RNA Research and Splicing

Identification of cis-Acting Elements that Regulate Influenza A Virus Segment 7 Differential mRNA Splicing

This study identifies cis-acting elements that regulate splicing balance between influenza A virus segment 7 mRNA1 and mRNA2, revealing key sequences that influence M1 and M2 protein expression.

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.

SRSF1 coordinates transcription and alternative splicing to modulate p53 and apoptosis

This study identifies SRSF1's role in coordinating transcription and alternative splicing, showing its impact on p53 regulation and apoptosis across multiple cell lines and cancer cohorts.

Single-molecule nascent RNA profiling reveals multiple layers of co-transcriptional splicing and their reprogramming by cold in Arabidopsis

This study uses pPOINT-seq to analyze co-transcriptional splicing in Arabidopsis, finding that cold exposure globally enhances splicing and alters intron processing patterns.

Two closely related RNA helicases, UAP56 and URH49, couple mRNA splicing and export pathways with their distinct complexes

This study identifies three splicing regulation patterns mediated by UAP56 and URH49 and their association with mRNA export pathways.

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.

Decoy and antisense RNA oligonucleotides targeting the EGFR exon 3 splice site suppress proliferation of A172 glioblastoma cells

The paper shows that decoy and antisense RNA oligonucleotides targeting EGFR exon 3 splice site reduce proliferation in A172 glioblastoma cells but not in A549 lung adenocarcinoma cells.

Multivalent Scaffolding by XIST E-Repeats Tunes RNA Binding Protein Cooperativity and Lowers the Phase Separation Threshold

The paper characterizes the biophysical interactions between XIST E-Repeats and RNA-binding proteins, revealing cooperative binding and phase separation behavior that informs XIST's chromatin-modulating function.

Germ granules function as stress-responsive hubs to protect germ cell resilience

This study shows germ granules in C. elegans act as stress-responsive hubs that reorganize RNA granule networks to protect germ cell viability during heat stress.

Targeting IGF2BP1 Creates a Mitotic Vulnerability in Colorectal Carcinoma

This study identifies IGF2BP1 as a regulator of mitotic integrity in CRC, showing that its inhibition creates a therapeutic vulnerability that synergizes with paclitaxel.

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.

The U6 snRNA capping enzyme Amus/MePCE is required for the stability of U6atac and the processing of introns with features of both major and minor classes

The paper identifies a role for Amus/MePCE in stabilizing U6atac and shows that some minor introns require both major and minor splicing pathways for processing.

Sequence architecture of RNA reveals key molecular signatures driving RNA phase separation

The paper develops a framework to predict RNA phase separation by analyzing sequence features and achieves high accuracy in distinguishing LLPS-associated RNAs from background RNAs.

Identification and functional characterization of novel murine DIS3L2 isoforms

The paper identifies and characterizes three novel DIS3L2 isoforms in murine macrophages and other cell lines, showing differences in exonucleolytic activity and interactome profiles.

Reference-free isoform discovery links unannotated RNA processing to disease risk

Torino, a reference-free framework for isoform discovery, identifies RNA processing patterns linked to disease risk by analyzing read coverage variation across species and disease states.

Nonsense-mediated decay constrains transposable element-driven evolutionary innovation

This study shows NMD limits TE-driven transcriptomic innovation by degrading TE-derived transcripts, affecting evolutionary novelty and cancer outcomes.

Pat1 globally activates deadenylation-dependent decapping to clear inefficiently translated oligo(A)-tailed transcripts

Sexually dimorphic alternative splicing and its erosion following the loss of sex in stick insects

The paper examines sex differences in gene expression and alternative splicing in stick insects, finding that splicing variation declines more rapidly than gene expression after the transition to asexuality.

The RES complex core subunits Snu17 and Bud13 buffer the spliceosome against intrinsically weak splicing signals in budding yeast

The paper investigates the role of RES complex subunits Snu17p and Bud13p in splicing efficiency in budding yeast, finding they buffer against weak splicing signals and are critical for inefficient intron splicing.

Decoding pseudoexon activation by deep intronic variants using a high-throughput minigene assay in the NF1 gene

The paper develops a high-throughput minigene assay to identify pseudoexon-activating variants in the NF1 gene and benchmarks splicing prediction tools.

A Cis-Element in magu-2 Mediates Apical mRNA Localization via Active Transport in C. elegans

A trans-splicing model for poly(A)-tail addition during VSG mRNA maturation in Trypanosoma brucei

The paper identifies a splicing enhancer sequence that recruits factors for VSG mRNA maturation and proposes a model where polyadenylated SL RNA precursors are substrates for trans-splicing.

scRBP infers cell-specific RNA-binding protein regulons from single-cell transcriptomes at gene and isoform resolution

scRBP infers cell-specific RNA-binding protein regulons from single-cell transcriptomes, resolving targets at gene and isoform levels and linking genetic risk to disease.

Alternative splicing use ratio is not conserved between human and mouse immune cells

The paper compares alternative splicing event use ratios between human and mouse immune cells and fibroblasts, finding most show significant differences.

RNA exosome-mediated RNA surveillance governs developmental timing in the human cerebellum

This study shows that RNA exosome dysfunction disrupts developmental timing and lineage fidelity in human cerebellar organoids, leading to neurodevelopmental defects.

Evolution of histone mRNA 3' end processing machinery in eukaryotes

This study reconstructs the evolution of histone mRNA 3' end processing machinery across eukaryotes, revealing broader conservation of SLBP and related factors than previously thought.

Long-term effects of the early life environment on alternative splicing

This study shows that early life environment has long-term effects on alternative splicing in pea aphids, independent of morph identity.

A high-resolution protein-RNA binding atlas for structure-aware interaction prediction and post-transcriptional regulatory modeling

The paper introduces ecCLIP for high-resolution RBP binding maps and Pythia for structure-aware RNA-protein interaction modeling, improving RNA half-life prediction and variant effect assessment.