RNA Research and Splicing

This study shows arginine methylation of LSM4 regulates alternative splicing in Arabidopsis, balancing responses to biotic and abiotic stress.

The paper shows that mRNA decay during T cell activation occurs through translation-dependent and independent pathways, with ribosome density determining the pathway used.

This study investigates the phase separation mechanism of the EWSLCD domain using biophysical methods, revealing tyrosine residues as key drivers of condensate formation.

This study identifies RBM41 as a paralog of U11/U12-65K in the minor spliceosome, showing distinct roles in splicing and spliceosome dynamics.

The paper identifies regulatory elements that control mRNA poly(A)-tail length and translation in vertebrate oocytes and embryos, showing conservation across species.

SPIT detects differential transcript usage in complex diseases by quantifying population heterogeneity and identifying subgroups with distinct DTU events, revealing new events in schizophrenia brain samples.

The paper combines full-length gene splicing assay and SpliceAI to analyze splicing effects of SPINK1 coding variants, finding less than 2% of variants significantly impact splicing.

This study identifies 413 APA-linked cancer susceptibility genes by integrating GWAS data with APA quantification, showing genetic variants associated with APA explain a large portion of cancer heritability.

This study identifies LARP4A and LARP4B as pro-tumorigenic RNA-binding proteins that promote sarcoma and carcinoma growth and metastasis through cell cycle regulation.

This study identifies RBM7 deficiency as a driver of breast cancer metastasis through MFGE8 splicing regulation and NF-kB pathway suppression.

The paper uses long-read sequencing to study mRNA isoform-specific ribosome association during neuronal differentiation, finding that alternative splicing in coding and untranslated regions affects translational control.

TREX identifies RNA-binding proteins interacting with specific RNA regions in living cells, revealing novel interactions in 45S rRNA and U1 snRNA.

This study shows coiled-coil domains can drive liquid-liquid phase separation in molecular models, with multimerization state playing a key role.

This study investigates how UPF1's ATPase autoinhibition and activation affect RNA binding kinetics and NMD efficiency, revealing that UPF1-RNA interaction kinetics are critical for NMD.

This study identifies and characterizes the extended RNA-binding domain of hnRNP U, revealing two RGG/RG elements that work redundantly to enhance RNA binding.

The paper analyzes alternative splicing patterns in immune cells across SARS-CoV-2 variants and vaccination statuses, finding variant- and vaccination-specific profiles and a unique splicing dynamic in vaccinated Omicron-infected individuals.

The paper investigates droplet size distributions in protein phase separation and finds they follow a scale-invariant log-normal function, suggesting universal behavior and a method to estimate critical concentration.

The paper introduces a reporter system to compare EJC-independent and EJC-enhanced NMD, showing differences in RNA and protein levels and varying readthrough responses to inhibitors.

ASTK is a software tool for alternative splicing analysis that identifies key sequence and epigenetic features influencing splicing inclusion levels across different AS types.

The paper shows that inhibiting the CPEB3 ribozyme increases CPEB3 protein and enhances memory by promoting mRNA polyadenylation and translation.

The paper identifies alternative polyadenylation as a key mechanism by which inverted Alu repeats regulate gene expression and contribute to disease.

The paper studies how the cytoplasm's crowded and active environment influences biomolecular condensate formation using a synthetic system and simulations.

This study investigates how MATR3 variants affect cryptic splicing repression, showing that some variants reduce protein solubility and impair RNA binding and splicing regulation.

The paper uses long-read RNA sequencing to study poly(A) tail dynamics across the oocyte-to-embryo transition in mice, revealing how deadenylation and readenylation regulate translation.

This study identifies SRSF1's novel ability to bind and unfold RNA G-quadruplexes, revealing new roles for its RS domain in RNA regulation.

The paper shows that stress-induced mRNA condensation increases mesoscale diffusivity in the cytoplasm, fluidizing it and aiding in the formation of Q-bodies.

betAS provides a method to analyze and visualize differential alternative splicing using beta distributions to quantify inclusion levels and their precision across groups.

This study develops scRAPID, a pipeline that predicts protein-RNA interactions from single-cell transcriptomic data, showing comparable or better performance than transcription factor-target interaction prediction.

The paper introduces VulExMap, a tool to identify vulnerable exons prone to splicing mutations, finding that only 27% of exons are vulnerable despite two-thirds of known disease-related mutations occurring in vulnerable exons.