<i>XIST</i> Is a Key Modulator Associated with the Adhesome Network

bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-24

Abstract A long non-coding RNA (lncRNA) known as the X-inactivation specific transcript ( XIST ) plays a central role in X chromosome inactivation – a transcriptional process that silences one of the two X chromosomes in females to ensure dosage compensation between males and females. Much research has been conducted on how XIST regulates X chromosome transcription critical to embryonic development, but recent studies suggest a non-canonical role for XIST in regulating cancer stem cells and cellular plasticity. As cell adhesion and adhesome genes are integral to the regulation of cancer stemness, we explored the previously unrecognized link between XIST and the adhesome network. By performing gene expression and gene ontology analysis on XIST -knockdown ovarian cancer cells, our study showed that XIST loss altered adhesome gene expression and downstream adhesion pathways. Using Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) datasets, we identified distinct correlations between XIST lncRNA and adhesome genes across normal and cancer tissue samples, which are associated with cell stemness. Furthermore, network analysis suggests that XIST may interact with specific adhesome genes within the cell nucleus. This interaction may have significant functional implications, as demonstrated by the hazard ratio analysis of XIST and adhesome gene expression in relation to clinical outcomes. Overall, our results show that among well-annotated functional lncRNAs, XIST appears to be a modulator strongly associated with the adhesome network and cell stemness. Our findings thus support a novel link between lncRNA-mediated epigenetic regulation of cell adhesion genes, highlighting XIST as a key regulator contributing to the adhesome network. Significance Statement This study identified that XIST , a long non-coding RNA essential for X-chromosome dosage compensation and embryonic development, plays a significant role in modulating the adhesome network. We found that XIST knockdown affected adhesion pathways in ovarian cancer cells, whereas XIST expression is strongly correlated with adhesome gene expression across all tissues. We observed that the interaction between XIST and adhesome genes changes significantly between tumors and normal tissues, and this altered interaction is associated with certain cancer outcomes. These findings reveal a possible link between lncRNA-mediated regulation and adhesome control that is associated with cell stemness signatures and the emergence of cancerous tissues.

A tunable, ultrasensitive threshold in enzymatic activity governs the DNA methylation landscape

Biophysical Journal · 2026-03-10

BET inhibition curbs macrophage inflammation, lipid accumulation, and atherogenesis by disrupting the YAP/TAZ-BRD4 axis

Journal of Leukocyte Biology · 2026-04-29

Macrophage dysfunction is hallmark of atherosclerotic disease, characterized by inflammation and uptake of oxidized low-density lipoproteins (oxLDL). We investigate the role of the epigenetic reader bromodomain-containing protein 4 (BRD4) in orchestrating macrophage responses through interactions with the mechanosensitive transcriptional coactivators YAP/TAZ. Suppression of BRD4 via bromodomain and extra-terminal motif (BET) protein inhibitors (BETi) unveils a remarkable capacity to mitigate YAP/TAZ-driven inflammation. Knockdown of YAP, TAZ or BRD4 in macrophages shows a significant convergence of inflammatory genes under the regulatory purview of these transcriptional regulators. In addition, persistent activation of YAP and TAZ initiates a partial inflammatory phenotype in macrophages, which is effectively ameliorated with BETi. Notably, CD36 and low-density lipoprotein (LDL) receptor-1 (LOX1), pivotal receptors involved in uptake of oxidized low-density lipoprotein (oxLDL), emerge as direct YAP/TAZ targets. We employed a BD2-specific BETi, ABBV-744, in an AAV-PCSK9-induced atherosclerosis model to test the therapeutic potential of BET inhibition. Although reduction in cholesterol levels is modest, BETi substantially curtails plaque formation, diminishing macrophage infiltration, and suppressing the upregulation of YAP/TAZ and oxLDL uptake receptors associated with atherogenesis. Intriguingly, even in conditions marked by heightened YAP/TAZ expression induced by myeloid cell-targeted YAP/TAZ overexpression, BETi effectively dampens inflammation, mitigates foam cell formation, and disease progression. Our work underscores the considerable promise of targeting the YAP/TAZ-BRD4 axis as a therapeutic strategy for averting atherosclerosis, thereby disrupting the relentless cycle of inflammation, mechanosensory responses, and oxLDL uptake characteristic of atherosclerosis progression.

DNMT3s and TETs adjust CpG methylation canyon width to regulate gene expression and cell fate

SSRN Electronic Journal · 2026-01-01

BPS2025 - Nucleosome placement and polymer mechanics explain genomic contacts on 100 kbp scales

Biophysical Journal · 2025-02-01

Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data

Bioinformatics · 2025-10-18 · 2 citations

MOTIVATION: Stochastic gene expression and cell-to-cell heterogeneity have attracted increased interest in recent years, enabled by advances in single-cell measurement technologies. These studies are also increasingly complemented by quantitative biophysical modeling, often using the framework of stochastic biochemical kinetic models. However, inferring parameters for such models (i.e., the kinetic rates of biochemical reactions) remains a technical and computational challenge, particularly doing so in a manner that can leverage high-throughput single-cell sequencing data. RESULTS: In this work, we develop a chemical master equation model reference library-based computational pipeline to infer kinetic parameters describing noisy mRNA distributions from single-cell RNA sequencing data, using the commonly applied stochastic telegraph model. The approach fits kinetic parameters via steady-state distributions, as measured across a population of cells in snapshot data. Our pipeline also serves as a tool for comprehensive analysis of parameter identifiability, in both a priori (studying model properties in the absence of data) and a posteriori (in the context of a particular dataset) use-cases. The pipeline can perform both of these tasks, i.e. inference and identifiability analysis, in an efficient and scalable manner, and also serves to disentangle contributions to uncertainty in inferred parameters from experimental noise versus structural properties of the model. We found that for the telegraph model, the majority of the parameter space is not practically identifiable from single-cell RNA sequencing data, and low experimental capture rates worsen the identifiability. Our methodological framework could be extended to other data types in the fitting of small biochemical network models. AVAILABILITY AND IMPLEMENTATION: All code relevant to this work is available at https://github.com/Read-Lab-UCI/TelegraphLikelihoodInfer, archival DOI: https://doi.org/10.5281/zenodo.16915450.

Bacteria detect neutrophils via a system that responds to hypochlorous acid and flow

eLife · 2025-09-01

Abstract Neutrophils respond to the presence of bacteria by producing oxidative molecules that are lethal to bacteria, including hypochlorous acid (HOCl). However, the extent to which bacteria detect activated neutrophils or the HOCl that neutrophils produce, has not been understood. Here we report that the opportunistic bacterial pathogen Pseudomonas aeruginosa upregulates expression of its fro operon in response to stimulated neutrophils. This operon was previously shown to be activated by shear rate of fluid flow in the environment. We show that fro is specifically upregulated by HOCl, while other oxidative factors that neutrophils produce including H2O2, do not upregulate fro. The fro-dependent response to HOCl upregulates the expression of multiple methionine sulfoxide reductases, which relieve oxidative stress that would otherwise inhibit growth. Our findings suggest a model in which the detection of shear rate or HOCl activates the fro operon, which serves as an early and sensitive host-detection system for P. aeruginosa that improves its own survival against neutrophil-mediated host defenses. In support of this model, we found that the fro operon is activated in an infection model where flow and neutrophils are present. This response could promote the bacterium’s pathogenicity, colonization of tissue, and persistence in infections.

Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read sequencing

bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-11

Faithful epigenetic inheritance across cell divisions is essential to maintaining cell identity and involves numerous epigenetic modifications, whose roles in establishing chromatin architecture are less understood. Technological approaches to temporally order epigenetic modifications throughout the cell cycle often face limitations in sequence resolution and rely on potentially damaging mitotic labeling or conversion steps. Herein, we present M ethylation P seudotime A nalysis T hrough read-level H eterogeneity (MPATH), a label- and conversion-free method to infer post-replication DNA strand maturity from methylation patterns across single molecules. We use MPATH to temporally order hydroxymethylation throughout mitotic inheritance, revealing that CpGs within cis-regulatory elements undergo transitions between methylation states at sub-cell-cycle timescales. When applied to long reads generated by NOMe-seq, MPATH uncovered relationships between nucleosome occupancy and DNA maturity. Finally, extension of MPATH to phased reads reveals allele-specific trends in pseudotime distribution associated with X chromosome activity. Our findings suggest that when coupled with multimodal sequencing strategies, MPATH could provide valuable insights into chromatin restoration dynamics.

Nucleosome placement and polymer mechanics explain genomic contacts on 100 kb scales

Nucleic Acids Research · 2025-07-19

The 3D organization of the genome-in particular, which two regions of DNA are in contact with each other-plays a role in regulating gene expression. Several factors influence genome 3D organization. Nucleosomes (where ∼100 base pairs of DNA wrap around histone proteins) bend, twist, and compactify chromosomal DNA, altering its polymer mechanics. How much does the positioning of nucleosomes between gene loci influence contacts between those gene loci? And to what extent are polymer mechanics responsible for this? To address this question, we combine a stochastic polymer mechanics model of chromosomal DNA including twists and wrapping induced by nucleosomes with two data-driven pipelines. The first estimates nucleosome positioning from ATAC-seq data in regions of high accessibility. Most of the genome is low accessibility, so we combine this with a novel image analysis method that estimates the distribution of nucleosome spacing from electron microscopy data. There are no fit parameters in the biophysical model. We apply this method to IL-6, IL-15, CXCL9, and CXCL10, inflammatory marker genes in macrophages, before and after inflammatory stimulation, and compare the predictions with contacts measured by conformation capture experiments (4C-seq). We find that within a 500-kb genomic region, polymer mechanics with nucleosomes can explain 71% of close contacts. These results suggest that, while genome contacts on 100 kb scales are multifactorial, they may be amenable to mechanistic, physical explanation. Our work also highlights the role of nucleosomes, not just at the loci of interest, but between them, and not just the total number of nucleosomes, but their specific placement. The method generalizes to other genes, and can be used to address whether a contact is under active regulation by the cell (e.g. a macrophage during inflammatory stimulation).

Author response: Bacteria detect neutrophils via a system that responds to hypochlorous acid and flow

2025-09-01

Neutrophils respond to the presence of bacteria by producing oxidative molecules that are lethal to bacteria, including hypochlorous acid (HOCl). However, the extent to which bacteria detect activated neutrophils or the HOCl that neutrophils produce, has not been understood. Here we report that the opportunistic bacterial pathogen Pseudomonas aeruginosa upregulates expression of its fro operon in response to stimulated neutrophils. This operon was previously shown to be activated by shear rate of fluid flow in the environment. We show that fro is specifically upregulated by HOCl, while other oxidative factors that neutrophils produce including H2O2, do not upregulate fro. The fro-dependent response to HOCl upregulates the expression of multiple methionine sulfoxide reductases, which relieve oxidative stress that would otherwise inhibit growth. Our findings suggest a model in which the detection of shear rate or HOCl activates the fro operon, which serves as an early and sensitive host-detection system for P. aeruginosa that improves its own survival against neutrophil-mediated host defenses. In support of this model, we found that the fro operon is activated in an infection model where flow and neutrophils are present. This response could promote the bacterium’s pathogenicity, colonization of tissue, and persistence in infections.