ATAC-seq

Single-cell multi-omics identify OTP and NOVA1 as regulators of leptin action in hypothalamic feeding circuits

This study uses single-cell multi-omics to identify OTP and NOVA1 as key regulators of leptin action in hypothalamic feeding circuits, revealing cell-type-specific transcriptional and regulatory changes.

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.

RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure

This paper introduces RAD-seq, a method to quantify RNA accessibility by protein binding, and shows it can detect RBP footprints and RNA structure changes under stress.

Circadian feeding rhythm loss drives sex-specific β-cell dysfunction in diet-induced obesity

This study shows that diet-induced obesity disrupts circadian β-cell function more in male mice than females, with time-restricted feeding partially restoring these effects.

Caudate nucleus aging and its association with brain disorders

This study examines caudate nucleus aging across species and diseases, identifying shared and disorder-specific age-related changes in cell types and regulatory features.

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.

Genome-wide loss of chromatin accessibility coexists with selectively elevated RNA abundance in nutrient-starved U2OS cells

This study shows that during nutrient starvation, chromatin accessibility decreases genome-wide, but RNA abundance increases selectively in stress-adaptive genes, indicating limited predictive power of ATAC-seq for transcript abundance.

Continuous Topological Accessibility (RFA) as a 3D-Aware GRN Filter: Anticorrelation with eQTL and No Prediction of ΔRNA

This paper introduces RFA, a 3D-aware GRN filter, and finds it anticorrelates with eQTL via local distance-decay but does not predict ΔRNA.

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.

ChAI-Net learns a regulatory code for chromatin co-accessibility

The paper introduces ChAI-Net, a deep learning model that predicts chromatin co-accessibility from DNA sequences in mouse embryonic stem cells, revealing sequence motifs that govern coordinated TF binding.

Dysplastic Alveolar Basaloid Cells Provide a Protective Barrier via KRT17-Stratifin Complex during Chronic Fibrosis

The paper identifies KRT17-Stratifin complex as a protective barrier in dysplastic alveolar basaloid cells during chronic fibrosis, revealing mechanisms of alveolar metaplasia and its functional relevance.

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.

Single-nucleus multiome profiling reveals osteocyte-centered remodeling of human subchondral bone across osteoarthritis severity

The paper uses single-nucleus multiome sequencing to analyze subchondral bone in OA, finding increased osteocyte SMAD2/3 activity and chondrocyte-derived FN1 signaling with disease severity.

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.

An invariant network architecture with broadly expressed regulators distinguishes cell-type from cell-state identity in situ

The paper constructs state-level regulatory networks in mouse liver hepatocytes, revealing an invariant sub-network of broadly expressed TFs that defines cell-type identity, distinct from state-specific variations.

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.

mito-overview: a mitochondrial report software

mito-overview integrates mitochondrial coverage, allele fractions, annotations, and read co-occurrence to identify and analyze candidate variants in mitochondrial genomic reports.

Characterisation of cis-regulatory elements and genome wide enhancer prediction in Heliconiini butterflies

This study characterizes cis-regulatory elements and predicts enhancers in Heliconiini butterflies using ATAC-seq and histone modification data, revealing temporal divergence and developing a CNN for enhancer prediction.

XChrom: a cross-cell chromatin accessibility prediction model integrating genomic sequence and cellular context

XChrom predicts chromatin accessibility across cells and genomic regions using genomic sequence and cell identity, outperforming existing methods and enabling cross-species analysis.

Integrating sequence-to-omics predictions and personal multi-omics for rare variant prioritization

The paper introduces Watershed-DL, a framework integrating sequence-to-omics predictions and multi-omics data to prioritize rare variants, finding it increases prioritized variants by 61.4% and identifies candidate disease alleles.

Tandem repeat variation shapes immune cell type-specific gene expression

The paper identifies immune cell type-specific gene expression regulated by tandem repeats using multi-omics data from large cohorts.

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.

CDH1 loss remodels gene expression and lineage identity in human mammary epithelial cells

This study shows that CDH1 loss in human mammary epithelial cells remodels gene expression and lineage identity toward a luminal progenitor-like state, contributing to ILC oncogenesis.