ATAC-seq

Cyclin C nuclear release and mitochondrial dysfunction define molecular signatures of MED13L Syndrome

The paper identifies mitochondrial dysfunction and cyclin C mislocalization as consistent features of MED13L syndrome, linking them to clinical severity and suggesting potential biomarkers.

IF1 restrains excessive elevation of the mitochondrial membrane potential and safeguards the epithelial state of human iPSCs

This study shows that IF1 limits mitochondrial membrane potential elevation and prevents epithelial-mesenchymal transition in human iPSCs by inhibiting ATP hydrolysis.

SOX2 can associate with chromatin directly by binding to DNA or indirectly via association with other chromatin-bound proteins

This study shows SOX2 can regulate gene expression both directly via DNA binding and indirectly through interactions with other chromatin proteins.

Clonal memory in human embryonic stem cells biases fate potential during endoderm differentiation

This study shows that clonal memory in human embryonic stem cells influences fate potential during endoderm differentiation by heritable chromatin states.

Purinergic receptor activation rectifies autism-associated endothelial dysfunction

This study shows that purinergic receptor activation can correct endothelial dysfunction linked to autism in a mouse model by restoring bioenergetic function and cerebrovascular reactivity.

Conserved Neuronal-like and Secretory Programs Define the Spatial Architecture of Gastroenteropancreatic Neuroendocrine Tumors

This study identifies conserved neuronal-like and secretory programs in GEP-NETs and links them to spatial microenvironmental niches and metastatic potential.

In vivo multimodal lineage tracing of mammalian development by DeepTrack barcoding

The paper introduces DeepTrack, a lineage tracing model that combines cellular barcoding with single-cell multi-omics to study cell fate transitions and molecular changes during mammalian development.

Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions

TCOF1 dosage is limiting for transitional human neural crest cells; its enhancers buffer promoter output against MYC fluctuations rather than amplifying it, a pattern seen across 14 dosage-sensitive promoters.

mmVelo: A deep generative model for estimating cell state-dependent dynamics across multiple modalities

mmVelo estimates cell state-dependent dynamics across multiple modalities using deep generative modeling, validated on mouse and human data.

Targeted ATAC-see (tATAC-see): A Visual Assay for Target-Specific Chromatin Profiling

tATAC-see captures target-specific chromatin states using a visual assay, showing dynamic remodeling in aging models and LAD resistance.

Erosion of regenerative regulation: age-associated shifts in the skeletal muscle fiber epigenome and transcriptome

The paper identifies age-associated changes in the skeletal muscle epigenome and transcriptome, revealing shifts in chromatin accessibility and gene expression linked to metabolic and senescence pathways.

Context-dependent regulatory networks connect Alzheimer's disease genetics to microglial inflammatory responses

This study develops cEpiNets to connect Alzheimer's disease genetics to microglial inflammatory responses by integrating epigenomic data across contexts.

A multi-tissue epigenomic atlas links the sheep non-coding genome to domestication and complex traits

SheepEpimap combines 516 histone CUT&Tag, ATAC-seq and RNA-seq datasets from 43 sheep tissues to annotate 2.93 million cis-regulatory elements and 145,407 allele-specific variants for trait interpretation.

DPF3a couples H3K36me2-dependent chromatin remodeling to genome architecture during myogenesis

This study identifies DPF3a as a chromatin remodeler that regulates myogenesis through three-dimensional genome organization rather than local chromatin accessibility.

Early life stress affects the transcription and chromatin accessibility of spermatogonial cells

This study shows early-life stress alters the transcriptome and chromatin accessibility of mouse spermatogonial cells, with molecular signatures persisting into adulthood.

Addressing technical variations in ATAC-seq data and improving motif accessibility analyses

The paper introduces three R/bioconductor packages to address technical variations in ATAC-seq data and improve motif accessibility analysis.

GATA3-extension mutants rewire lineage identity in luminal breast cancer

The paper shows that eGATA3 mutations alter transcriptional regulation and lineage identity in luminal breast cancer without losing DNA-binding function.

Trust-Aware Sequence-to-Function Modelling in Regulatory Genomics

The paper introduces RegTrust-XAI, a trust-aware framework for sequence-to-function models in regulatory genomics, showing how reliability, explanation validity, and sequence novelty are distinct properties.

Public-Data Reanalysis Links MS4A4A to M2-like Human Myeloid States and Supports a Predicted Four-Pass Transmembrane Fold

The paper reanalyzes public datasets to show MS4A4A is associated with M2-like myeloid states and finds AlphaFold does not support a predicted MS4A4A-MS4A6A interaction.

RapidMACS: MACS3-identical peak calling, 50x faster

RapidMACS provides a faster narrow peak caller for ATAC-seq and related data, achieving 3.5 to 51x speed improvements over MACS3 while producing identical output.

Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEAD

Loss of extracellular matrix-integrin signaling switches off YAP/TEAD and lets prostate adenocarcinoma organoids turn neuroendocrine; LATS inhibition reverses it, and combined YAP, NOTCH and AR inhibition fully reprograms them.

Implicit Hierarchical Tensor Decomposition of Single-Cell Four-Omics Data Reveals Cell-Type-Associated Enhancer--Promoter Regulatory Programs

The paper develops a tensor decomposition framework to integrate single-cell four-omics data and identifies cell-type-associated enhancer-promoter regulatory programs.

Antimicrobial cetylpyridinium chloride disrupts the mitochondrial electron transport chain as potently as cyanide, via cardiolipin interference at cytochrome C

AUF1-Engineered Intestinal Organoids Enhance Epithelial Barrier Repair and Mucosal Regeneration in Experimental Colitis

This study shows that restoring AUF1 in intestinal organoids improves epithelial barrier function and mucosal healing in colitis models.

Integrated Analysis of Skeletal Muscle Transcriptional Networks Characterizes Dysregulation in Pathways and Trait-Associated Regulatory Regions in Type 2 Diabetes

The paper identifies dysregulated pathways and candidate driver genes in skeletal muscle from individuals with type 2 diabetes using co-expression networks and single-nucleus RNA-seq data.

Expression status transition of NOTCH1 accompanies chromatin remodeling in human early retinal progenitor cells

The paper examines NOTCH1 expression changes in human retinal progenitor cells and links them to chromatin remodeling using single-cell RNA-seq and ATAC-seq data.

Chemical Interrogation and Reprogramming of ATAT1-Mediated Tubulin Acetylation

This study develops chemical tools to measure, inhibit, and visualize ATAT1-mediated tubulin acetylation, enabling controlled manipulation of microtubule stability.

BART-spatial unravels biologically significant transcriptional regulators from spatial omics data

BART-spatial identifies transcriptional regulators from spatial omics data by integrating spatial and pseudotemporal information with TR binding profiles, outperforming existing methods.

ATP Synthase Activity Couples Bioenergetics to Mitochondrial Translation

This study shows mitochondrial translation is sensitive to ATP synthase activity, with matrix GTP availability identified as a key constraint.

Chromatin is a long-range force generator that regulates plasma membrane tension and cell integrity independently of gene expression

The paper investigates how chromatin organization affects cell mechanics during NETosis, finding that chromatin decompaction increases plasma membrane tension and cell volume independently of gene expression.