multiome

A Minimal Synthetic Cleavage Module Enables Selective Degradation of Pathogenic r(CUG) Repeats in Cells

This study develops a synthetic cleavage module that selectively degrades pathogenic r(CUG) repeats in cells, reducing DM1-associated pathology without DNA damage.

Aging activates latent enhancers that can be reversed withexercise

This study identifies age-acquired enhancers in mouse hearts and shows that exercise can reverse their activation.

Integrated transcriptomic and epigenomic profiling of human cartilage reveals coordinated changes in fibronectin expression, splicing, and receptor signaling during osteoarthritis progression

This study profiles human cartilage across OA grades, revealing changes in fibronectin expression, splicing, and receptor signaling during disease progression.

Impact of RNA modification and IL-12 boosts on mRNA-LNP vaccine-elicited CD8+ T cell responses

This study compares CD8+ T cell and antibody responses in non-human primates using different ratios of modified and unmodified mRNA-LNP vaccines with IL-12 boosting.

Two closely related RNA helicases, UAP56 and URH49, couple mRNA splicing and export pathways with their distinct complexes

This study identifies three splicing regulation patterns mediated by UAP56 and URH49 and their association with mRNA export pathways.

Single-Nucleus Profiling Reveals Neuronal Metabolic Collapse During the Transition to Alzheimer's Disease Dementia

This study uses single-nucleus RNA-sequencing and multiome data to identify neuronal mitochondrial gene suppression as a driver of Alzheimer's dementia, revealing genetic and epigenetic mechanisms underlying cognitive resilience.

Multiplex-GCN Predicts Clinically Actionable Tumor Microenvironment Subtypes in Pancreatic Cancer

The paper develops a multi-layered GCN to identify TME-guided PDAC subtypes, revealing seven subtypes with distinct molecular and prognostic features.

Identification of gene kinetics patterns improves RNA velocity and cell fate prediction using JuloVelo

JuloVelo improves RNA velocity and cell fate prediction by incorporating gene kinetics patterns, outperforming existing methods across multiple differentiation programs.

The DGKK mRNA is a primary target of the Prader-Willi syndrome-associated snoRNA SNORD116

The paper identifies DGKK as the primary target of SNORD116, showing increased DGKK RNA and protein levels upon SNORD116 depletion in human and mouse models.

MINT Block: multivariate integration across independent studies to identify multi-omics signatures

MINT Block integrates multi-omics data across studies to identify generalisable signatures while accounting for study-specific variation, improving prediction accuracy.

Optimal transport reveals unresolved cells in single cell multi-omics

This paper introduces optimal transport to explicitly reveal cell correspondences in single-cell multi-omics, improving integration and label transfer by identifying and removing ambiguous cells.

The Alzheimer's disease risk gene ABCA7 regulates microglial lysosomal and lipid homeostasis and promotes phagocytosis to maintain neuronal health

This study shows ABCA7 deficiency in microglia disrupts lysosomal and lipid homeostasis, impairs phagocytosis, and negatively affects neuronal health in Alzheimer's disease.

The m6A motif is an anti-3' splice site

The paper shows that the m6A writer spares canonical 3' splice sites from methylation, allowing efficient splicing despite cotranscriptional methylation.

Dysregulation of epithelial differentiation architecture underlies field cancerization in head and neck cancer

This study identifies molecular and architectural changes in normal-adjacent field tissue in HNSCC that disrupt epithelial differentiation and may promote cancer development.

Cirrhosis-associated immune dysfunction reflects impaired intestinal CD8ab⁺ intraepithelial lymphocyte compartmentalization

The paper investigates immune dysfunction in cirrhosis by analyzing CD8ab⁺ intraepithelial lymphocytes and identifies CCL25-CCR9 axis disruption as a key factor.

A surviving beta cell subpopulation enriched in patients with T1D

Regulon-based clustering of islet scRNA-seq finds an IRF1-high, cytokine-driven beta cell state with reduced identity and autoantigen genes, enriched in type 1 diabetes donors.

NECTIN4 defines a subtype-dependent tumor state coupling enfortumab vedotin targetability to antitumor immunity in bladder cancer

The paper identifies NECTIN4 as a subtype-dependent determinant of tumor state and antitumor immunity in bladder cancer, linking its expression to response to enfortumab vedotin and checkpoint inhibitors.

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.

Dysregulation of FMR1 Splicing in Human Fragile X Syndrome

This study identifies FMR1-217 mis-splicing in FXS as a result of CGG repeat expansion, R-loop formation, and impaired Pol II elongation, with potential therapeutic rescue via splice-switching ASOs.

Layer-to-cell-class correspondence is gene-specific for pyroptosis-related transcription in human skin

Epidermal NLRP1, PYCARD and CASP4 versus dermal GSDMD polarity in systemic sclerosis skin is reproduced by same-donor cell-class pseudobulk for PYCARD and GSDMD, but rarely NLRP1.

A Wolbachia pipientis protein confers resistance to virus infection in Drosophila melanogaster

The paper identifies a Wolbachia protein that enhances Drosophila resistance to virus infection via the IMD pathway.

Spatially-resolved multimodal profiling identifies functionally-heterogeneous cancer-associated fibroblasts associated with poor radiotherapy outcomes in muscle-invasive bladder cancer.

This study identifies functionally heterogeneous cancer-associated fibroblasts in muscle-invasive bladder cancer linked to poor radiotherapy outcomes.

ZNF121 recruits YTHDF2 to modulate mRNA stability

The paper identifies ZNF121 as a cofactor that enhances YTHDF2-mediated mRNA decay by facilitating its binding to target transcripts, thereby modulating mRNA stability and cell-cycle regulation.

Beyond codon optimality: codon pairs regulate mRNA stability dependent on translation

The paper identifies codon pairs and amino acid pairs as regulators of mRNA stability in zebrafish, showing context-dependent decay mechanisms involving deadenylation and decapping.

ERBB2 establishes the timing of progesterone priming required for uterine receptivity

This study shows ERBB2 controls the timing of progesterone responsiveness in the uterus, ensuring proper receptivity for implantation.

N6-methyladenosine promotes temozolomide resistance through non-canonical regulation of mRNA stability in glioblastoma cells

This study shows that m6A methylation stabilizes genes involved in temozolomide resistance in glioblastoma, and inhibiting METTL3 can restore drug sensitivity.

Mammalian spermatogenesis at single-cell resolution downstream of genetic perturbations in meiotic double-strand break repair

Single-nucleus RNA+ATAC profiling of 32 mice shows asymmetric PRDM9 binding drives asynapsis, pachytene cell loss, aneuploidy and multi-megabase crossover redistribution, tuned by a chromosome 15 locus.

ALS-associated exitron splicing produces UBQLN2 isoforms with distinct properties

The paper identifies an exitron in UBQLN2 that generates an alternatively spliced isoform with distinct properties linked to ALS.

Associations between striatal neurochemical changes and resting-state functional connectivity following transcranial temporal interference stimulation

This study investigates whether 20-Hz tTIS modulates striatal neurochemical markers and functional connectivity, finding group-dependent associations between Glx changes and network alterations.

A root pathogen drives rhizosphere enrichment of antagonistic Pseudomonas and induces production of an antimicrobial metabolite

This study shows that a root pathogen activates antimicrobial production in beneficial bacteria, enhancing plant defense against itself.