ATAC-seq

Rapid kinetics of H+ transport by membrane pyrophosphatase: evidence for a direct-coupling mechanism

The paper measures H+ transport kinetics in mPPase using a stopped-flow assay and finds that hydrolysis, not pyrophosphate binding, directly couples to H+ transport.

A Biophysical Model for ATAC-seq Data Analysis

This paper proposes a biophysical model for analyzing ATAC-seq data and evaluates its benefits for integrating multiome data with single-cell RNA-seq.

Deaminase-mediated chromatin accessibility profiling with single-allele resolution

The paper introduces ACCESS-ATAC, a method that improves TF binding site prediction resolution and reveals allele-specific co-occupancy patterns in HepG2 and K562 cells.

Epigenomics of embryogenesis in turbot (Scophthalmus maximus)

This study creates a comprehensive epigenomic atlas of turbot embryogenesis, revealing chromatin dynamics and regulatory elements important for development and aquaculture.

Cell-type-resolved chromatin accessibility in the human intestine identifies complex regulatory programs and clarifies genetic associations in Crohn's disease

The paper constructs a cell-type-resolved chromatin accessibility atlas in the human intestine and identifies regulatory programs and genetic variants associated with Crohn's disease.

A lineage-resolved multimodal single-cell atlas reveals the genomic dynamics of early C. elegans development

This study constructs a lineage-resolved single-cell multimodal atlas of early C. elegans development, revealing genomic dynamics and zygotic genome activation mechanisms.

Dysregulated RNA splicing induces regeneration failure in alcohol-associated liver disease

The paper identifies dysregulated RNA splicing in alcohol-associated liver disease as a cause of regeneration failure, highlighting ESRP2 deficiency and its impact on key signaling pathways.

Combined analysis of chromatin accessibility, promoter interactions and whole genome sequencing solved the missing heritability in gastric cancer

The paper identifies novel genetic mechanisms underlying missing heritability in HDGC-like families by integrating chromatin accessibility, promoter interactions, and whole-genome sequencing data.

Epigenetic Regulation of Inflammatory NF-κB Target Genes by IFN-γ via IRF1

This study shows IFN-γ enhances TLR-induced inflammatory gene expression through IRF1, which is critical for synergistic activation of genes like IL6 and TNF in human monocytes.

ARID1A governs the silencing of sex-linked transcription during male meiosis in the mouse

This study shows ARID1A is essential for silencing sex-linked genes during male meiosis by regulating H3.3 localization and DNA repair.

Atheroprone Flow Activates SMAD-FOXO1 to drive Endothelial-to-Mesenchymal Transition and Atherosclerosis

This study identifies SMAD/FOXO1 complexes that mediate EndoMT in response to atheroprone flow, showing their role in atherosclerosis and suggesting targeting this interaction could reduce disease progression.

A negatively-charged region within carboxy-terminal domain maintains proper CTCF DNA binding

The paper identifies a negatively-charged region in CTCF's C-terminal domain that weakens DNA binding and chromatin accessibility through an autoinhibitory mechanism.

Cells transit through a quiescent-like state to convert to neurons at high rates

The paper identifies a quiescent-like state with reduced nuclear size and transcriptional activity that enables efficient TF-mediated conversion of fibroblasts to neurons.

Integration of single cell omics with biobank data discovers trans effects of SREBF1 abdominal obesity risk variants on adipocyte expression of more than 100 genes

The paper integrates single-cell omics with biobank data to show SREBF1 risk variants affect adipocyte gene expression in trans, impacting abdominal obesity.

Transcriptome and chromatin accessibility landscapes across 25 distinct human brain regions expand the susceptibility gene set for neuropsychiatric disorders

The paper maps transcriptomic and chromatin accessibility profiles across 25 human brain regions and identifies genes linked to neuropsychiatric disorder risk.

multiDGD: A versatile deep generative model for multi-omics data

multiDGD is a deep generative model for multi-omics data that learns shared representations and enables data integration and association detection.

Integrated analysis and systematic characterization of the regulatory network for human germline development

The paper integrates multi-omics data to characterize the regulatory network governing human germline development and identifies key factors and interactions involved.

Aberrant expression of histone H2B variants reshape chromatin and alter oncogenic gene expression programs

This study shows that H2B variants alter chromatin structure and oncogenic gene expression, suggesting they may be early cancer biomarkers and therapeutic targets.

Combining multiple stressors unexpectedly blocks bacterial migration and growth

The paper shows that combining physical and chemical stressors significantly reduces bacterial growth and migration, contradicting previous studies that used single stressors.

Chromatin Remodelling in Damaged Intestinal Crypts Orchestrates Redundant TGFβ and Hippo Signalling to Drive Regeneration

The paper identifies revSCs as regenerative cells in damaged intestinal crypts, showing TGFβ and Hippo pathways are critical for their function and intestinal regeneration.

Single cell variant to enhancer to gene map for coronary artery disease

This paper links CAD GWAS variants to causal genes in SMCs using single-cell chromatin accessibility and Hi-C data, creating a scV2E2G map for disease mechanism discovery.

A genome-wide ATLAS of liver chromatin architecture reveals that sex dictates diet-induced nucleosome dynamics

The paper maps liver chromatin architecture using ATAC-seq and shows sex is the main factor driving diet-induced nucleosome dynamics in mice.

Comprehensive genome annotation of the model ciliate Tetrahymena thermophila by in-depth epigenetic and transcriptomic profiling

This study improves gene annotation in Tetrahymena thermophila by integrating transcriptomic and epigenetic data, adding new genes and UTRs while identifying antisense transcripts.

Uncovering functional lncRNAs by scRNA-seq with ELATUS

The paper introduces ELATUS, a computational framework for detecting functional lncRNAs from scRNA-seq data, showing improved detection and biological relevance compared to traditional methods.

Deciphering gene regulatory programs underlying functionally divergent naive T cell subsets

The paper identifies gene regulatory programs distinguishing naive CD8+ T cell subsets using RNA-seq and ATAC-seq data, revealing novel regulators and transcriptional networks.

Multimodal single-cell profiling reveals neuronal vulnerability and pathological cell states in focal cortical dysplasia

This study uses multi-omics single-cell profiling to identify chromatin and transcriptomic changes in FCD type II, revealing altered cell states and neuronal vulnerability.

Multi-Omics Single-Cell Analysis Reveals Key Regulators of HIV-1 Persistence and Aberrant Host Immune Responses in Early Infection

This study uses single-cell RNA and ATAC sequencing to identify KLF2 as a key regulator of HIV-1 persistence and Th17 cell dysfunction in early infection.

Repeated shifts in sociality are associated with fine-tuning of highly conserved and lineage-specific enhancers in a socially flexible bee

The paper identifies enhancer activity differences between social and solitary populations of Lasioglossum albipes, linking cis-regulatory variation to social behavior evolution.

scCancerExplorer: a comprehensive database for interactively exploring single-cell multi-omics data of human pan-cancer

scCancerExplorer provides an interactive database for exploring single-cell multi-omics data across 50 cancer types, integrating genomic, epigenomic, and transcriptomic data.

Understanding Complex Chromatin Dynamics of Primary Human Neutrophils During PMA Induced NETosis

The paper examines chromatin dynamics in primary human neutrophils during PMA-induced NETosis, identifying early chromatin changes linked to NOX-dependent NET formation.