RNA Research and Splicing

Human Kidney Alternative Splicing Information Illuminates Cardiovascular-Kidney-Metabolic Syndrome Risk

The paper identifies splicing variants in human kidney tissue associated with kidney function and cardiovascular-kidney-metabolic syndrome traits using long-read RNA sequencing and QTL analysis.

BAV-LLPS: A database of bacterial, archaea and virus liquid-liquid phase separation proteins

The paper introduces BAV-LLPS, a database of LLPS proteins from bacteria, archaea, and viruses, containing over 5,000 proteins with annotations and structural models.

OLIGONUCLEOTIDES TARGETING THE SPLICE ACCEPTOR SITE DOWNSTREAM OF A MICROEXON AS AN INNOVATIVE THERAPY FOR AUTISM

The paper demonstrates that splice-switching antisense oligonucleotides (SSOs) targeting the downstream splice acceptor site of a microexon can modulate microexon inclusion and restore protein levels of ASD risk genes.

Structural and mechanistic insights into Dis3L2 mediated degradation of structured RNA

This study investigates the structural and mechanistic role of Dis3L2 in RNA degradation, identifying a critical residue involved in double-stranded RNA processing.

SpliceDecoder: A High-Throughput Tool for Guiding the Functional Interpretation of Differential Splicing Events

SpliceDecoder prioritizes biologically meaningful splicing events by predicting their impact on transcript productivity, protein sequence, and functional domains.

Amino acids bind to phase-separating proteins and modulate biomolecular condensate stability and dynamics

The paper investigates how amino acids interact with phase-separating proteins to modulate biomolecular condensate stability and dynamics.

Alternative splicing fine-tunes modular protein interfaces to control protein localisation

This study shows that alternative splicing modulates protein interfaces to control localization by altering exon structure and charge distribution.

MntJULiP and Jutils: Differential splicing analysis of RNA-seq data with covariates

The paper introduces MntJULiP and Jutils for differential splicing analysis of RNA-seq data, incorporating covariates to identify age and sex-related splicing patterns in GTEx brain samples.

Ribonucleoprotein (RNP) condensates modulate survival in response to Mars-like stress conditions

This study shows that RNP condensates in yeast help survive Mars-like stress conditions, including shock waves and perchlorate, by forming P-bodies and modulating gene expression.

CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing

CAR-SPLASH identifies RNA kinetic switches that regulate alternative splicing based on transcription speed, with potential therapeutic applications using antisense oligonucleotides.

Coordination of nuclear RNA processing by speckle-localized kinase TAOK2

This study identifies TAOK2 as a kinase that regulates splicing and export of both viral and cellular transcripts by phosphorylating SRRM1/2, maintaining nuclear speckle structure and function.

Vitamin B12 alleviates Verheij syndrome-like defects via phospholipid remodeling in a C. elegans PUF60 spliceosomopathy model

This study identifies vitamin B12 as a suppressor of Verheij syndrome-like defects in a C. elegans PUF60 model by restoring metabolic balance and splicing.

Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals

The paper quantifies NMD efficiency across human tissues and individuals, identifies tissue-specific and inter-individual variability, and links NMD efficiency to genetic factors and clinical outcomes.

An SR45-dependent exonic splicing enhancer is essential for regulating alternative splicing in Arabidopsis

The paper identifies an SR45-dependent exonic splicing enhancer essential for regulating alternative splicing in Arabidopsis, showing its role in intron splicing efficiency and phenotypic rescue.

RNA-binding proteins provide specificity to the PAN2-PAN3 mRNA deadenylation complex

This study shows that the PAN2-PAN3 deadenylation complex can be recruited to specific mRNAs via RNA adaptors, adding to the specificity of mRNA degradation.

Cataloging the potential functional diversity of Cacna1e splice variants using long-read sequencing

The paper uses long-read sequencing to catalog Cacna1e splice variants in rat thalamus and computationally identifies four functionally distinct isoforms.

The DND1-NANOS3 complex shapes the primordial germ cell transcriptome via a heptanucleotide sequence in mRNA 3'UTRs

The paper identifies an RNA sequence motif recognized by the DND1-NANOS3 complex in germ cells and shows its role in regulating mRNA expression.

Mapping genetic effects on splicing in ten thousand post-mortem brain samples reveals novel mediators of neurological disease risk

The paper maps genetic effects on splicing in 10,725 brain samples, identifying 68,358 cis-sQTLs and 97 loci where splicing mediates neurological disease risk.

NQO1 phase condensation promotes stress granule assembly to facilitate pancreatic carcinogenesis

This study identifies NQO1's role in promoting stress granule assembly via phase separation to drive pancreatic carcinogenesis, independent of ROS.

Defining the roles of the Integrator, NEXT, and nuclear exosome complexes in Drosophila oogenesis

This study identifies the essential role of Integrator, NEXT, and nuclear exosome complexes in Drosophila oogenesis by showing their necessity for RNA degradation and preventing aberrant RNA accumulation.

eIF4E assembly into C. elegans germ granules is essential for its repressive function

The paper shows that IFE-1 assembly into P granules is essential for its repressive function in C. elegans germ cells.

Mutual homeostasis of charged proteins

The paper identifies a homeostatic mechanism called interstasis that co-regulates the dosage of proteins with low complexity domains through RNA-based negative feedback.

Determining off-target effects of splice-switching antisense oligonucleotides using short read RNAseq in neuronally differentiated human induced pluripotent stem cells

This study uses RNAseq to assess off-target effects of three splice-switching AONs in human cells, identifying splicing changes and showing variability in AON-induced effects.

Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain

The paper uses long-read sequencing to identify novel RNA isoforms in neuropsychiatric risk genes, revealing previously undetected exons and isoforms that may contribute to disease mechanisms.

Angel Wing: a class of alternative splicing regulators in animals

This study identifies Angel wing (Anw) as an alternative splicing regulator, showing its role in muscle function and disease relevance in humans.

SpliceUp: Predicting SF3B1 mutations in individual cells via aberrant splice site activation from scRNA-seq data

SpliceUp detects SF3B1-mutant cells in scRNA-seq data by analyzing aberrant splicing signatures, improving detection from low-coverage datasets.

Investigating Amino acid Enrichments and Patterns in Phase-Separating Proteins: Understanding Biases in Liquid-Liquid Phase Separation

The paper identifies enriched peptide motifs in phase-separating proteins and validates their role in LLPS through computational analysis and experimental testing.

Transcriptome-wide outlier approach identifies individuals with minor spliceopathies

The paper identifies individuals with minor spliceopathies by analyzing transcriptome-wide splicing outliers in RNA-seq data from rare disease cohorts.

Biobank-scale Bayesian TWAS reveals splicing-mediated mechanisms of complex disease

The paper uses Bayesian TWAS to identify splicing-disease associations across multiple cohorts, revealing causal mechanisms in immune, vascular, and metabolic traits.

Predicting Saturation Concentrations of Phase-Separating Proteins via Thermodynamic Integration

This paper introduces two thermodynamic integration schemes to accurately calculate saturation concentrations of phase-separating proteins in simulations, enabling comparison with experimental data.