RNA Research and Splicing

Detection of a sequence feature for recursive splicing

The paper identifies sequence features associated with recursive splicing and develops a classifier to detect these features.

Biomolecular condensates provide a unique environment for redox-mediated protein crosslinking

This study shows that fluorescently tagged proteins in biomolecular condensates undergo crosslinking due to excitation-induced ROS, leading to condensate solidification and highlighting redox regulation of condensate properties.

Repurposed hnRNPC binds mature mRNAs and safeguards the mitotic transcriptome

This study identifies two hnRNPC-RNP populations in mitotic cells and shows hnRNPC binds mature mRNAs, stabilizing the mitotic transcriptome.

Endosomal hitchhiking and NDR kinase signaling coordinate SsdA-mRNP localization

This study identifies SsdA-mRNP localization in Aspergillus nidulans hyphae as dependent on endosomal hitchhiking and NDR kinase signaling, revealing spatial regulation during polarized growth.

TREX2 component PCID2 scaffolds alternative SAC3-based subcomplexes with distinct RNA processing and export function

The paper identifies novel SAC3-based subcomplexes of the TREX2 complex, revealing distinct RNA processing and export functions through interactions with PCID2 and other subunits.

Emergence of rigidity percolation and critical behavior in tunable protein condensates

This study investigates how protein condensates transition from liquid-like to networked states through tunable interactions, revealing critical behavior and percolation transitions linked to biological function.

Premature cleavage and polyadenylation in the minor intron of PTEN modulate its expression and generates a functional long non-coding RNA in breast cancer

The paper identifies a novel mechanism where premature cleavage and polyadenylation of the minor intron in PTEN generates a functional lncRNA, PINC, which modulates cellular proliferation in breast cancer.

Machine Learning Models Reveal the Role of Ionization-Dependent Partitioning in Condensate Formation

The paper uses machine learning to show that ionization-dependent partitioning, captured by logD, is key to predicting small molecule behavior in biomolecular condensates.

snoFlake: A network model for snoRNA-RBP complexes reveals SNORD22 as a U5 snRNP-associated splicing regulator

snoFlake identifies snoRNA-RBP complexes and reveals SNORD22 as a splicing regulator by interacting with U5 snRNP components.

AI-Driven Reconstruction of the Research Paradigm for Phase Separation in Membraneless Organelle

This paper introduces an AI-driven paradigm to predict and analyze protein phase separation propensity, identifying novel membraneless organelle candidates through integration of physical mechanisms and machine learning.

Decoding Mutually Induced Conformational Changes in Non-Canonical Recognition of U1 SL4 snRNA by ULD of SF3A1 during Early Spliceosome Assembly

This study investigates the structural and dynamic basis of non-canonical recognition between SF3A1 ULD and U1 snRNA SL4 during spliceosome assembly, revealing dual recognition mechanisms and the impact of mutations on protein-RNA interactions.

ALTERNATIVE SPLICING OF A CODING GENE PRODUCES A NUCLEAR REGULATORY LONG NON-CODING RNA

The paper shows alternative splicing generates regulatory lncRNAs from protein-coding genes in Arabidopsis, forming autoregulatory RNA-protein feedback loops under dark conditions.

Nonsense mutations can increase mRNA levels

This study shows that nonsense mutations can increase mRNA levels in S. pombe, challenging the conventional understanding of NMD and its impact on transcript abundance.

Single-cell full-length transcriptome of human lung reveals genetic effects on isoform regulation beyond gene-level expression

The paper presents an isoform-level lung cell atlas using single-cell long-read RNA-sequencing, revealing genetic effects on isoform regulation that improve cell-type classification and identify novel variants associated with lung cancer risk.

Autoregulation of three yeast ribosomal protein genes by splicing inhibition

The paper shows that splicing inhibition autoregulates three yeast ribosomal protein genes by inserting introns into GFP and observing repression.

UFMylation anchors splicing factors at the ER to reprogram nuclear splicing

The paper identifies a retrograde signaling pathway where UFMylation of ER ribosomes anchors splicing factors at the ER, linking translational stress to nuclear RNA processing and altering membrane-associated gene expression.

Localization-dependent activation of the DEAD-box ATPase Vasa by eLOTUS domains

This study identifies how eLOTUS domains activate Vasa by promoting its RNA and ATP binding through a charged disordered sequence, revealing a localization-dependent regulatory mechanism.

Beyond gene length: Exon-intron architecture and isoform potential in the evolution of eukaryotic complexity

The paper shows that exon count increases beyond a certain point in eukaryotic evolution and saturates at ~10 exons per gene, suggesting it contributes to genomic complexity.

Novel examples of NMD escape through alternative intronic polyadenylation

The paper identifies NMD escape through alternative intronic polyadenylation by analyzing GTEx data and demonstrates tissue-specific isoform switches in several genes.

Kinetic logic of uridylation-mediated RNA decay

This study investigates how uridylation mediates RNA decay in Drosophila by showing how Tailor generates oligo(U) intermediates and how Dis3l2 decodes these to initiate decay.

The tumour suppressor RBM5 activates the helicase DHX15 to regulate splicing

This study identifies RBM5's role in regulating splicing by activating DHX15 and blocking spliceosome progression, with implications for cancer-related splicing dysregulation.

Microenvironmental Determinants of Reaction Kinetics in Biomolecular Condensates Probed with Protein Ligation

The paper investigates how the microenvironment within biomolecular condensates affects reaction kinetics using protein ligation as a model, identifying effective concentration, hydrophilicity, and water activity as key factors.

Quantitative prediction of nonsense-mediated mRNA decay across human genes by genomic language model and large-scale mutational scanning

The paper develops a model to predict nonsense-mediated mRNA decay (NMD) across human genes using genomic data and mutational scanning, showing improved accuracy and revealing quantitative rules of NMD implementation.

Cellular fitness is determined by ribosomal protein S12-mediated release of a truncated Xrp1

The paper identifies a post-transcriptional mechanism where ribosomal protein S12 regulates Xrp1 expression through alternative splicing, leading to cell death in unfit cells.

FUS and TAF15 safeguard the critical functions of the ribonucleoprotein network formed by EWSR1 and newly synthesized RNA

This study shows that EWSR1 forms a ribonucleoprotein network with nascent RNA, and its loss leads to compensatory reorganization of FUS and TAF15, revealing functional redundancy in maintaining nascent RNA homeostasis.

Intron Retention Controls Localization of lncRNAs PURPL and MALAT1 to Promote Cell Proliferation and Migration

The paper identifies U2AF2's role in intron retention of lncRNAs PURPL and MALAT1, showing how this process affects their localization and promotes cell proliferation and migration.

Nuclear Speckle Dynamics are Controlled by Polyphosphate Inhibition of CLK Proteins

This study identifies polyphosphate as a regulator of nuclear speckle dynamics by inhibiting CLK3 kinase, affecting splicing factor organization and RNA splicing.

ER tethering and active transport govern condensate diffusion during hyperosmotic stress

The paper uses live-cell tracking to show that hyperosmotic stress causes HOPS condensates to exhibit sub-diffusion due to ER tethering and super-diffusion via microtubule transport.

Nuclear speckle protein SON safeguards efficient splicing of GC-rich genes

This study identifies SON as a critical factor for splicing GC-rich genes, showing its role in stabilizing weak splice sites and enhancing gene expression efficiency.

Nascent transcripts of LL2R tandem repeat nucleate locus-specific RNP condensates recruiting splicing factors

The paper identifies LL2R tandem repeats in chicken that form RNP condensates by recruiting splicing factors, revealing their role in nuclear compartment formation.