ATAC-seq

MYC drives endothelial transformation and dedifferentiation in angiosarcoma

This study shows MYC drives endothelial transformation and dedifferentiation in angiosarcoma by promoting lineage plasticity and cell growth.

Integrative Multi-omics Analysis of the Human Skeletal Muscle Response to Endurance or Resistance Exercise: Findings from the Molecular Transducers of Physical Activity Consortium (MoTrPAC)

In 174 sedentary adults, resistance exercise changed more muscle molecular features than endurance exercise across omes and time points; network analysis nominates MEF2A and NFIC as regulatory hubs.

Accurate Reconstruction of Adaptive Immune Receptor Repertoires from FACS-partitioned B and T Cell Subsets

The paper develops computational methods to accurately reconstruct adaptive immune receptor repertoires from partitioned B and T cell subsets, showing improved accuracy compared to pooling sub-repertoires.

Epigenome Alterations and 3D Chromatin Architecture Remodeling in Inflammatory Macrophage Activation under Diabetic Conditions

This study investigates how diabetic conditions alter the 3D chromatin architecture and epigenome of macrophages, revealing disease-associated rewiring of the 3D epigenome and potential therapeutic targets.

Degraded myelin is associated with cold hypersensitivity in paclitaxel-induced peripheral neuropathy

In paclitaxel-treated mice, cold hypersensitivity outlasts mechanical hypersensitivity and coincides with reduced myelin gene expression, lower chromatin accessibility at Egr2/Yy1 motifs, and fragmented sciatic nerve myelin.

Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types

The paper introduces optimized fluorescence-activated nuclei sorting (FANS) protocols to isolate cell-type-specific nuclei from human and mouse brain tissue for multi-omic analysis.

PWK genetic background reprograms heterochromatin and malignant epithelial states in Neu-driven mammary tumors

The paper shows that the PWK genetic background alters transcriptional programs, heterochromatin organization, and malignant epithelial state trajectories in NeuT mammary tumors.

Kidzoi Enables Cell-Type-Specific Regulatory Activity and Variant Effect Prediction in Kidney

Kidzoi is a kidney-specific sequence-to-function model that improves variant effect prediction and chromatin accessibility prediction in proximal tubule cells.

Jasmonate-induced expansion of the MYC2 cistrome occurs within a preconfigured chromatin landscape

This study defines the native MYC2 cistrome in Arabidopsis under basal and JA-induced conditions, showing that JA treatment expands MYC2 binding sites while chromatin accessibility remains largely unchanged.

Signaling by a tyrosine-sulfated peptide balances growth and osmotic stress response in rice

Overexpressing rice peptide OsPSY8 lengthens roots but lowers osmotic stress survival, while knockout raises it; OsWRKY24 represses the OsPSY8 promoter and is induced by PEG.

Genome-wide discovery of cis-regulatory elements in a large genome

The paper develops resources to identify cis-regulatory elements in the Parhyale hawaiensis genome using ATAC-seq and sequence conservation analysis.

EWS::WT1 Isoform-Dependent Regulation of Neogenes in Desmoplastic Small Round Cell Tumors

This study identifies DSRCT-specific neogenes regulated by the EWS::WT1 fusion protein and shows their potential as biomarkers and therapeutic targets in desmoplastic small round cell tumors.

HDAC inhibitor treatment restores transcriptome, chromatin accessibility and memory deficits in a mouse model for Down syndrome

Induction of hysteretic chromatin states by CRISPRa reveals locus-specific encoding of transcriptional memory

The paper uses CRISPRa to show that transcriptional memory can be induced in MSCs through locus-specific activation, linked to H3K27me3 loss and increased transcription factor reacquisition.

Single-Nucleus Multi-Omic Atlas Maps Regulatory Architecture and Non-Coding Variant Effects across Adult Human Tissues

The paper constructs a single-nucleus multi-omic atlas of adult human tissues, identifying regulatory elements and variant effects across 21 tissues.

Role of Uridine Phosphorylase 1 (UPP1) in Pancreatic β-Cell Physiology and Its Dysregulation in Obesity and Type 2 Diabetes

This study investigates the role of UPP1 in β-cell function and shows that UPP1 deficiency impairs uridine-potentiated GSIS and MAPK activation in mice and humans.

Transcriptional networks underlying tumour plasticity in small-cell lung cancer

This study identifies a novel intermediate cell state and a regulatory network in SCLC that drives lineage plasticity and immunogenicity.

A druggable chromatin vulnerability in suppressive neutrophils restores antitumor immunity

This paper identifies a druggable chromatin vulnerability in suppressive neutrophils that can restore antitumor immunity through mSWI/SNF antagonists.

Discrepancies between ChIP-seq and CUT&Tag histone mark profiles are explained by GC content and chromatin accessibility

Controlling for DNA dosage with Whole Genome Sequencing improves ATAC-seq peak calling

This paper improves ATAC-seq peak calling by integrating whole-genome sequencing data to control for DNA dosage biases, enhancing peak accuracy and relevance to gene regulation.

A temporal threshold in TGF-β signaling separates reversible tissue adaptation from persistent NK cell effector dysfunction

This study shows that prolonged TGF-β signaling causes persistent NK cell dysfunction through epigenetic changes, while short-term signaling leads to reversible effects.

A single-nuclei multiomics resource across four brain regions prioritises human neural cell types influencing brain-related traits

The paper integrates multiomic data from human brain nuclei with GWAS statistics to prioritize neural cell types associated with brain-related traits.

CardioChrom Reconstructs the Human Cardiac Virtual Epigenome from Single-Nucleus Transcriptomes

CardioChrom reconstructs chromatin accessibility and histone modifications from single-nucleus RNA data in human heart failure, improving prediction accuracy and identifying regulatory changes in endothelial cells.

Glucocorticoid receptor activation reorganizes Wnt/LEF1 regulatory circuitry associated with therapeutic response in B-cell acute lymphoblastic leukemia

This study shows that GR activation reorganizes Wnt/LEF1 regulatory circuitry in B-ALL, influencing therapeutic response and resistance through chromatin state changes and gene regulation.

Refinement of the Pathogenic T Cell Receptor Motif Suggests Type 17 CD8+ T Cells Initiate HLA-B*27-associated Autoimmunity

The paper identifies a broader pathogenic T cell receptor motif linked to HLA-B*27-associated autoimmune diseases and shows these T cells express a Type 17 program.

ATACofthesnake: A scalable framework for analyzing multifactorial and time course chromatin accessibility data

The paper introduces ATACofthesnake, a scalable framework for analyzing multifactorial and time course chromatin accessibility data, providing a structured workflow to handle such data reproducibly.

BOTANIC-1: a series of long-context plant genomic foundation models in the agentic era

Bidirectional Mamba2 plant genomic language models (318M to 3.2B parameters) trained on 320 land-plant genomes top a 22-task frozen-model aggregate; a small variant reaches 131,072 bp context.

FFPE-CUTAC: A Single Assay, Multiple Layers

FFPE-CUTAC is a new assay for analyzing FFPE tissues that provides regulatory and copy-number profiles, showing robustness over time and compatibility with RNA-seq.

Variation in enhancer activity across brain regions defines neurological disease risk and shapes cellular pathology

The paper identifies brain region-specific enhancers linked to neurological disease risk and shows their role in cellular pathology using enhancer activity data and GWAS integration.

A blastema in sea star larvae integrates wound signaling to drive regeneration-specific and developmental gene expression patterns.

The paper identifies a regeneration-induced blastema cell state in sea star larvae and shows how wound signals drive distinct gene regulatory networks for regeneration.