucleotides.

Post-transcriptional regulation of cyclin A and cyclin B mRNAs is mediated by Bruno 1 and Cup, and further fine-tuned within P-bodies

This study shows that Bruno 1 and Cup regulate cyclin A and B mRNAs, with P-bodies modulating cyclin B mRNA levels in a stage-specific manner.

Identification of Human Pathways Acting on Nuclear Non-Coding RNAs Using the Mirror Forward Genetic Approach

The paper introduces a single-cell method called Mirror to identify human pathways acting on nuclear non-coding RNAs, revealing key components and disease links.

Stochastic splicing and deterministic inclusion of variable exons promote diversification of Down Syndrome Cell Adhesion Molecule expression

The paper investigates stochastic and deterministic mechanisms of Dscam alternative exon inclusion in Drosophila and honey bees, revealing experience-directed splicing patterns.

Dysregulation of alternative splicing patterns in the ovaries of reproductively aged mice

This study identifies age-related alternative splicing changes in mouse ovaries, showing increased isoform diversity and functional impacts on mitochondrial genes.

RBPSignal: A deep learning approach for predicting RNA-Protein binding signals

RBPSignal predicts RNA-protein binding signals using deep learning and identifies sequence motifs, validated against eCLIP data and existing databases.

Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay

The paper identifies the amino acid preceding a premature termination codon as a key determinant of nonsense-mediated mRNA decay efficiency.

Deep Transcriptomics Reveals Cell-Specific Isoforms of Pan-Neuronal Genes

The paper uses single-cell RNA-Seq to analyze splicing patterns in C. elegans neurons, identifying cell-specific isoforms and regulatory factors.

Dominant variants in major spliceosome U4 and U5 small nuclear RNA genes cause neurodevelopmental disorders through splicing disruption

The paper identifies de novo variants in RNU4-2 and RNU5B-1 as causes of neurodevelopmental disorders by disrupting splicing, with variant location and allele phase influencing clinical severity.

From Pan-Life Phase Insights to PhaseHub: Analyzing Condensate Complexity

The paper analyzes phase-separating proteins across 1,106 species to reconstruct the evolutionary history of protein condensation and identifies phase separation-regulated signaling hubs.

RNA polymerase III transcription-associated polyadenylation promotes the accumulation of noncoding retrotransposons during infection

The paper identifies polyadenylation as a mechanism driving SINE RNA accumulation during gammaherpesvirus infection, linking Pol III transcription to mRNA-like processing.

Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

The paper investigates the structural determinants of inverted Alu-mediated backsplicing in the HIPK3 gene using SHAPE-JuMP and finds that long-range Alu-mediated base pairs are required for circularization, but not full-length Alu elements.

Decay drives RNA abundance regulation using three distinct regulatory mechanisms

The paper identifies three regulatory mechanisms by which RNA decay influences RNA abundance changes in Arabidopsis, including synergistic, oppositional, and decay-alone effects.

The RNA binding proteins Ddx6 and Ddx61 support development in mRNA-decay deficient pnrc2 mutants

The paper shows that Ddx6 and Ddx61 compensate for mRNA decay defects in pnrc2 mutants by regulating translation and poly(A) tail length.

Long non-coding RNA hsr-omega provides scaffolding for the nuclear domain B-body.

This study identifies hsr-omega as an RNA scaffold for the Drosophila B-body and shows its role in maintaining nuclear protein homeostasis.

Small molecule inhibition of CPSF3 impacts R-loop distribution

The paper tests the effect of CPSF3 inhibitors YT-II-100 and JTE-607 on R-loop formation, finding global increases but no effect on specific R-loop positive control genes.

Isoswitching in human brain development and aging

The paper identifies isoswitching, a phenomenon of isoform usage changes in human brain development and aging, and shows it can predict age across the lifespan using RNA-seq data.

A novel splicing graph allows a direct comparison between exon-based and splice junction-based approaches to alternative splicing detection

The paper introduces a splicing graph to compare exon-based and splice junction-based alternative splicing detection methods, revealing discrepancies and integrating results.

Comprehensive Profiling of RBM20-Regulated CaMKIIδ Splice Variants Across the Heart, Skeletal Muscle, and Olfactory Bulbs.

The paper identifies tissue-specific CaMKIIδ splice variants of the Camk2d gene in the heart, skeletal muscle, and olfactory bulbs and shows RBM20 regulates their expression.

Integrative CRISPR Screens and RNA-Omics Discover an Essential Role for PUF60-3' Splice Site Interactions in Cancer Progression

The paper identifies PUF60's role in cancer progression by combining CRISPR screens and RNA-omics, showing its splicing activity supports TNBC proliferation and is a potential therapeutic target.

MARK4 enhances stress granule formation and increases tau accumulation

This study shows MARK4 enhances stress granule formation and promotes tau accumulation through interactions with TIA1.

Tissue specific function of the Drosophila 7SK snRNP in controlling motoneuron synaptic growth

This study shows that loss of Larp7 or 7SK RNA in Drosophila impairs locomotion and axonal growth, with the 7SK complex regulating transcription of long genes with high GC content promoters.

Single-molecule multimodal timing of in vivo mRNA synthesis

This study directly sequences pre-mRNA to resolve transcription and processing at single-molecule resolution, revealing delayed splicing and m6A methylation preceding splicing.

Maximal Efficacy of Alternative Splicing is Ensured by Balanced Efficiency of U1 and U2AF

The paper analyzes RNA-seq data to show that U1 and U2AF splicing efficiencies follow a Weibull distribution, with balanced efficiency maximizing overall splicing efficacy.

Neural microexons modulate arousal states via cAMP signalling in zebrafish

This study shows that srrm3 regulates arousal states in zebrafish via cAMP signaling, with mutations causing hyperarousal and transcriptional changes.

Defining the mechanisms and properties of post-transcriptional regulatory disordered regions by high-throughput functional profiling

The paper identifies regulatory sequences in disordered regions of RNA binding proteins and shows how they modulate mRNA decay through interactions with core machinery.

Developmental dynamics and axonal transport of cerebral cortex projection neuron mRNAs in vivo

The paper investigates mRNA dynamics and axonal transport in cerebral cortex projection neurons in vivo, identifying cis-regulatory elements and transport mechanisms for specific mRNA classes.

New Insights into nuclear import and nucleolar localization of yeast RNA exosome subunits

This study characterizes the subcellular localization and nuclear import mechanisms of yeast RNA exosome subunits, revealing their nucleolar distribution and interactions with importins and cofactors.