RNA Research and Splicing

Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib

The paper quantifies transcriptional readthrough in CML cells after imatinib treatment and shows it precedes alternative splicing changes and resistance development.

Competition for the conserved branch point sequence influences physiological outcomes in pre-mRNA splicing

The paper shows QKI competes with SF1 for branch point sequences, repressing splicing and causing lethality in yeast.

Phase separation of PGL-3 driven by structured domains that oligomerize and interact with terminal RGG motifs.

This study identifies that structured domains in PGL-3 drive phase separation through oligomerization and interaction with RGG motifs, independent of RNA.

Non-translated mRNA levels determine P-body properties

The paper shows that non-translated mRNA levels influence the biophysical properties and composition of processing bodies (PBs) under different stress conditions.

Holistic meta-analysis of Caenorhabditis elegans germ granule proteomics reveals complex dynamics and new candidate granule associated proteins

The paper performs a meta-analysis of C. elegans germ granule proteomics data to identify dynamic protein interactions and novel candidate granule-associated proteins.

Dissecting the RNA binding capacity of the multi-RRM protein Rrm4 essential for endosomal mRNA transport

The paper investigates the RNA binding roles of Rrm4's RRM domains in Ustilago maydis, revealing how different RRM interactions influence mRNA transport and stability.

Alternative polyadenylation in the brain is altered by chronic ethanol exposure in a sex- and cell type-specific manner

The paper examines how chronic ethanol exposure alters alternative polyadenylation in the brain, revealing sex- and cell type-specific effects on gene regulation and neuronal function.

The Dark Side of Biomolecular Condensates: Quantifying the Role of Nucleic Acids

This study quantifies how nucleic acids influence liquid-liquid phase separation by analyzing oligonucleotide systems with varying properties and peptide interactions.

LENG8 mediates RNA nuclear retention and degradation in eukaryotes

This study identifies LENG8 as a conserved RNA nuclear retention factor that prevents misprocessed mRNAs and noncoding RNAs from being exported, ensuring proper nuclear quality control.

Inverted Alu repeats in loop-out exon skipping across hominoid evolution

The paper identifies inverted Alu pairs that promote exon skipping through RNA stem-loop structures and shows their evolutionary significance in hominoid genomes.

Coordination of sequential RNase activities in an ancient molecular machine

The paper studies the evolution of the RNA exosome, showing how an ancient active RNase evolved into a regulatory hub coordinating sequential RNase activities.

A linguistics-based algorithm for RBP motif and context discovery

This paper introduces a linguistics-based algorithm for discovering RNA-binding protein motifs and their sequence contexts, showing improved accuracy over existing methods.

Comparative analysis of wavelength-specific UV stress granule formation

This study compares UV-induced stress granule formation across UVA, UVB, and UVC in three cell types, finding cell-type specificity and lack of oxidative stress involvement.

Muscle LIM Protein is a Non-Canonical RNA-Binding Protein that Engages in RNA-Dependent Cytoskeletal Assemblies

This study identifies MLP as a non-canonical RNA-binding protein in cardiomyocytes and shows its RNA-dependent interaction with cytoskeletal complexes.

Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer progression

The paper uses long-read RNA sequencing to analyze isoform diversity in ovarian cancer, identifying key isoform-level changes associated with disease progression and clinical outcomes.

Rapid reversible RNA isoform switching during loss and recovery of turgor in Arabidopsis thaliana

The paper identifies rapid reversible RNA isoform switching in Arabidopsis thaliana during water deficit and recovery, revealing new protein products and mechanisms of stress response.

Molecular mechanism of coilin interaction with core snRNPs

The paper identifies the molecular mechanism by which coilin distinguishes mature from immature snRNPs through its C-terminus containing an RNA-binding region and a Tudor-like domain that interacts with Sm proteins.

Exon inclusion signatures enable accurate estimation of splicing factor activity

The paper estimates splicing factor activity from exon inclusion changes, identifying cancer-related splicing programs and their association with patient survival and cancer hallmarks.

Conservation of extended sequence and structure in the branchpoint-to-3' splice site region upstream of neural microexons

The paper investigates sequence and structural features of neural microexons in humans and chickens, showing dynamic regulation and structural accessibility in the branchpoint-to-3' splice site region.

Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer

The paper identifies a metastasis-suppressive regulatory axis involving RBMS3 and TXNIP by analyzing mRNA stability in breast cancer using a deep-learning framework.

Arc Capsids Facilitate the Transfer of Muscleblind.

This paper shows Arc interacts with Mbnl1 RNA in a neuronal activity-dependent manner, facilitating transsynaptic transfer of Mbnl1 RNA through extracellular vesicles in Drosophila and mammals.

Heat stress-induced condensation of G3BP1 in perinuclear P-bodies in C. elegans' germline

This study investigates the role of GTBP-1 in heat stress response in C. elegans germline, showing its involvement in stress granule formation and reproductive homeostasis.

Alternative 3' Polyadenylation Responses to Acute Ethanol Exposure Differ Between Drosophila Populations

The paper identifies population-specific alternative polyadenylation (APA) responses to acute ethanol exposure in Drosophila melanogaster, showing genotype- and population-dependent shifts in 3' UTR length.

Analysis of genes co-evolved with Igf2bp RNA-Binding Proteins provides insights into post-transcriptional regulatory networks

This paper reviews the evolutionary analysis of genes coevolved with Igf2bp proteins, highlighting their roles in neural development and cancer.

The Kinetic Intron Hypothesis

The paper proposes the Kinetic Intron Hypothesis to model intron length by exploring hypothetical dynamics of intron RNA synthesis and degradation, presenting preliminary data on novel intron characteristics.

Splicing Isoforms Associated to TGFb-Induced Myofibroblast Activation

The paper identifies 5 alternative splicing events associated with TGFβ-induced myofibroblast activation using RNA-Seq and validates them in independent datasets.

Exercise modulation of the alternative splicing landscape in human tissues

This study examines how acute endurance and resistance exercise alter alternative splicing in human skeletal muscle, adipose tissue, and blood, identifying 5102 differential splicing events and their regulatory mechanisms.

RNA G-quadruplexes mediate cooperativity in HNRNPH binding and splicing regulation

The paper investigates how RNA G-quadruplexes enable cooperative binding of HNRNPH and regulate splicing, showing clinical relevance in breast cancer.

Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles

The paper shows that MALAT1 long noncoding RNA forms condensates with splicing factors to regulate hypoxia-induced alternative splicing near nuclear speckles.

RNA-specific local translation is patterned by condensates for multinucleate cell growth

The paper shows that Whi3 condensates regulate local translation in syncytial fungi, linking condensate composition and RNA features to spatially patterned translation during cell growth.