RNA Research and Splicing

Probing RNA-protein interactions in the early mouse embryo

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.

Synergy of RNA Concentration, RNA Binding Proteins, and RNA Palindrome Drives clustering of oskar mRNA in vivo

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

Efficient co-transcriptional splicing enforces rapid microexon definition and inclusion by SRRM4

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

Single-cell atlas of transcript usage remodelling in antiviral immune responses across human populations

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.

Molecular characterization of Cdh12-SCON conditional knockout mice reveals unexpected splicing changes

The paper characterizes the SCON system in Cdh12 conditional knockout mice, revealing unintended splicing changes that affect mRNA expression.

Coordinated alternative splicing decisions via stepwise exon definition

The paper shows that intron retention and alternative exon choice are coupled through multistep exon recognition by the spliceosome, which is disrupted in cancer.

In Vivo Massively Parallel Reporter Assay Reveals Sequence Determinants of mRNA Localization in Astrocytes

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

Targeting of the nuclear RNA exosome to chromatin by HP1 affects the transcriptional programs of liver cells.

This study shows that HP1 interacts with the RNA exosome, affecting RNA degradation and transcriptional programs in liver cells, with implications for cancer biology.

Programmable artificial RNA condensates in mammalian cells

This paper introduces programmable artificial RNA condensates in mammalian cells that can be controlled for subcellular localization and molecular recruitment.

A Mammalian Genomic Signature Shaped by Single Nucleotide Variants Regulates Transcriptome Integrity and Diversity

The paper identifies a genomic signature, G-tract-AG motifs, that regulates transcriptome integrity and diversity through repression of AG usage and SNV-induced splicing activation.

Competition between protein-RNA clustering and phase separation drives re-entrant phase behavior of hnRNPA1

This study shows that hnRNPA1 phase separation is suppressed at high RNA concentration due to competition with protein-RNA cluster formation, with specific RNAs promoting clusters more effectively than unspecific ones.

CNOT10 is involved in TTP-mediated AU-rich element containing mRNA metabolism, independent of mRNA decay regulation

The paper investigates TTP's role in reducing ARE-containing mRNA levels through interactions with CNOT10, distinct from its known mRNA decay function.

Arabidopsis TITAN LIKE is required for U12-type intron splicing, especially for AT-AC subtypes

This study shows that Arabidopsis TTL is essential for U12-type intron splicing, especially AT-AC introns, and identifies distinct spliceosomal functions from DROL1.

Augmented prediction of multi-species protein--RNA interactions using evolutionary conservation of RNA-binding proteins

MuSIC predicts cross-species RBP-RNA interactions using evolutionary conservation and label smoothing, outperforming existing methods and quantifying variant effects on binding.

Cryo-EM structures of the CDK11-cyclin L-SAP30BP complex reveal mechanisms of CDK11 regulation

The paper presents the cryo-EM structure of the CDK11-cyclin L-SAP30BP complex, revealing mechanisms of CDK11 regulation and inhibitor selectivity.

PABPC1 Modulates Immunoglobulin pre-mRNA Alternative Polyadenylation

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.

Recurrent LINE 1 exonization drives transcriptome remodelling in NSCLC

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

hnRNPA2B1 Modulates Early TIA1 Recruitment into Stress Granules through an RNA-Dependent Assembly Mechanism

Genetic compensation in β-actin mutants occurs independently of mutations that destabilize β-actin mRNA

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

Sequence and structure of protein binding sites in RNA impact biomolecular condensates

The paper investigates how RNA-protein binding site context, not just valence, affects biomolecular condensate properties in Ashbya gossypii.

Membranes arrest the coarsening of mitochondrial condensates

The paper investigates how mitochondrial membranes regulate the size and dynamics of condensates, showing that membranes prevent coarsening by limiting condensate growth.

U2 snRNP recognizes the branch site through a loaded-spring strand-invasion mechanism

This study reveals a loaded-spring mechanism by which U2 snRNP recognizes the branch site through spontaneous strand invasion driven by conformational energy release.

Direct RNA-seq provides evidence for an antiterminator function of the yeast Hrp1 protein on RNA polymerase II transcripts

The paper uses direct RNA sequencing to show Hrp1 affects RNA polymerase II termination and polyA site selection in yeast.

Transcriptome-Wide Alternative Splicing Analysis Implicates Complex Events in Bipolar Disorder

This study performs a transcriptome-wide alternative splicing analysis in bipolar disorder, identifying complex splicing events and candidate genes associated with the disorder.

The glp-1 3' untranslated region regulates germline proliferation and promotes reproductive fecundity through multiple mechanisms

This study investigates how the glp-1 3'UTR regulates germline proliferation and fecundity through interactions with RNA-binding proteins POS-1 and GLD-1, revealing distinct mechanisms for each.

Evaluating splicing factor and kinase network crosstalk through global phosphoproteomics

The paper investigates crosstalk between splicing factors and kinase networks using phosphoproteomics and RNA-seq data, showing significant changes in phosphorylation and kinase activity upon splicing factor knockdown.

A long-read RNA sequencing and polysome profiling framework reveals transposable element-driven transcript diversity and translational rewiring in glioblastoma

This study combines long-read RNA sequencing and polysome profiling to show that transposable elements drive transcript diversity and alter translation in glioblastoma stem cells.

SMG7 and eIF4A constitute a homeostatic module controlling P-body condensation and function of Meiotic bodies

The paper identifies SMG7 and eIF4A as a regulatory module that controls P-body condensation and function of meiotic bodies in Arabidopsis.

PCBP1 regulates alternative splicing of AARS2 in congenital cardiomyopathy

This study identifies PCBP1's role in regulating AARS2 alternative splicing and its impact on heart development and congenital cardiomyopathy.

CFIm25-Dependent Alternative Polyadenylation in AKT2 mRNA Programs Macrophage Polarization

This study shows CFIm25 regulates macrophage polarization by controlling AKT2 mRNA polyadenylation, promoting M1 traits and suppressing M2 features.