ATAC-seq

Rapid generation of marsupial induced pluripotent stem cells suitable for use in next-generation conservation

This study generates transgene-free iPSCs from the fat-tailed dunnart, demonstrating their pluripotency and potential for use in conservation biotechnology.

Genome-wide chromatin accessibility during early embryogenesis in a generalist cichlid fish

This study maps genome-wide chromatin accessibility in A. calliptera embryos across three stages, revealing dynamic changes in regulatory elements and transcription factor activity during early development.

Aging activates latent enhancers that can be reversed withexercise

This study identifies age-acquired enhancers in mouse hearts and shows that exercise can reverse their activation.

A subtype-specific gene regulatory program controls differential circuit integration of deep CA3 pyramidal neurons

The paper identifies ST18 as a regulator of deep CA3 pyramidal neuron identity, showing its role in restricting a superficial-like program and shaping circuit integration through molecular and electrophysiological changes.

Local chromatin, 3D genome folding and transposon cargo shape Sleeping Beauty transposition

This study identifies factors influencing Sleeping Beauty transposition, showing chromatin context, cargo size, and transcriptional activity affect efficiency and reintegration patterns.

SMARCA4 MUTATIONS PROMOTE CHEMOTHERAPY RESISTANCE IN T-ACUTE LYMPHOBLASTIC LEUKEMIA THROUGH ALTERED CHROMATIN REMODELING AT AP1-ASSOCIATED REGULATORY REGIONS

This study shows SMARCA4 mutations in T-ALL lead to chemotherapy resistance by altering chromatin remodeling at AP-1 regulatory regions, reducing stress response genes.

Revamped transposon-induced hepatocellular carcinoma model reveals deep similarities of cancer-driver landscapes across mice and humans

The paper develops a new transposon-induced model to identify cancer drivers in mice and shows similarities in driver landscapes between mice and humans.

Visualizing the Epigenetic Landscape of Aging and Cellular Reprogramming: Optimized ATAC-see for Cells and Tissues

The paper optimizes ATAC-see for high-throughput chromatin accessibility imaging in aging and reprogramming, revealing age-related chromatin changes and reprogramming-induced remodeling.

Elevated mitochondrial metabolism in Down syndrome iPSCs reduces commitment to neuroectoderm

This study shows that increased mitochondrial metabolism in Down syndrome iPSCs impairs neuroectoderm commitment by reducing ciliation, and this effect can be reversed by inhibiting mitochondrial calcium uptake.

A MultiOmics time-resolved systems map of gene regulation in Toxoplasma gondii

This study creates a time-resolved multi-omics map of gene regulation in Toxoplasma gondii by integrating perturbation data with single-cell measurements, revealing regulatory networks and novel interactions.

Epigenetic Remodeling Increases Plasticity of Bovine Fibroblasts Without Improving Embryo and Stem Cell Development

This study evaluates a multi-target small-molecule cocktail, GUSTC, to reduce repressive heterochromatin marks in bovine fibroblasts, enhancing reprogramming potential without improving embryo development.

Transient Partial Inhibition of DNA Polymerase α Promotes Chromatin Plasticity and Enhances Human Cell Reprogramming

Transient low-dose inhibition of DNA polymerase α enhances human cell reprogramming by promoting chromatin plasticity while maintaining genomic stability.

Multi-omics analysis reveals chromatin and transcriptomic remodeling in hippocampal CA1 following adolescent social isolation

Two weeks of post-weaning isolation in male mice altered expression of 106 CA1 genes, enriched for myelination, while chromatin accessibility shifted only at nominal significance and tracked expression weakly.

Maternal Folate Nutrition Programs Adult Hematopoietic Stem Cell Function Through Mitochondrial Remodeling

This study shows maternal folate levels influence adult hematopoietic stem cell function through mitochondrial and chromatin changes in offspring.

Hepatocyte nuclear factor-1β recruits the nucleosome remodeling and deacetylase complex to activate gene transcription

This study identifies HNF-1β's role in recruiting the NuRD complex to activate gene transcription through chromatin remodeling and acetylation.

Unpacking Chromatin Accessibility with Fiber-seq

This paper introduces Fiber-seq, a method for detecting chromatin accessibility on individual DNA fibers, and provides guidelines for its proper use and analysis.

Integration of ATAC and RNA-sequencing identifies chromatin and transcriptomic signatures in classical and non-classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation

The paper integrates ATAC-seq and RNA-seq data from zebrafish osteoblasts to identify chromatin and transcriptomic signatures and mechanisms of entpd5a regulation.

A multi-omics resource of B cell activation reveals genetic mechanisms for immune-mediated diseases

This study profiles B cell activation states using multi-omics data to identify genetic mechanisms underlying immune-mediated diseases.

Epigenomic heterogeneity and spatial organization during human reprogramming

This study examines epigenomic and spatial changes during human reprogramming, finding distinct molecular and spatial patterns in productive versus unsuccessful trajectories.

SP1 tethers NR2F2 to drive atrial cardiomyocyte identity

The paper identifies SP1 as a transcription factor necessary for human atrial cardiomyocyte identity, showing it interacts with NR2F2 to drive gene regulation.

HyARQ: a Snakemake workflow for allele-specific read counting and quality control in F1 hybrids

HyARQ is a Snakemake workflow for allele-specific read counting and quality control across multiple assays in F1 hybrids, showing accurate recovery of parental proportions.

ZBTB7B is a Master Regulator of Salivary Acinar Cell Function

The paper identifies ZBTB7B as a master regulator of salivary acinar cell function through transcriptional and regulatory analyses in human and mouse salivary glands.

Ctcf deficiency in myofibers induces pathological genome reprogramming toward the spontaneous development of myopathy

This study shows that Ctcf deficiency in myofibers leads to genome reprogramming and myopathy by disrupting 3D genome structure and gene regulation.

Deciphering auditory neuroprogenitor stemness for large-scale neuronal screening

The paper characterizes the molecular and metabolic changes in auditory neuroprogenitors induced by CHIR-DS treatment and demonstrates their utility in neuronal screening.

Engineered regulatory states resolve context-dependent genetics in macular degeneration

The paper uses CRISPR activation to engineer regulatory states in RPE-1 cells, revealing hidden genetic effects in AMD by analyzing chromatin accessibility and transcriptional interactions.

KAS-CUT&Tag for direct mapping of transcription bubbles

N3-kethoxal labeling of single-stranded DNA within CUT&Tag maps Pol II transcription bubbles; bubble density tracks nascent transcription, shifts with transcription inhibitors and TFIIS loss, and peaks at histone genes.

STEER-seq: a recombinase based platform for pooled multimodal single-cell perturbation screening

STEER-seq enables pooled single-cell perturbation screening in hiPSCs by using defined genomic integration and barcode tracking to study transcription factor effects on cell identity.

Hyperosmotic stress induces rewiring of 3D chromatin interactions

One hour of 200 mM sorbitol collapses most chromatin loops in human cells while several hundred transient, cohesin-dependent, CTCF-independent loops form at active promoters, preceding anchor-gene activation.

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.

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.