376 papers
This study reveals that a mouse-specific retrotransposon drives developmentally regulated alternative transcription start site switching in the Ash2l gene to generate a truncated protein isoform, which primes developmental promoters via histone modifications to control embryogenesis and cell fate decisions.
This study demonstrates that medulloblastoma-associated mutations in the RNA helicase DDX3X/DED1 confer rapamycin resistance by selectively enhancing the translation of unstructured, pro-growth mRNAs while suppressing structured transcripts, thereby allowing tumor cells to bypass TORC1-mediated stress controls.
This paper introduces the NP-hard Maximum Agreement Secondary Structure (MASS) problem, which simultaneously clusters RNA secondary structures and identifies shared structural motifs, and provides exact algorithms and scalable heuristics that outperform existing methods by effectively summarizing structural diversity and conserved features in RNA ensembles.
This study employs an integrative structural dynamics approach to elucidate how the dual-role chromatin reader Cti6 and transcription factors Ash1 and Ume6 dynamically engage the Sin3 deacetylase complex, revealing competitive and defined assembly mechanisms that facilitate crosstalk between gene repression and activation.
Using a massively-parallel reporter assay and deep learning models in lung epithelial cells, this study identifies 29 severe COVID-19 risk variants that allele-specifically modulate enhancer activity, revealing their potential to alter gene expression and influence disease outcomes.
The paper introduces InvDNA, a deep learning framework that designs single-stranded DNA sequences directly from all-atom backbone coordinates, achieving over a twofold improvement in sequence recovery and a 44.4% success rate in folding into predefined conformations compared to existing methods.
This study reveals that during influenza infection, Myc expression in upper airway basal cells is essential not only for epithelial regeneration but also for orchestrating mucosal immunity by recruiting CD8+ NKT-like effector cells via a CXCL10-CXCR3 axis, thereby establishing basal cells as specialized sentinels that coordinate tissue repair and immune defense.
By applying a stochastic modeling framework to Tabula Muris Senis single-cell RNA sequencing data, this study quantifies mitochondrial DNA deletion dynamics in mouse limb muscle, revealing that rare mutation events followed by rapid clonal expansion drive accumulation over approximately three months, with specific gene disruptions influencing heteroplasmy levels.
This study characterizes the molecular epidemiology of Chikungunya virus outbreaks in Kenya from 2017 to 2020, revealing that Indian Ocean Lineage strains with fitness-enhancing mutations caused geographically distinct but related transmission clusters in Mombasa and Dadaab-Hagadera, while identifying specific clinical symptoms that can aid in differentiating Chikungunya from other acute febrile illnesses in resource-limited settings.
This study demonstrates that relocating a specific eight-amino acid "Z-appendage" variant from the collagen IV α3 chain to the α5 chain in Alport syndrome mice shifts the pathology from glomerular basement membrane defects to marked thickening of Bowman's capsule, thereby revealing a critical bioactive role for the collagen IV α565-α121 scaffold in maintaining the structural integrity of Bowman's capsule.
This study demonstrates that the phospholipid-binding protein Annexin A2 is essential for maintaining pulmonary surfactant function and preventing lung stiffness during injurious ventilation by regulating surfactant composition, specifically the levels of POPG, suggesting it as a potential therapeutic target for ARDS.
This study demonstrates that in Drosophila male cells lacking roX RNA, the failure of the dosage compensation complex to activate X-linked genes is bypassed by the rapid acquisition of extra X chromosomes, which restores the essential X-to-autosome expression ratio and viability.
This study demonstrates that circadian rhythms regulate macrophage responses to SARS-CoV-1 and SARS-CoV-2 spike proteins by driving time-dependent immunometabolic states characterized by central metabolic and mitochondrial changes rather than classical immune activation.
This study demonstrates that exposure to the PFAS compounds PFOA and GenX induces cell type-specific cytotoxicity and distinct perturbations in p53-mediated DNA damage response and TGF-β/SMAD inflammatory signaling pathways across human skin, liver, kidney, and colon cell lines, with GenX generally exhibiting lower toxicity than PFOA.
This paper introduces two novel platforms, scGOAT-seq and GlycoScope, which utilize human lectins to integrate functional glycan accessibility into single-cell and spatial multiomic profiling, thereby revealing stimulus-specific glycan remodeling and spatially resolved glycan programs in immune cells and follicular lymphoma that were previously undetectable by existing methods.
This study demonstrates that the evolutionarily conserved GTPase Drg1 localizes to the outer mitochondrial membrane to coordinate cytoplasmic translation with mitochondrial function, thereby ensuring mitochondrial integrity, dynamics, and energy production.
This study reveals that cancer-associated mutations in the TIP60 chromodomain allosterically disrupt its trimeric assembly and acetyl-CoA docking, thereby impairing histone acetyltransferase activity and the subsequent activation of DNA repair genes under genotoxic stress.
This study utilizes bioinformatic analysis of proteomic data from goat atrial tissue to reveal that atrial fibrillation triggers a coordinated mitochondrial adaptation involving oxidative phosphorylation enrichment and HSPA9-mediated regulation of respiratory chain complexes.
This study reveals that the R6K plasmid-encoded silencer Sfx selectively targets its own conjugal transfer operon by cooperating with the Rho factor to arrest transcription elongation and utilizing phase separation to form stable, competitor-resistant nucleoprotein filaments, thereby partitioning the genome into distinct regulatory niches.
This study demonstrates the potential of intraperitoneal vivo-morpholino injections for transient gene knockdown in adult threespine stickleback, achieving successful knockdown of the *Spi1b* gene in the spleen despite variable delivery efficiency across target organs.