ATAC-seq

Common origin for effector and regulatory Follicular and Tissue-Adapted CD4+ T cells in Non-Small Cell Lung Cancer

The paper identifies a common origin for effector and regulatory CD4+ T cells in non-small cell lung cancer through single-cell analysis, revealing their plasticity and role in immune responses.

Beckwith-Wiedemann syndrome multiomic analysis of hepatoblastoma uncovers unique tumor heterogeneity and cellular landscapes, including transition cells leading to tumor formation

This study uses multiomic analysis to identify WNT pathway enrichment and transition cells in BWS hepatoblastoma, revealing unique tumor heterogeneity and potential targets for intervention.

ZNF180 modulates tumor intrinsic immunotherapy resistance in melanoma through driving plasticity

This study identifies ZNF180 as a driver of immunotherapy resistance in melanoma by promoting tumor plasticity and immune suppression through mechanisms involving MHC-I loss, CD155 expression, and CD4 T-cell exclusion.

Library Size in Spatial ATAC-seq: Technical Confounder or Biology?

This study shows that library size in spATAC-seq data is biologically informative and that standard normalization methods can obscure important biological signals.

Chronic Cadmium Exposures and Hyperglycemia Additively Drive Mitochondrial Dysfunction in Hepatic Cells: Key Implications for MASLD Etiopathogenesis

This study shows chronic cadmium exposure combined with hyperglycemia worsens mitochondrial dysfunction in liver cells, suggesting a role in MASLD development.

Integrative proteo-genomic profiling uncovers key biomarkers of lapatinib resistance in HER2-positive breast cancer

The paper identifies a nine-marker signature of lapatinib resistance in HER2-positive breast cancer using integrative multi-omics analysis, revealing novel biomarkers and chromatin dynamics associated with drug resistance.

Beneficial and detrimental consequences of AHR activation in intestinal infection

This study examines how prolonged AHR activation, either through genetic means or environmental pollutants, affects immune responses to intestinal infection, finding differential impacts on infection clearance and immune cell function.

Coupling CRISPR Scanning with Targeted Chromatin Accessibility Profiling using a Double-Stranded DNA Deaminase

This paper introduces TDAC-seq, a method combining CRISPR perturbations with chromatin accessibility profiling to study cis-regulatory elements at single-nucleotide resolution.

Trimodal Single-Cell Gene Regulatory Networks Reveal Principles of Stemness Loss and Cell Fate Acquisition in Human Hematopoiesis

The paper establishes dynamic enhancer-based gene regulatory networks in human hematopoiesis, revealing that stemness loss and lineage acquisition are temporally and mechanistically uncoupled.

Lipopolysaccharide Induces Trained Innate Immune Tolerance in the Heart Through Interferon Signaling in a Model of Stress-Induced Cardiomyopathy

This study shows that LPS pretreatment protects hearts from ISO-induced injury through TLR4-mediated interferon signaling, involving both cell-autonomous and non-cell-autonomous mechanisms.

The limited effects of AAV2 vectors on host chromatin accessibility and nuclear architecture are consistent with a favorable safety profile

Long-read single-cell genome, transcriptome and open chromatin profiling links genotype to phenotypes.

SPLONGGET enables comprehensive genotype-phenotype analysis by integrating long-read single-cell genome, transcriptome, and open chromatin profiling in thousands of cells.

Disrupted transcriptional networks regulated by CHD1L during neurodevelopment underlie the mirrored neuroanatomical and growth phenotypes of the 1q21.1 copy number variant

The paper identifies CHD1L as a key regulator of neurodevelopmental processes, showing its role in shaping neuroanatomical and growth phenotypes linked to 1q21.1 copy number variants.

Epigenomic regulation of human oligodendrocyte myelination properties, relation to age and lineage

The paper investigates how epigenomic factors like chromatin accessibility and histone modifications affect human oligodendrocyte myelination and age-related vulnerability to injury.

Chd4 remodels chromatin to control retinal cell type specification and lineage termination

This study shows that Chd4 remodels chromatin to control retinal cell fate by repressing progenitor identity and promoting rod photoreceptor production, without affecting the competence windows for early vs. late cell-type production.

Real-time Biomechanical Characterisation of Cytoskeletal Remodelling

This study uses Q-AFM to track real-time biomechanical changes in hMSCs during cytoskeletal remodelling induced by disruptors.

Human Papillomavirus Genomes Associate with Active Host Chromatin during Persistent Viral Infection

This study shows HPV31 genomes associate with active host chromatin regions, linking viral persistence to transcriptional activity and integration sites in cervical cancers.

Multi-omics analysis reveals genetic regulatory mechanismsof muscle traits in wild and domesticated Bactrian camels

The paper integrates multi-omics data from Bactrian camels to identify regulatory mechanisms and genetic variants influencing muscle traits.

Ectomesenchymal identity emerges via relief of Twist1transcript destabilization

The paper identifies a vertebrate-specific regulatory mechanism for Twist1 expression in cranial neural crest cells, linking enhancer activity to transcript destabilization.

Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma

The paper identifies a mature dendritic cell subtype associated with improved immune response and prognosis in melanoma patients treated with anti-PD-1 checkpoint inhibitors.

Hypoxic stress dysregulates functions of glioma-associated myeloid cells through epigenomic and transcriptional programs

This study shows hypoxia alters myeloid cell functions in glioblastoma by changing gene expression and chromatin accessibility, affecting immune cell markers and transcription factor regulation.

CUT&TIME captures the history of open chromatin indeveloping neurons

The paper introduces CUT&TIME, a method to map historical chromatin accessibility in single cells during neurogenesis, revealing early changes in promoter accessibility linked to cell-fate commitment in retinal ganglion cells.

Unveiling causal regulatory mechanisms through cell-state parallax

The paper introduces GrID-Net, a graph neural network that detects causal locus-gene associations using cell-state parallax, uncovering noncoding mechanisms affecting 132 genes in schizophrenia.

Diverse epigenomic mechanisms underpin transcriptional dysregulation in Polycomb-altered acute myeloid leukemia

This study investigates how PRC2 depletion in AML affects epigenomic and transcriptional changes, revealing altered chromatin accessibility, H3K27me3 levels, and gene expression patterns that impact cell phenotype and treatment response.

Lineage-Specific Epigenomic Mapping of Proximal and Distal Fallopian Tube Epithelium Reveals Mesenchymal/Wnt-Driven Tumor Phenotype Diversification

The paper compares epigenomic and transcriptional differences between proximal and distal fallopian tube epithelium in mouse models, revealing distinct tumor subtypes driven by EMT and WNT pathways.

CD39 defines a cytotoxic tumor-associated NK cell state responsive to NKG2A blockade in lung cancer

The paper identifies CD39+ tumor-associated NK cells as a cytotoxic effector state in NSCLC responsive to NKG2A blockade through multiomic analysis.

Chromatin accessibility and heat stress gene expression in the reef-building coral, Acropora millepora

This study examines chromatin accessibility in the coral Acropora millepora under heat stress, finding that open chromatin regions correlate with gene expression patterns and stress responses.

TRAFICA: An Open Chromatin Language Model to ImproveTranscription Factor Binding Affinity Prediction

TRAFICA improves TF-DNA binding affinity prediction by integrating open chromatin features and in vitro binding profiles, outperforming existing tools in both in vitro and in vivo settings.

Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression changes in the hippocampus

This study identifies cell-type-specific chromatin accessibility and gene expression changes in the hippocampus following novel environment exposure using single-nucleus multiomics and bulk RNA-seq.

Fatty acid metabolism controls plasma membrane cholesterol accessibility via ATGL-dependent phospholipid remodeling

This study shows that fatty acid metabolism regulates plasma membrane cholesterol accessibility through ATGL-dependent phospholipid remodeling, affecting membrane fluidity and cholesterol signaling.