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.