RNA Research and Splicing

Nanos downregulates maternal mRNAs in germline during Drosophila early embryogenesis

The paper identifies maternal mRNAs downregulated by Nanos in Drosophila PGCs at the blastoderm stage, prior to zygotic genome activation.

SLBP-independent control of maternal histone mRNA

The paper identifies an SLBP-independent mechanism for maintaining maternal histone mRNA stability in C. elegans oogenesis, mediated by the PETISCO complex and TOST-1.

NORAD orchestrates KLC1-mediated SFPQ transport via liquid-liquid phase separation

This study identifies NORAD as a regulator of axonal transport through liquid-liquid phase separation, showing its role in SFPQ transport and neuronal function.

Aging-associated alternative splicing programs conserved between human and mouse tissues

The paper identifies aging-associated alternative splicing programs in human and mouse tissues using scRNA-seq and introduces LeafletFA for discovering coordinated splicing programs.

GLA-3 Mediates Stress Response in Caenorhabditis elegans Germ Cells: A key role of the Tristetraprolin (TTP) Family

This study investigates the role of GLA-3, a TTP homolog in C. elegans, in stress response and germ cell function, showing its importance in stress granule formation and germ cell survival.

Parallel ZNF598 and GIGYF2 pathways mediate conserved collision-dependent mRNA decay with distinct endonucleolytic features

The paper shows that two pathways, ZNF598 and GIGYF2, mediate mRNA decay due to ribosome collisions in yeast and mammals, with distinct endonucleolytic features.

A reaction-diffusion model captures the essence of liquid-liquid phase separation

This paper develops a reaction-diffusion model to simulate liquid-liquid phase separation, showing how diffusivity and interactions affect droplet formation and stability.

Human Messenger RNA Harbors Widespread Noncoding Splice Isoforms

The paper identifies 15,836 noncoding splice isoforms in human mRNA from 7,298 protein-coding genes, showing tissue-specific expression and association with cancer.

metaAPA: a tool for integration of PolyA site predictions from single-cell and spatial transcriptomics

metaAPA integrates polyA site predictions from multiple tools to provide high-confidence and subset-supported sites for single-cell and spatial transcriptomics data.

Alternative splicing in pediatric central nervous system tumors highlights oncofetal candidate CLK1 exon 4

The paper analyzes splicing in 729 pediatric brain tumors, identifies splicing-defined subgroups, and highlights CLK1 exon 4 as an oncofetal event linked to tumor prognosis.

Nonequilibrium phases of a biomolecular condensate facilitated by enzyme activity

The paper investigates how DEAD-box helicase activity influences the dynamic behavior of RNA-based biomolecular condensates through nonequilibrium mechanisms.

Alternative splicing dynamics during human cardiac development in vivo and in vitro

This study maps alternative splicing dynamics during human cardiac development and identifies splicing markers in iPSC-derived cardiomyocytes, revealing both similarities and differences with native cardiac splicing patterns.

The apoptosis gene BCL-X splice isoforms have opposing effects in diabetic kidney disease: potential treatment target and prognostic value

The paper investigates the role of BCL-X splice isoforms in diabetic kidney disease, finding that increased BCL-XS promotes apoptosis and correlates with renal function decline, suggesting it as a biomarker and therapeutic target.

Exploiting the polypharmacology of alectinib for synergistic RNA splicing disruption with RBM39 degraders

This paper combines RBM39 degradation and SRPK1 inhibition to disrupt RNA splicing in neuroblastoma, showing synergistic anti-cancer effects in cell lines and a mouse model.

DDX3X syndrome mutations lock DDX3X-RNA conformational states to drive persistent pathological condensation and neuronal death

This paper shows that DDX3X syndrome mutations cause solid-like stress granules and neuronal death by altering DDX3X-RNA conformation.

A filamentous scaffold for gene regulation

The paper determines the structure of a filamentous NONO/SFPQ heterooligomer using cryo-EM, revealing its organization and functional differences between the components.

RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria

The paper introduces CRASP-Seq, a method to identify gene regulators of alternative splicing, and finds ZNF207 regulates LMNA splicing in progeria by interacting with U1 snRNP.

CrosSplice: A Pipeline for Identifying Rare Splice-Site Creating Variants from Cross-Tissue Transcriptome Data

CrosSplice identifies rare splice-site creating variants using cross-tissue transcriptome data, discovering clinically relevant variants missed by conventional methods.

SF3A2 deacetylation at lysin 10 mitigates myocardial pathological remodeling by reprogramming cardiomyocyte metabolism

This study shows that SF3A2 deacetylation at K10 reduces myocardial remodeling by altering cardiomyocyte metabolism, including glucose and fatty acid metabolism.

Single-cell alternative polyadenylation analysis reveals mechanistic insights of COVID-19-associated neurological and psychiatric effects

The paper analyzes single-cell alternative polyadenylation (APA) in frontal cortex cells from COVID-19 patients and controls, identifying APA changes linked to neurological and psychiatric sequelae.

Hollow condensates emerge from gelation-induced spinodal decomposition

The paper investigates the formation of hollow biomolecular condensates driven by gelation-induced spinodal decomposition using a phase-field model.

Absence of MBP 3' UTR in Mice Disrupts mRNA Transport, Myelination, and Motor Learning

Enzyme-driven phase separation of synthetic condensates enables self-organizing compartments and protective microenvironments

The paper shows how coupling enzymatic reactions to phase separation creates self-regulating compartments that modulate mRNA stability and levels.

Alternative splicing contributes to plasticity and regulatory divergence in locally adapted house mice from the Americas

This study examines alternative splicing variation in house mice from different climates, showing its role in adaptation and plasticity through diet-dependent gene regulation.

SF3B1K700E rewires splicing of cell-cycle regulators

The paper identifies SF3B1K700E-induced splicing changes in K562 cells that affect cell cycle regulators, with functional consequences in mitosis and cancer survival.

Genomic stop codon scanning reveals quantitative principles of nonsense-mediated mRNA decay

The paper quantitatively analyzes NMD activity for various PTCs in the LMNA gene, revealing new positional and sequence context dependencies beyond existing binary rules.

Transcription-dependent phase coexistence of mitochondrial nucleoids and RNA granules

This study shows that active mitochondrial transcription sustains phase coexistence between mt-nucleoids and mtRNA granules through nascent RNA.

Transcripts of vaccinia virus postreplicative genes do not contain a 5' methylguanosine cap

The paper shows that vaccinia virus postreplicative mRNAs lack a 5' methylguanosine cap and have nontemplated poly(A) leaders, controlled by promoter sequences.

RNA secondary structures modulate hnRNPH1-mediated alternative splicing of cold-shock protein RBM3

This study identifies RNA G-quadruplex remodelling as the key mechanism by which temperature modulates hnRNPH1-mediated alternative splicing of RBM3.

Conserved RNA helicase Vasa regulates ribonucleoprotein condensates through protein interaction and mRNA recruitment

This study investigates the role of Vasa in regulating Oskar condensate material properties through protein and mRNA interactions in germ granules.