RNA Research and Splicing

This study shows how sequence hydrophobicity affects the stability and organization of heterotypic biomolecular condensates, providing design principles for synthetic condensates.

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

Parnet is a CLIP-seq-based foundation model for RNA sequence representation learning that outperforms existing methods in binding profile prediction and generalizes across tasks.

This study identifies DYRK1B as a regulator of processing body abundance through phosphoproteomics and functional assays.

Flipper identifies differential RNA binding behavior using eCLIP data with improved normalization and separation of expression/splicing effects from true binding changes.

The paper reconstructs a transcript-resolved catalogue of human enhancer RNAs, identifies their splice junctions, and provides tools for further study.

This study identifies RNA binding domains in HNRNPR, showing that RRM3 and a C-terminal charged region are critical for RNA binding, and reveals specific interactions with G-quadruplexes.

This study shows that specific pseudouridines in the U2 branch site recognition region affect branch site recognition during pre-mRNA splicing in yeast.

This study identifies STRs associated with alternative splicing in human brain tissue and links some to disease-related GWAS signals.

SpliceImpactR identifies and predicts the impact of alternative RNA processing events on protein function across the human transcriptome, revealing widespread context-dependent effects on the proteome.

The paper identifies a structural gate in pre-mRNA that regulates U1 recruitment and nutrient-stress adaptation in yeast.

This study maps sex-specific RNA-RNA and RNA-DNA interactions in Drosophila cells using RD-SPRITE, revealing CLAMP's role in spliceosome targeting and RNA regulation.

The paper presents cryo-EM structures of human spliceosomes showing how SDE2, FAM32A, and Prp18 regulate 3' splice site selection by counteracting distal bias and stabilizing weaker proximal sites.

This study shows that stress granule fusion is coordinated by mitochondria, enhancing cell viability and stress adaptation.

This study shows that inhibiting CPSF73, an mRNA 3' end processing enzyme, reduces cancer cell proliferation and reverses the mesenchymal state by altering alternative polyadenylation (APA) patterns and 3'UTR lengths in multiple cancer cell lines.

The paper reanalyzes TE-gene splicing in Drosophila brain data, showing TE exonisation is common and validates previous findings despite conflicting results from another study.

This study identifies FMR1 as a translational enhancer of oskar in Drosophila oocytes and reveals how its RNA-binding domains regulate opposing translation functions through phase separation.

The paper identifies a Type II RhlB helicase in Pseudomonas aeruginosa that forms toxic condensates, which are resolved by RNase E through antagonizing phase separation.

This study identifies PAIP1 as a cofactor for mRNA export and shows it couples nuclear to cytoplasmic mRNP remodeling and poly(A) homeostasis, affecting mRNA stability and development.

This study identifies splicing dysregulation in SF-mutated cancers and demonstrates that antisense oligonucleotides can correct aberrant splicing and restore tumor suppressor function.

The paper systematically analyzes eight pathogenic EXOSC3 variants in yeast to determine their functional consequences on RNA exosome function.

This study shows how RNA and protein interactions influence the aging of FUS condensates through molecular mechanisms involving LARKS and cross-β-sheet structures.

The paper identifies the structured mRNA element 45ABC in plant RBP45 genes, showing it mediates auto- and cross-regulatory feedback via alternative splicing, balancing RBP45 expression and function.

scPAISO identifies and quantifies alternative polyadenylation sites in scRNA-seq data using Read1, improving PAS detection and isoform quantification accuracy.

The paper identifies two perispeckle networks that partition interchromatin space, showing differential gene expression associations compared to nuclear speckles.

This study identifies ELAVL1 and ELAVL4 as co-regulators of MSI1-dependent translational activation in Xenopus and mammals.

This study shows that electrostatic interactions between intrinsically disordered regions drive G3BP1 condensate ageing, with RNA modulating these interactions and delaying dynamic arrest.

LLPSense predicts and modulates condition-dependent protein phase separation using machine learning, revealing new insights into disease mechanisms and enabling programmable condensates.

The paper introduces susceptibility as a measure of how biomolecular condensates respond to solute perturbations, showing large variations in response across different condensates and solutes.