ATAC-seq

PATTY corrects open chromatin bias for improved bulk and single-cell CUT&Tag profiling

PATTY corrects open chromatin bias in CUT&Tag data using ATAC-seq and machine learning, improving detection of histone modifications and cell clustering in single-cell analyses.

BPabZIP, a new bZIP protein motif that promotes binding near, and displacement of, nucleosomes

The paper identifies a new bZIP protein motif, BPabZIP, that facilitates nucleosome displacement and binding near nucleosomes in human cells.

Multimodal single-cell analysis uncovers transcription factor networks underlying T-cell aging

This study uses multimodal single-cell analysis to identify transcription factor networks involved in T-cell aging.

Systematic mapping of chromatin dysregulation driven by viral transcriptional regulators at scale

The paper maps chromatin dysregulation caused by viral transcriptional regulators using PROD-ATAC, identifying vTRs that remodel chromatin and reveal shared host transcription factor networks.

Astrocytes transform the transcriptomic and epigenetic landscape of developing cortical neurons to promote activity via intrinsic excitability control

This study shows astrocytes alter the transcriptomic and epigenetic landscape of developing cortical neurons, promoting intrinsic excitability and influencing disease-related pathways.

Developmental and regulatory logic of cannabis glandular trichomes resolved by single cell multiomics

This study uses single-cell multiomics to resolve the developmental and regulatory logic of Cannabis sativa glandular trichomes, identifying new cell types and regulatory programs.

Stag2 dependent chromatin remodeling enforces the erythroid-specific Gata1 cistrome

This study investigates how Stag2-dependent chromatin remodeling influences Gata1's function in erythropoiesis, revealing its role in lineage-specific gene regulation and dyserythropoiesis in MDS.

Structural dynamics insights into principles underlying the fitness of new broadly potent AAVs

The paper develops a new AAV engineering workflow, scAAVengr-Hunt, to create potent vectors and identifies a structural mechanism underlying their broad species and tissue potency.

Cellular stemness identifies high-risk ductal carcinoma in situ and offers a therapeutic interception opportunity

This study identifies stemness features in luminal hormone-responsive cells within DCIS that correlate with invasive progression and shows that targeting FOXA1 reduces tumor growth.

TDP-43 regulates chromatin looping and gene transcription through binding and stabilizing DNA G-quadruplex structures

This study shows TDP-43 binds and stabilizes DNA G-quadruplexes, enhancing chromatin looping and gene expression in K562 and HepG2 cells.

A chromatin accessibility map of pea aphid brain and embryo identifies tissue-specific regulatory elements

The paper generates a chromatin accessibility map of pea aphid brain and embryo using ATAC-seq, identifying tissue-specific regulatory elements and their relationship to gene expression.

Strain diversity drives heterogeneous responses to tuberculosis combination therapy

This study examines drug response patterns in diverse Mycobacterium tuberculosis strains to combination therapy, finding that strain-specific sensitivity varies more than genetic distance.

Single-nucleus epigenomic dysregulation unmasks genetic risk-associated neurodegenerative glia states

The paper identifies glial cell-specific regulatory elements and genetic risk modifiers in tau-related dementias using single-nucleus epigenomic profiling.

Temporal Transcriptomics Identifies Isoform-specific Trans-regulation by Multiple lncRNAs in Human iPSCs

The paper identifies six lncRNAs that regulate gene expression in trans in human iPSCs, revealing isoform-specific effects and a systemic response to doxycycline exposure.

MNS induces antiviral protection and suppresses inflammation

This study shows that MNS reduces viral infection and inflammation in cell and animal models by suppressing inflammatory pathways and altering chromatin accessibility.

The Onset of Myeloid Differentiation in Hematopoietic Progenitors In Vivo is Coordinated with S-phase Progression

This study shows that myeloid differentiation in hematopoietic progenitors starts during S phase and is linked to chromatin changes and HOXA9 activity.

Inflammation-induced epigenetic memory restores oligodendrocyte progenitor cell regenerative capacity in the aged central nervous system

This study shows that inflammation-induced epigenetic memory in OPCs improves remyelination in aged mice by enhancing differentiation and reducing axonal damage.

Integrative Genomic, Single-Cell, and Functional Profiling of the CD48-CD244 Axis and NK-Cell Dysfunction in Multiple Myeloma

The paper investigates the CD48-CD244 axis in multiple myeloma, showing CD48 enhances NK-cell activation but contributes to NK exhaustion and poor prognosis.

VIDEO - Visual Integration of Drosophila Enhancer Organization: A tool for integrating and visualizing chromatin accessibility, in vivo transcription factor binding and motif occurrence in tissue-specific differentially expressed genes

VIDEO is a web-based tool that integrates and visualizes chromatin accessibility, TF binding, and motif occurrence in tissue-specific genes to explore gene regulation in Drosophila.

Chromatin State Distinguishes Injury-Responsive from State-Stabilizing Transcriptional Programs in Hybrid Hepatocytes

The paper identifies chromatin features distinguishing injury-responsive from state-stabilizing transcriptional programs in hybrid hepatocytes using multi-omics data.

Failure of Bacillus Calmette-Guerin Therapy in Patients with Bladder Cancer is Characterized by Immune Dysfunction Associated with Activator Protein 1

This study identifies immune dysfunction linked to AP-1 in BCG non-responders with NMIBC, suggesting pre-existing immunosenescence contributes to early recurrence.

Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer

This study shows BET + MAPK inhibitors improve efficacy against BRAFV600E CRC by inducing epigenetic reprogramming and cellular plasticity through enhancer dynamics disruption.

Spatiotemporal regulation of arbuscular mycorrhizal symbiosis at cellular resolution

This study uses spatial transcriptomics and TRAP-seq to analyze gene expression dynamics in arbuscular mycorrhizal symbiosis, revealing spatiotemporal regulation of nutrient exchange and defense responses.

Comparative multi-omics of the macrophage response to infection with Mycobacterium tuberculosis complex bacteria reveals pathogen-driven epigenomic reprogramming

This study uses multi-omics approaches to analyze how M. bovis infection reprograms the epigenome of bovine alveolar macrophages, identifying key genes and pathways involved in the host response.

UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility

UniversalEPI predicts cell type-specific and differential chromatin interactions using DNA sequence and ATAC-seq data, showing robust performance across cell types and conditions.

Photoaged microplastics disrupt endothelial stretch-sensitive ion channels to impair calcium signaling and vascular integrity

This study shows photoaged microplastics impair endothelial calcium signaling and vascular integrity by disrupting Piezo1-Notch mechanotransduction.

Agentic systems are adept at solving well-scoped, verifiable problems in computational biology

This paper introduces CompBioBench, a benchmark for evaluating agentic systems in computational biology, showing strong performance across diverse tasks.

MOAflow: how re-design a pipeline with Nextflow streamlines data analysis

The paper redesigns an existing MOA-seq analysis pipeline using Nextflow to improve scalability and efficiency, resulting in a containerized and reproducible workflow.

In vivo CRISPR-based screen identifies ZC3H12C as a mediator of CAR-T cell dysfunction in solid tumors

The paper identifies ZC3H12C as a mediator of CAR-T cell dysfunction in solid tumors through an in vivo CRISPR screen and validates its role using single-cell RNA and ATAC-seq.

ATAC-seq of Low-Input and Cryopreserved Primordial Germ Cells Reveals Functional Enhancers

The paper optimizes ATAC-seq for low-input and cryopreserved chicken primordial germ cells, identifying PGC-specific chromatin regions and their functional roles.