RNA Research and Splicing

Decoding Condensate Composition Reveals Tunable Interactomes and Functions of Disordered Proteins

This study introduces PhaseID, a method to identify protein components in LLPS condensates formed by IDRs, revealing how LLPS tunes interaction selectivity and enables new cellular functions.

piRNAs safeguard splicing and RNA fidelity

This study shows piRNAs regulate pre-mRNA splicing in C. elegans to maintain transcript isoform fidelity and proteome integrity by delaying splice completion and modulating splice-site selection.

IsoformMapper: A Web Application for Protein-Level Comparison of Splice Variants through Structural Community Analysis

The paper introduces IsoformMapper, a web tool that compares protein isoforms through structural community analysis, showing how alternative splicing affects protein function in Arabidopsis.

Substitutions in RNA-binding protein Hrp1 map a potential interaction surface with the yeast RNA polymerase II elongation complex

The paper identifies Hrp1 as an RNAP II anti-termination factor and shows specific substitutions in Hrp1 and Rpb3 affect termination by altering protein interactions.

Aberrant splicing in human cancer has a large-scale functional impact on transcription factors

The paper identifies 2,118 aberrant splicing events affecting 718 transcription factors across 14 cancer types, showing functional perturbations in TFs due to cancer-specific alternative splicing.

An autism spectrum disorder mutation in Topoisomerase 3B causes accumulation of covalent mRNA intermediates by disrupting metal binding within the zinc finger domain

This study shows that an autism-linked TOP3B mutation causes mRNA covalent intermediates by disrupting metal binding in the zinc finger domain, leading to neuronal toxicity.

Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB

The paper shows PRMT5 promotes chromatin escape of mRNAs by methylating SNRPB, affecting splicing and nuclear export.

CSDE1 regulates miR-20a-5p/ TMBIM6 axis in melanoma

The paper identifies a regulatory axis involving CSDE1, miR-20a-5p, and TMBIM6 in melanoma, showing CSDE1 enhances TMBIM6 expression through post-transcriptional mechanisms.

Biomolecular condensates of Eya drive transcriptional co-activation associated with eye development

This study identifies Eya biomolecular condensates as transcription hubs in eye development, showing their dynamic state is essential for co-activation and linked to disease.

Single molecule imaging of transcription dynamics, RNA localization and fate in T cells

This study uses single-molecule FISH to analyze cytokine mRNA dynamics in T cells, revealing transcriptional heterogeneity and post-transcriptional regulation by HuR.

A gene set collection of RBP target genes

The paper compiles a gene set collection of RBP target genes derived from eCLIP-seq data to enable functional enrichment analysis of gene lists.

Thermodynamic principles of enzymatic regulation in biomolecular condensates from reaction-coupled molecular modeling

This study uses a thermodynamic model to show how enzymatic reactions regulate biomolecular condensates by coupling reaction kinetics to local molecular environments, revealing two general principles.

A microexon confers functional divergence of the actin nucleator Arp2/3

The paper investigates the functional impact of a microexon in the Arp2/3 actin nucleator, showing it alters function in specific contexts despite similar bulk polymerization activity.

Massively parallel assay of human splice variants reveals cis-regulatory drivers of disease-associated and cell type-specific splicing regulation

The paper develops COMPASS, a method to assess splicing variant effects across cell types, identifying disease-associated variants and cell type-specific splicing programs.

The AMPK-related kinase NUAK1 regulates neuronal morphogenesis through the RNA splicing co-factor SON

This study identifies NUAK1 as a regulator of alternative splicing in cortical neurons through phosphorylation of SON, linking it to neurodevelopmental processes and ZTTK syndrome.

Human Mendelian disease and in vivo mutagenesis screening define the molecular architecture of the U8 snoRNA

The paper identifies molecular domains in the U8 snoRNA affected by LCC mutations and shows how U8 function impacts stability through a post-transcriptional mechanism.

mRNA initiation and termination are spatially coordinated

The paper identifies a spatial coordination between mRNA initiation and termination sites, proposing a 'Positional Initiation-Termination Axis' that influences isoform diversity.

mRNA poly(A)-tail length is a battleground for coronavirus-host competition

This study shows coronavirus infection limits PABPC1 activity, destabilizing short-tailed host mRNAs and enabling viral mRNAs to maintain specific poly(A)-tail lengths through synthesis and capping mechanisms.

Plant Cleavage Factor I complex is essential for precise cleavage and polyadenylation site determination

This study identifies the plant CFI complex components and shows their essential role in cleavage and polyadenylation site selection, with defects in morphological development and gene expression.

SRSF12 is a primate-specific splicing factor that induces a tissue-specific gene expression program

This study identifies SRSF12 as a primate-specific splicing factor that induces tissue-specific gene expression programs in human cells.

A Unifying Mechanism for Shared Splicing Aberrations in Splicing Factor Mutant Cancers

This study identifies a shared trans-acting mechanism in splicing factor mutant cancers that drives retained intron (RI) splicing defects through DDR-induced AMPK-AKT imbalance and SRSF1 hypophosphorylation.

Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3' splice sites

The paper identifies sequence and structural differences between SF3B1-sensitive and resistant cryptic 3' splice sites, showing SF3B1-sensitive sites are weaker and less structurally distinct.

NRDE2 Interacts with an Early Transcription Elongation Complex and Widely Impacts Gene Expression

This study identifies NRDE2 interactions with transcription and splicing factors and shows its broad impact on gene expression and splicing in human cells.

A network of RS splicing regulatory proteins controls light-dependent splicing and seedling development

The paper identifies RS splicing regulatory proteins as key regulators of light-dependent splicing and seedling development in Arabidopsis.

UPF1 shuttles between nucleus and cytoplasm independently of its RNA binding and ATPase activities

This study shows UPF1 shuttles between nucleus and cytoplasm without needing its RNA binding or ATPase activities, with RNA binding causing cytoplasmic retention.

Long-read Sequencing of Nascent RNA from Budding and Fission Yeasts

This paper describes methods for isolating and analyzing nascent RNA using long-read sequencing in budding and fission yeasts to study RNA processing and transcription dynamics.

A Dynamical Density Functional Theory Framework for Non-Equilibrium Phase Dynamics in Biomolecular Condensates

The paper develops a dynamical density functional theory framework to model non-equilibrium phase dynamics in biomolecular condensates, integrating experimental data with molecular descriptors to capture long-timescale processes.

Cytoplasmic poly-adenosine binding proteins modulate susceptibility of mRNAs to RNA-binding protein-directed decay

This study shows that PABPCs modulate PUM1/2-mediated mRNA decay by protecting poly(A) tails, with PABPC levels determining mRNA susceptibility to degradation.

Sequence-encoded interactions program internal condensate architecture

The paper shows how molecular interactions can encode multiphase architecture in cellular condensates and demonstrates a framework for engineering such structures with multiple coexisting phases.

Abnormal expression of splicing regulators RBFOX and NOVA is associated with aberrant splicing patterns at the Neurexin-3 gene in a monogenic autism spectrum disorder

The paper investigates splicing regulator dysregulation in Pitt-Hopkins Syndrome neurons and identifies aberrant splicing of the Neurexin-3 gene linked to impaired synapse organization and reduced electrical activity.