RNA Research and Splicing

Engineering Heterotypic Biomolecular Condensates with Synthetic Peptides for Controlled Spatial Organization and Liquid-like Nature

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

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.

PARNET: A CLIP-SEQ-BASED FOUNDATION MODEL FOR RNA SEQUENCE REPRESENTATION LEARNING

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.

Phosphoproteomics identifies the DYRK1B protein kinase as a regulator of processing bodies

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

Flipper: An advanced framework for identifyingdifferential RNA binding behavior with eCLIP data

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

Reconstructing the human enhancer RNA transcriptome

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

Contributions of Folded and Disordered Domains to RNA Binding by HNRNPR

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.

Pseudouridines in the U2 Branch Site Recognition Region Differentially Contribute to Branch Site Recognition during Pre-mRNA Splicing

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

The contribution of short tandem repeats to splicing variation in the human cortex

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

SpliceImpactR maps alternative RNA processing events driving protein functional diversity

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.

A starvation-remodeled pre-mRNA structure controls U1 recruitment and nutrient-stress adaptation in yeast

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

Mapping genome-wide RNA-RNA and RNA-DNA interactions in nuclear hubs of male and female Drosophila cells

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.

Structural basis for alternative 3' splice site selection in the human spliceosome active center

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.

Stress granule fusion is a mitochondria-coordinated process for stress adaptation

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

Targeting CPSF73, the mRNA 3' End Processing Endonuclease, Moves Cancer Cells Away from the Mesenchymal State

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.

Transposons contribute to splice-isoform diversity in the Drosophila brain

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.

Granule microenvironment regulates the dual functions of FMR1

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 fungal RNA-binding protein Ssd1 represses Sun4 protein abundance through recognition of 5' UTR structural and sequence elements

RNase E resolves toxic condensates by counteracting phase separation of Type II RhlB helicases

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.

PAIP1 couples mRNA export to cytoplasmic mRNP remodeling and poly(A) homeostasis

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.

Systematic comparison of pathogenic variants of the RNA exosome gene EXOSC3/RRP40 in Saccharomyces cerevisiae reveals variant-specific functional consequences

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

Compositional control of FUS condensate ageing through aggregation-prone interaction networks

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 structured mRNA element 45ABC mediates auto- and cross-regulation of RBP45 genes via alternative splicing

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.

Identification and quantification of alternative polyadenylation sites in single cell RNA-seq data using scPAISO

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

Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space

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

ELAVL1 and ELAVL4 are required for Musashi-dependent translational activation

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

Competing Molecular Interactions Govern the Dynamical Arrest of G3BP1 Condensates

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

A machine learning framework for predicting and modulating condition-dependent protein phase separation

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

Susceptibility and Regulation of Biomolecular Condensates by Solutes

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.

Switch-TRIBE: Lineage-specific high-resolution profiling of endogenous RNA-protein interactions

Switch-TRIBE profiles RNA-protein interactions in Drosophila neural stem cells, identifying cell-type specific targets and revealing regulatory strategies of RBPs in neurogenesis.