ATAC-seq

Sociality changes Gene Essentiality

The paper shows social interactions in phages distort gene essentiality by masking true fitness costs through complementation, and proposes an MOI-based strategy to classify sociality.

Probabilistic network modeling identifies RBPJ as a driver of stemness in Merkel cell carcinoma

This study uses probabilistic network modeling to identify RBPJ as a key regulator of stemness in Merkel cell carcinoma, showing its potential as a therapeutic target.

A GATA2-PROX1-FOXC2 regulatory axis integrates shear stress signaling with lymphatic vascular development

The paper identifies a GATA2-PROX1-FOXC2 regulatory axis that integrates shear stress signaling with lymphatic vascular development, showing dosage-dependent cooperation between GATA2 and FOXC2.

Single-cell multiomics of neuron activation reveals context-specific genetics of brain disorders

The paper identifies context-specific genetic effects in neuronal activation using single-cell multiomics, revealing NPD risk variants and genes active during stimulation.

Novel Drosophila cis-regulatory elements can be uncovered by footprinting transcription factor binding sites in ATAC-seq data

The paper uses ATAC-seq data and TF footprinting tools to identify novel cis-regulatory elements in Drosophila embryos, finding that many TF binding sites lie outside known enhancers.

Schistosoma japonicum Histone Acetyltransferase 1 (SjHAT1): A Novel Anti-schistosomal Drug Target

This paper identifies SjHAT1 as a potential drug target for schistosomiasis by showing its essential role in parasite survival and reproduction through functional and expression analyses.

TOX enforces the immunosuppressive program of tumor-infiltrating regulatory T cells

This study identifies TOX as a critical regulator of tumor-infiltrating regulatory T cells, showing its role in maintaining immunosuppression and its potential as a therapeutic target.

Quantitative trait loci mapping of gene expression and chromatin accessibility in primary fibroblast reveals shared allelic effects between Latin American and European ancestries

The paper maps gene expression and chromatin accessibility QTLs in fibroblasts from European and Latin American ancestries, finding high concordance and shared regulatory mechanisms.

Chromatin accessibility–transcription coupling is dynamically reconfigured during Arabidopsis embryo maturation

The paper investigates the relationship between chromatin accessibility and transcription during Arabidopsis embryo development, finding that their coupling is regulated rather than fixed.

MULTIPLE DEFECTS IN MOUSE STEM CELL BASED EMBRYO MODELS LACKING ALL HOX FUNCTION

This study shows that mouse gastruloids lacking all HOX function can elongate but fail to form endoderm and properly segment mesoderm, suggesting HOX proteins are needed to posteriorize anterior structures.

Donor-matched iPSC model reveals context-dependent T2D genetic signals in fibro-adipogenic progenitors

The paper uses donor-matched iPSC-derived FAPs to show that T2D GWAS signals are enriched in adipogenic FAP subtypes under high-insulin exposure.

Large-scale prediction of transcription factor binding across human cell types informs regulatory genomics and reveals promiscuous occupancy associated with chromatin contacts

The paper predicts transcription factor binding across 43 human cell types using ATAC-seq data and a new platform, revealing promiscuous occupancy and chromatin contacts.

WNT signaling in human pluripotent stem cells promotes HDAC2-dependent epigenetic programs and development of retinoic acid-responsive mesoderm

This study shows that WNT signaling in hPSCs promotes mesoderm development through HDAC2-dependent epigenetic programs and RA responsiveness, enhancing T cell generation.

ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets

ScriptManager v1.0 provides a unified framework for reproducible and scalable analysis of genomics and epigenomics data across diverse assays.

Multimodal Hypersampling of the adult human heart resolves tissue-specific cell states and disease-associated variants

This paper creates a detailed heart atlas using multimodal data to identify cell states and disease-associated genetic variants in specific heart regions.

iSCORE-PD: an isogenic stem cell collection to research Parkinson Disease

The paper generates a collection of 65 isogenic human stem cell lines with PD-associated mutations to study Parkinson's disease, revealing that most genetic variation comes from cell culture rather than genome editing.

Annotation-Based Gene-Peak Links Improve Regulatory Network Prediction of Gene Expression in Human Kidney Multi-Omics

This paper introduces an annotation-based gene-peak linkage method that improves gene expression prediction from chromatin accessibility in human kidney multi-omics data.

Multi-layered characterization of ~700,000 conserved noncoding elements within the human genome

The paper characterizes ~700,000 conserved noncoding elements in the human genome, showing many have cis-regulatory potential and are enriched in TAD centers.

Single-nucleus multiomic analysis reveals modulation of the gene regulatory circuit landscape in pituitary cell types during mouse estrous cycle.

The paper uses single-nucleus multiomics to study pituitary cell changes during the mouse estrous cycle, finding stage-dependent gene regulatory circuits and validated ETS2-driven gene expression patterns.

Common γ-chain cytokines induce an epigenomically plastic precursor-like KIT+ ILC2 state linked to immune disease susceptibility

This study identifies KIT+ ILC2s as an epigenomically plastic state linked to immune disease susceptibility and shows that STAT5 activation by cytokines induces this phenotype.

A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species

HiCFoundation is a Hi-C-based model that integrates chromatin structure with epigenomic regulation across species, improving analysis of 3D genome architecture and single-cell data.

Enhancer pioneering activity of Wnt/β-catenin signaling

This study shows Wnt/β-catenin signaling can establish new regulatory elements by remodeling chromatin, beyond its traditional role as a molecular switch.

Population-scale detection of methylation outliers from long-read genome sequencing

METAFORA calls depth-aware, covariate-adjusted methylation outlier regions from PacBio and Nanopore long reads; in 551 rare-disease genomes, outliers tracked structural variants, repeat expansions, and imprinting defects.

Scalable Hypothalamic Arcuate Neuron Differentiation from Human Pluripotent Stem Cells Suitable for Modeling Metabolic and Reproductive Disorders

This paper describes a scalable method to differentiate human pluripotent stem cells into hypothalamic arcuate neurons, which can model metabolic and reproductive disorders.

Cytokine-induced Chromatin Accessibility in Whole Blood Neutrophils Links to Sepsis Transcriptional 1 States

The paper uses ATAC-Seq to study chromatin accessibility in neutrophils stimulated with inflammatory factors, finding stimulus-specific programs linked to sepsis transcriptional states.

Lineage-specific chromatin poising enforced by ETS-IRF composite elements determines the divergent interferon responses of plasmacytoid dendritic cells and epithelial cells

This paper identifies lineage-specific chromatin accessibility differences at IFN gene loci in pDCs and epithelial cells, revealing ETS-IRF composite elements as key regulators of divergent interferon responses.

circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics

The paper introduces circVDJ-seq for efficient T cell receptor profiling from single-cell and spatial multi-omics data, revealing distinct immune microenvironments and T cell clonality patterns in various clinical contexts.

Epigenetic de-repression of basal cell metaplasia in aging AT2 cells is a risk factor for idiopathic pulmonary fibrosis (IPF).

This study identifies age-related epigenetic changes in AT2 cells that promote basal cell metaplasia, contributing to idiopathic pulmonary fibrosis.

Interplay between β-catenin transcriptional and cell-cell junction activity regulates homeostasis and collective dynamics in the intestinal epithelium

This study investigates how β-catenin's dual roles in Wnt signaling and cell-cell junctions affect intestinal epithelial homeostasis and collective dynamics.

Deciphering the limitations of immortalized hepatocyte cell lines for the study of liver cis-regulatory elements

This study compares cis-regulatory elements in immortalized liver cell lines to primary liver tissue using ATAC-seq, finding significant differences in transcription factor binding and gene regulation.