RNA Research and Splicing

phyloDS: phylogeny-aware differential splicing across species, beyond reference annotations

phyloDS identifies differentially used orthologous splice junctions across species by improving orthology definition, statistical testing, and sequence-level validation.

Targeting CLK1 by CRISPR tools and pharmacological inhibition modulates the innate immune response and dengue virus replication

The paper shows that CLK1 inhibition enhances antiviral defenses against dengue virus by boosting IFN-stimulated gene expression and reducing viral replication.

A unified framework for quantitative splicing and transcript prediction

This paper introduces SpliceAI2, a deep learning model that improves identification and quantification of splice-altering variants and their effects on transcripts and disease.

IsoGraph resolves coordinated transcript choice and gene abundance in the aging human brain

IsoGraph identifies age-associated transcript-usage signals in human brain transcriptomes, distinguishing them from gene abundance and cellular composition effects.

Non-equilibrium modeling of flux through biomolecular condensates

This study introduces TRACE, a computational model to simulate molecular transport through biomolecular condensates, revealing how sequence composition, molecule stiffness, and host-guest interactions influence flux.

Probing Genomic Foundation Models with Splice-Variant Perturbations

This paper evaluates genomic foundation models using splice-variant perturbations, finding they match task-specific networks and generalize across mutation types.

Fine-tuning genomic models on rare splicing events identifies a novel biomarker of TDP-43 pathology

Direct monitoring of unfolded nascent polypeptides by the CCR4-NOT complex contributes to protein quality control through selective mRNA deadenylation and decay

The paper identifies the role of the CCR4-NOT complex in recognizing unfolded nascent polypeptides and triggering mRNA deadenylation and decay to maintain protein quality control in yeast.

MDS-causing mutations of ZRSR2 impair minor intron splicing by reducing its interaction with SF3B complex

Blockiness as Determinant of Liquid Phase Formation by Polypeptide-Like Polymers in Stickers-Spacers Paradigm

This study shows how sequence blockiness affects liquid-liquid phase separation in polypeptide-like polymers through coarse-grained simulations and mean-field theory.

Pumilio proteins license viral noncoding RNA engagement with target mRNAs

The paper identifies PUM1 and PUM2 as cofactors for viral noncoding RNAs HSUR1 and HSUR2 in mRNA repression, showing PUM binding is required for productive HSUR-mRNA engagement.

The Spliceosome Scaffold Component BCAS2 Promotes Pancreatic Cancer Progression through Weak 5 Splice Site Dependent Splicing Regulation

This study identifies BCAS2 as a critical regulator of PDAC progression by promoting alternative splicing of weak 5' splice sites, specifically enhancing SOS1 exon 21 inclusion and RAC-signaling activation.

RNA synthesis and degradation regulate biomolecular condensates through non-equilibrium feedback

This study shows RNA synthesis and degradation dynamically regulate transcriptional condensates through non-equilibrium feedback, affecting their composition and stability.

Exitron-type splicing of intrinsically disordered regions recurs across jawed vertebrates despite sequence divergence: donor-proximal cis control in TARDBP

The paper identifies exitron-type splicing events in IDR-coding sequences across jawed vertebrates, showing donor-proximal cis control in TARDBP despite sequence divergence.

RBFOX2 restrains oncogenic cell plasticity in Group 3 medulloblastoma

This study identifies RBFOX2 as a suppressor of oncogenic cell plasticity in Group 3 medulloblastoma by regulating alternative splicing and cytoskeletal dynamics.

Cajal bodies shape the nuclear transcriptome, intron retention and transcripts redistribution in Arabidopsis roots under hypoxia

This study shows that Cajal bodies in Arabidopsis roots regulate transcript retention and processing during hypoxia, affecting gene expression and stress tolerance.

nHOTAIRM1 scaffolds ANXA11-dependent assemblies to drive axonal mRNA localization in human motor neurons

This study identifies nHOTAIRM1's role in axonal mRNA localization by scaffolding ANXA11-dependent transport assemblies in human motor neurons.

S. cerevisiae Cwc15p Tunes the Spliceosome Active Site for Remodeling and Catalysis

This study investigates the role of Cwc15p in S. cerevisiae splicing, finding it stabilizes and facilitates structural transitions of the spliceosome active site, important for splicing under nonoptimal conditions.

Global Regulatory Functions of the Human CCR4-NOT Complex in mRNA Deadenylation and Decay

The paper identifies the regulatory roles of the CCR4-NOT complex in mRNA deadenylation and decay by analyzing transcriptome-wide effects of subunit depletion.

Post-transcriptional dysregulation precedes morphological transformation in chemically induced liver cancer

The paper identifies post-transcriptional changes in liver tissue before morphological transformation in chemically induced cancer.

Phosphorylation tunes electrostatically driven protein-RNA interactions

This study quantifies how phosphorylation modulates electrostatic interactions between charged IDPs and RNA, showing that phosphorylation reduces binding affinity linearly with net charge.

Long-range transport of biomolecular condensates by Marangoni effect

The paper identifies the Marangoni effect as a mechanism for intracellular transport of biomolecular condensates using C. elegans zygotes and in vitro experiments.

Sequential Design of Experiments enables accessible and efficient multidimensional mapping of single- and multi-protein condensates

This paper introduces a sequential Design of Experiments framework to study multidimensional biomolecular condensation, revealing protein-specific interactions and context-dependent behaviors in RNA-binding condensates.

Temporal gating dictates stress-induced transcript export from the nucleus

The paper shows that transcription timing, not sequence features, determines nuclear export of stress-induced mRNAs in human cells.

A systematic delineation of 3' UTR regulatory elements and their contextual associations

The paper identifies 3'UTR regulatory elements using synthetic inserts and a deep learning model, revealing their effects on gene expression and nuclear-cytoplasmic partitioning, and highlights disease-relevant variants.

Stepwise Ligand Capture Primes PKR for Activation and RNA Discrimination

This study reveals how PKR's dsRBDs work together to enable selective RNA recognition and activation through a two-step ligand sampling mechanism.

RNA splicing factor mutations drive myeloid neoplasm oncogenesis through protein complex poisoning

This study identifies how RNA splicing factor mutations drive myeloid neoplasm by disrupting proteomic networks through mis-splicing, validated via single-cell transcriptomics and proteomics.

Synapsin-1 and actin form ordered nanoscale assemblies

This study investigates how synapsin-1 and actin form ordered nanoscale assemblies through phase separation, showing that actin scaffolds retain structural memory for condensate reformation.

A combinatorial pre-mRNP retention factor network couples nuclear speckle architecture to splicing quality control

The paper identifies a network of RNA-binding proteins that retain pre-mRNPs in nuclear speckles, linking splicing status to nuclear retention and speckle organization.

Pumilio and Brain tumor regulate the expression of Smaug during the Drosophila maternal-to-zygotic transition

This study shows that Pumilio and Brain tumor regulate Smaug mRNA degradation during the Drosophila maternal-to-zygotic transition, preventing ectopic Smaug protein expression and ensuring proper mRNA clearance.