RNA Research and Splicing

The paper investigates DDX53's role in human germ cells using TCam-2 cells, showing its involvement in RNA metabolism, splicing, and potential interactions with RNA molecules.

This study uses direct RNA sequencing to analyze epitranscriptomic changes in brain cells, revealing m6A modification patterns linked to Alzheimer's disease progression.

SMARTIE improves the analysis of RNA editing data to identify and rank RBP target RNAs by integrating statistical tests with confidence-weighted features.

The paper introduces Granule-seq to analyze RNA composition in stress granules and FUS condensates, finding they are distinct RNA compartments with different transcript enrichments and recruitment mechanisms.

This study shows CDK12 and CDK13 suppress distinct intronic polyadenylation sites, leading to premature termination and novel peptides in cancer.

This study investigates how PUF60 expression changes affect splicing patterns and reveals a phosphorylation-mediated regulatory mechanism in mouse stem cells.

The paper introduces SHARCLIP to map RNA-RNA, RNA-protein, and protein-protein contacts in cells, revealing structural mechanisms of splicing and therapeutic targets.

This study identifies an alternative splicing event in MSI2 that determines its subcellular localization and regulatory function.

This study identifies sex-specific gene expression differences in hemp by analyzing polyadenylation patterns and shows that these differences emerge after germination.

This study visualizes and characterizes the diffusivity of NEAT1-1 in live cells, revealing its presence in a distinct diffusive state within the nucleoplasm.

The paper investigates alternative splicing of microexons in human peripheral tissues using transcriptomic data, finding that microexon dysregulation may reflect a broader splicing homeostasis collapse rather than a primary disease driver.

This study identifies CDKL5-mediated phosphorylation of nELAVL as critical for regulating RNA metabolism and condensate communication, essential for visual cortex maturation.

The paper introduces WATER, a method to analyze temporal gene expression, and shows that minor spliceosome inhibition disrupts developmental timing by redistributing molecular programs.

This paper introduces Polymer-Assisted Condensation (PAC) to explain repulsion-driven layering in biomolecular condensates, showing it forms stable core-shell structures without relying on interfacial tension hierarchies.

This paper presents a protocol for minigene assays to validate splice-altering variants using locus-specific design, gene synthesis, and long-read sequencing.

The paper shows that 3'UTR-3'UTR interactions drive Wnt gene activation by enabling co-translational protein complex assembly, independent of protein abundance.

The paper investigates how nuclear speckles regulate splicing and stem cell function in muscle stem cells during activation, injury, and aging.

This study shows synthetic transcriptional condensates exhibit dynamic behaviors driven by RNA synthesis and degradation, revealing how reaction kinetics influence condensate formation and function.

This study shows SRSF1 regulates 3'-end site selection through mechanisms both independent and dependent on U1 snRNP, affecting RNA isoform determination in breast cancer.

The paper adapts REMORA to study RNA-binding protein functions in early mouse embryos, identifying direct regulatory roles for several RBPs, including Alyref in 3' polyadenylation control.

The paper investigates factors driving oskar mRNA clustering in Drosophila embryos, finding that RNA concentration, Staufen, and RNA palindromes collectively promote dimerization and oligomerization.

The paper investigates how SRRM4 facilitates efficient co-transcriptional splicing of microexons, showing that upstream intron removal enables rapid microexon inclusion in neurons.

The paper creates a single-cell atlas of transcript usage changes during antiviral immune responses in humans, showing lineage-specific and ancestry-related variations across influenza and SARS-CoV-2 infections.

The paper develops an in vivo MPRA method to identify sequence determinants of mRNA localization in astrocytes and finds diverse regulatory mechanisms are used.

The paper investigates PABPC1's role in alternative polyadenylation during B cell development, finding it primarily shortens and downregulates its targets in a context-dependent manner.

This study identifies recurrent LINE-1 exonization events in NSCLC that generate new transcript isoforms, contributing to transcriptome diversity without affecting gene expression levels.

This study shows genetic compensation in ACTB mutants occurs via SRF/MRTF-A transcriptional feedback, independent of mutant mRNA expression or degradation.