ATAC-seq

Stage-dependent chromatin accessibility remodeling defines an architectural state in facioscapulohumeral muscular dystrophy myoblasts

The paper identifies a stage-specific chromatin accessibility state in FSHD myoblasts that resolves during differentiation, showing architectural remodeling uncoupled from DUX4 target loci.

Genome compartments guide protamine replacement and genome stability during spermiogenesis

This study maps chromatin accessibility and protamine incorporation during spermiogenesis, revealing compartment-specific dynamics and their role in genome stability.

Immortalized AT2 Cell Lines from Healthy and IPF Lungs Enable 2D and 3D Cultures

The paper generates immortalized AT2 cell lines from healthy and IPF lungs that maintain key biological features in 2D and 3D cultures, providing a platform for lung disease research.

Enhanced EBNA2-dependent activity in EBV-transformed B cells from patients with multiple sclerosis

This study shows that EBNA2 activity is increased in MS patients, altering gene expression and chromatin accessibility in EBV-transformed B cells.

Presenilin 1 (PS1) located at mitochondrial inner membrane regulates mitochondrial cristae junction proteins arrangement and cristae formation in HEK293 cells

This study shows PS1 localizes to mitochondrial inner membrane and regulates cristae structure by modulating protein interactions at cristae junctions, leading to mitochondrial dysfunction in Alzheimer's disease.

Reprogramming of neuronal genome function and phenotype by astrocytes

This paper shows that astrocytes reprogram neuronal gene expression and chromatin accessibility, affecting thousands of genes and regulatory elements, including those linked to schizophrenia and Alzheimer's disease.

Epigenetic remodeling via HDAC6 inhibition amplifies anti-tumoral immune responses in myeloid leukemia cells

This study shows HDAC6 inhibition enhances anti-tumoral immune responses and chemosensitivity in myeloid leukemia cells by upregulating RNase T2 and improving chromatin accessibility.

TFBSpedia: a comprehensive human and mouse transcription factor binding sites database

The paper constructs a comprehensive TFBS database by integrating multiple resources and evaluates their accuracy using independent datasets.

G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome

This study shows that G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome by stabilizing G4s, which enhances chromatin accessibility and promotes gene expression in BLM-deficient cells.

Mycobacterial infection uncovers plasticity of Kupffer cells

The paper investigates KC plasticity in mycobacterial infections, finding that KClow cells derived from bona fide KCs exhibit unique antimycobacterial activity and adaptability.

Single cell multiomic analysis of the impact of Delta-9-tetrahydrocannabinol on HIV infected CD4 T cells

This study investigates how THC affects HIV-infected CD4 T cells using single-cell multiomic analysis, finding no effect on HIV reactivation but altered gene expression and chromatin accessibility.

SIRT6 Activation Improves Intervertebral Disc Health in the Aging Spine

This study shows that activating SIRT6 with MDL-800 improves intervertebral disc health in aged mice by enhancing autophagy, reducing senescence, and improving matrix quality.

Rewiring of 3D Enhancer-Promoter Interactome Underlies Diabetic Endothelial Dysfunction

The paper identifies RBBP6-mediated degradation of JUNB as a mechanism causing 3D enhancer-promoter disruption and endothelial dysfunction in diabetes.

Cell-type specific impact of opioid use disorder and HIV on the human forebrain and cerebellum

This study examines the cell-type specific effects of opioid use disorder and HIV on the human brain, identifying changes in gene regulation, metabolism, and immune responses across different brain regions.

Early feature extraction drives model performance in high-resolution chromatin accessibility prediction: A systematic evaluation of deep learning architectures

The paper evaluates deep learning architectures for high-resolution chromatin accessibility prediction, finding that early feature extraction, not downstream architecture, primarily determines performance.

Features affecting Cas9-Induced Editing Efficiency and Patterns in Tomato: Evidence from a Large CRISPR Dataset

The paper analyzes a large CRISPR dataset in tomato to identify factors affecting Cas9 editing efficiency and repair patterns, finding chromatin accessibility and genomic context are key determinants.

Pioneer factor IRF1 unlocks latent enhancers to rewire chromatin and immunometabolism in inflammatory macrophages

This study identifies IRF1 as a pioneer factor that remodels chromatin and drives metabolic reprogramming in inflammatory macrophages through enhancer activation and transcriptional control.

Nuclear Myosin 1 links genomic architecture to adipose tissue remodeling, metabolic inflammation and obesity in mice

This study shows NM1 regulates adipose tissue remodeling, metabolic inflammation, and obesity in mice by controlling chromatin accessibility and gene expression during adipogenesis.

Differential chromatin accessibility between pre- and post-natal stages highlights putative causal regulatory variants in pig skeletal muscle

The paper identifies stage-specific regulatory variants in pig skeletal muscle by analyzing chromatin accessibility, molecular QTLs, and GWAS data across prenatal and postnatal stages.

Expanding the fly eye gene regulatory network: from Drosophila to the hoverfly Episyrphus balteatus.

The paper compares the gene regulatory network of compound eye development between Drosophila and Episyrphus balteatus, finding conserved and species-specific regulatory interactions.

A chromosome-level assembly and functional genomic resources for the model annelid Capitella teleta

The paper presents a chromosome-level genome assembly and functional genomic resources for Capitella teleta, improving upon an outdated reference and enabling better analysis of multi-omic data.

Transcriptomic and chromatin accessibility profiling unveils new regulators of heat hormesis in Caenorhabditis elegans

This study identifies new regulators of heat hormesis in C. elegans through transcriptomic and chromatin accessibility analysis, revealing tissue-specific responses and conserved factors involved in stress resilience and longevity.

Nardilysin regulates Slc2a2 expression through ISLET1 recruitment to an evolutionarily conserved enhancer in pancreatic β-cells

This study identifies NRDC's role in regulating Slc2a2 expression in pancreatic β-cells through direct interaction with an evolutionarily conserved enhancer and ISLET1 recruitment.

Regulatory network architecture constrains inflammatory responses in tissue-resident alveolar macrophages

The paper investigates gene regulatory networks in alveolar macrophages, finding that tissue-resident macrophages have more restrained inflammatory responses due to a stabilizing network involving PU.1 and CEBP/β.

Role of nuclear ATPases in nuclear mechanics and cell migration through confined spaces: opposite effects of BRG1 and cohesin

This study shows that BRG1 stiffens isolated nuclei and inhibits cell migration through tight spaces, while cohesin softens nuclei and enhances migration.

The regulatory landscape of optic fissure closure in the vertebrate eye

The paper identifies cis-regulatory elements and transcription factors involved in optic fissure closure using chicken embryos, linking them to human coloboma genes.

A novel iPSC model of Bryant-Li-Bhoj neurodevelopmental/neurodegenerative syndrome demonstrates the role of histone H3.3 in chromatin dynamics, neuronal differentiation, and maturation

This paper uses an iPSC model of BLBS to show that the H3.3 L48R variant disrupts chromatin dynamics, neuronal differentiation, and electrophysiological function.

CUT homeobox factors modulate chromatin accessibility in neurons

This study identifies CUT-dependent chromatin accessibility changes in neuronal nuclei using ATAC-seq in C. elegans.

A multi-omics atlas of human hindbrain development

This paper creates a multi-omics atlas of human hindbrain development, revealing cellular diversity, regulatory programs, and disease relevance.

SWI/SNF nuclear foci scaffold peripheral gene hubs for circadian chromatin control

This paper identifies MOR-containing SWI/SNF foci as perinuclear scaffolds that gate chromatin accessibility for circadian gene regulation, revealing a spatial mechanism for converting protein oscillations into transcriptional rhythms.