RNA Research and Splicing

Mapping NMD-coupled alternative splicing in iPSC-derived brain cells: a resource for therapeutic discovery

The paper maps NMD-coupled alternative splicing events in iPSC-derived brain cells and identifies therapeutic targets for neurodevelopmental disorders.

dirCLIP profiles variant-specific RNA-protein interactions via nanopore long-read sequencing

dirCLIP uses nanopore sequencing to profile variant-specific RNA-protein interactions, revealing isoform-selective binding and co-occurring sites with high concordance to short-read data.

BCLAF1 links RNA splicing to ATF4-dependent metabolic adaptation in acute myeloid leukemia

This study identifies BCLAF1 as a regulator linking RNA splicing to ATF4-dependent metabolic adaptation in AML, showing its role in sustaining leukemic cell survival and sensitivity to venetoclax.

Blocky proline/glutamine patterns in the SFPQ intrinsically disordered region dictate paraspeckle formation as a distinct membraneless organelle

The paper identifies blocky proline/glutamine patterns in the SFPQ IDR as essential for paraspeckle formation and segregation from nuclear speckles through phase separation.

Splicing regulation and intron evolution in the short-intron ciliate model of endosymbiosis Paramecium bursaria

This study investigates splicing regulation and intron evolution in Paramecium bursaria during endosymbiosis, finding that splicing enhances gene expression and older introns evolve toward shorter lengths and lower GC content for efficient splicing.

PCLIPtools: A Robust Framework for Identifying RNA-Protein Interaction Sites from PAR-CLIP experiments.

PCLIPtools improves PAR-CLIP data analysis by identifying high-confidence RNA-protein interaction sites with greater precision and speed than existing tools.

Sequence models conditioned on splicing factor expression predict splicing in unseen tissues

Splice Ninja predicts tissue-specific splicing events using splicing factor expression, achieving accurate results on unseen tissues.

Two components of the early ASH1 mRNA transport machinery undergo PUN motif-dependent liquid-liquid-phase separation

The paper shows that Loc1p and She2p undergo PUN motif-dependent liquid-liquid-phase separation, which is essential for early ASH1 mRNA transport.

Programmed Double-stranded RNA Formation Enables Meiotic Stage Transitions

The paper identifies dsRNA formation and NATs as a mechanism for selective mRNA clearance during meiosis, driven by transcription factors like Ndt80p.

Coacervate Droplets as a Liquefier for the Solid-to-Liquid Transition of RNA Aggregates

This paper demonstrates that coacervate droplets can reverse solid RNA-peptide aggregates into functional liquid droplets, offering a method to manage pathological aggregation.

SF3B1 Phosphorylation Prompts U2AF2 Dissociation for Widespread Control of pre-mRNA Splicing

This study shows SF3B1 phosphorylation reduces its binding to U2AF2, enabling widespread control of pre-mRNA splicing by promoting U2AF2 dissociation.

Common tissue-specific expressions and regulatory mechanisms of c-KIT isoforms with and without GNNK and GNSK sequences across five mammals

The paper analyzes c-KIT isoform expression across five mammals, finding conserved tissue-specific patterns and identifying regulatory factors for alternative splicing.

Variant-resolved prediction of context-specific isoform variation with a graph-based attention model

Otari predicts tissue-specific isoform abundance changes caused by genetic variants using a graph-based attention model trained on genomic and long-read transcriptome data.

Elevated levels of intracellular RNA lariats suppress the antiviral response

The paper shows that accumulation of intracellular RNA lariats in DBR1-null cells reduces antiviral response by desensitizing dsRNA sensors.

A High-Throughput, Flow Cytometry Approach to Measure Phase Behavior and Exchange in Biomolecular Condensates

This study develops a flow cytometry method to measure biomolecular condensate formation, colocalization, and exchange dynamics, revealing that condensate aging reduces molecular dynamics.

DNA-binding and dimerization of the SOG1 NAC domain are functionally linked with its ability to undergo liquid-liquid phase separation

This study shows that the SOG1 NAC domain can undergo liquid-liquid phase separation in vitro, dependent on DNA/RNA binding and dimerization.

Sarcomeric Remodelling in Human Heart Failure unraveled by single molecule long read sequencing

The paper uses single molecule long-read sequencing to analyze transcriptomes in heart failure patients and controls, identifying novel isoforms and convergent isoform changes across different cardiomyopathy types.

Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO

This paper reports covalent ligands targeting the RNA-binding protein NONO, showing they stabilize mRNA interactions, remodel transcriptomes, and suppress cancer cell growth with high specificity.

Comprehensive analysis of nonsense-mediated mRNA decay targets and activity in cardiomyocytes

The paper identifies NMD targets and activity in cardiomyocytes using SMG1 inhibition and RNA sequencing, showing conserved targets and reduced efficiency with UPF1/UPF2 knockdown.

Held out wings RNA binding activity in the cytoplasm during early spermatogenesis

This study identifies RNA-binding targets of the HOW(S) protein in Drosophila spermatogenesis using RIP-seq, revealing novel transcripts and motif preferences.

A Yeast-Based High-Throughput Screening Platform for the Discovery of Novel pre-mRNA Splicing Modulators

This paper develops a yeast-based high-throughput screening platform to identify small molecules modulating pre-mRNA splicing, identifying 4 compounds and showing one affects splicing in cancer cells with a splicing factor mutation.

Dilated cardiomyopathy-associated RNA Binding Motif Protein 20 regulates long pre-mRNAs in neurons

This study identifies RBM20 as a neuronal RNA-binding protein that regulates long pre-mRNAs, impacting synaptic protein expression and linking heart disease risk to neuronal function.

Lysine acetylation facilitates competitive recruitment of translation termination factor eRF3a by PABPC1 C-terminal domain

This study shows that acetylation of PABPC1 at K606 enhances its affinity for eRF3a, promoting competitive recruitment and modulating mRNA fate.

Mapping of CELF1-RNA interactions reveals post-transcriptional control of lens development

The paper maps CELF1-RNA interactions in mice lenses, showing CELF1 represses target mRNAs to regulate lens development and prevent cataracts.

Mitochondrial hitch-hiking of Mapt mRNA maintains Tau levels in axons

The paper identifies mitochondrial transport of MAPT mRNA via SYNJ2a/SYNJ2BP complex and shows its role in maintaining Tau levels and axonal growth in glutamatergic neurons.

Transient pH changes drive vacuole formation in enzyme-polymer condensates

This study investigates how transient pH changes induce vacuole formation in enzyme-polymer condensates using an in vitro model.

An elevated level of the mRNA exporter Mex67-Mtr2 in nuclear mRNPs impairs nuclear mRNA export

The paper shows that excess Mex67-Mtr2 in nuclear mRNPs impairs mRNA export, and overexpression of Nab2 or Yra1 suppresses this defect by reducing Mex67 levels.

LOTUS-domain proteins activate Vasa to drive germ granule assembly

This study identifies LOTUS-domain proteins as catalysts for Vasa activity in germ granule assembly across species, showing their role in recruiting Vasa and enhancing RNA binding.

Molecular Basis and Cellular Effects of Janus-Class-Driven Cytoplasmic PYK2 Coacervates

This study identifies a novel mechanism of phase separation driven by the Janus-class KFL region of PYK2, showing its role in kinase activation and cell adhesion.

Targeting EZH2 Oncogenic Splicing: Decoding the Regulatory Network and Antisense Correction

This study identifies splicing dysregulation in SF-mutated cancers and demonstrates that antisense oligonucleotides can correct aberrant splicing and restore tumor suppressor function.