ATAC-seq

NR2F2 regulation of interstitial to fetal Leydig cell differentiation in the testis: insights into differences of sex development

The paper identifies Nr2f2 as a regulator of interstitial to fetal Leydig cell differentiation in mice, linking its dysfunction to disorders of sex development.

Cell type mapping of mild malformations of cortical development with oligodendroglial hyperplasia in epilepsy using single-nucleus multiomics

This study uses single-nucleus multiomics to map cell types and molecular changes in MOGHE lesions, identifying disease-specific oligodendrocytes and heterotopic neurons with altered gene expression.

H3F3A K27M Mutations Drives a Repressive Transcriptome by Modulating Chromatin Accessibility, Independent of H3K27me3 in Diffuse Midline Glioma

Diversification of Dentate Gyrus Granule Cell Subtypes is Regulated by Neuregulin1 Nuclear Back Signaling.

The paper identifies a role for Neuregulin1 nuclear back signaling in regulating dentate gyrus granule cell subtype diversity, showing that its disruption leads to increased semilunar granule cell-like cells.

TCA cycle rewiring underpins implantation and histone acetylation programming

This study reveals that TCA cycle rewiring at implantation supports histone acetylation programming and pluripotency transitions in mouse embryos.

Multi-scale gene regulatory networks for resolving transcription factor and autoimmune variant impacts on human B cell fate dynamics

Targeting RhoA activity rejuvenates aged hematopoietic stem cells

This study shows that reducing RhoA activity in aged HSCs lowers nuclear tension, restores chromatin structure, and improves regenerative capacity and lineage balance.

Early epigenetic priming of regeneration studied with a novel transgenic epigenetic reporter

The paper uses a novel transgenic reporter to study epigenetic reprogramming during zebrafish fin regeneration, identifying early chromatin remodeling events and key factors required for regeneration.

Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner

The paper shows that Hmgb2 enhances astrocyte-to-neuron conversion by regulating chromatin accessibility of neuronal maturation genes in response to growth factors.

Characterization of non-coding variants associated with transcription factor binding through ATAC-seq-defined footprint QTLs in liver

The paper identifies 693 SNPs associated with transcription factor binding in liver ATAC-seq data by analyzing footprint quantitative trait loci (fpQTLs).

Single cell multi-omic whole genome sequencing and chromatin accessibility profiling reveals genome-epigenome coevolution in colorectal cancer

This paper introduces dATAC, a single-cell multi-omic method for simultaneous whole genome sequencing and chromatin accessibility profiling, revealing genome-epigenome coevolution in colorectal cancer.

A bifunctional imprinted lncRNA scaffolds NuRD-HDAC1 to couple cis-activation of Dio3 with trans-repression of the osteoblast chromatin landscape

The paper shows Dio3os scaffolds NuRD-HDAC1 to activate Dio3 in cis and repress thyroid-hormone-responsive osteogenic genes in trans.

Integration of functional genomics and statistical fine-mapping systematically characterizes adult-onset and childhood-onset asthma genetic associations.

This study integrates functional genomics and statistical fine-mapping to identify causal variants, regulatory elements, and effector genes for adult-onset and childhood-onset asthma.

Dynamin 1-mediated endocytic recycling of glycosylated N-cadherin sustains the plastic mesenchymal state to promote ovarian cancer metastasis

This study identifies DNM1 as a master regulator of EMT in ovarian cancer, showing it sustains the mesenchymal state through N-cadherin endocytic recycling and promotes metastasis.

Nuc3DMap delineates finer nucleosome-based three-dimensional chromatin architecture

Nuc3DMap integrates MNase-seq, Hi-C, and Micro-C data to delineate finer nucleosome-based 3D chromatin architecture and identifies distinct subtypes of chromatin features.

Neural stem cell epigenomes and fate bias are temporally coordinated during corticogenesis

The paper integrates single-cell transcriptomics and epigenomics to show how neural stem cells shift lineage bias and epigenetic states during mouse corticogenesis.

Nuclear actin-dependent Meg3 expression suppresses metabolic genes by affecting the chromatin architecture at sites of elevated H3K27 acetylation levels

This study shows that β-actin depletion increases Meg3 expression, which alters chromatin architecture and represses metabolic genes through promoter-enhancer interaction disruption.

Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms

The paper performs genotype inference from aggregated chromatin accessibility data to identify caQTLs and their links to gene expression and complex traits.

Identifying similar populations across independent single cell studies without data integration

The paper introduces CFS, a method to compare cell groups across datasets without integration, identifying conserved astrocyte subpopulations in mouse motor cortex and spinal cord.

Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq

The paper introduces a copy number normalization pipeline to distinguish differential signals in ATAC-seq and ChIP-seq driven by copy number differences from other factors.

A new class of OLD family ATPases Cran1 functions in cell cycle progression in an archaeon

This study identifies a new class of OLD family ATPases in archaea, showing Cran1 is essential for cell cycle progression rather than antiviral defense.

Cochlin-Expressing Memory B (COMB) Cells Are Enriched in Autoimmune Diseases and Display a Distinct Activation Profile

The paper identifies a novel memory B cell subset, COMB cells, enriched in autoimmune diseases and characterized by distinct transcriptional and epigenetic features.

Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate pathogenic variants in age-related macular degeneration

The paper creates a single-cell multiome atlas of RPE and choroid tissues to identify pathogenic variants and mechanisms in AMD using HiChIP, Activity-by-Contact, and STARR-seq.

Prior epigenetic status predicts future susceptibility to seizures in mice

The paper shows that epigenetic variation recorded in mice during development predicts seizure susceptibility, with specific loci linked to human epilepsy genes.

Multi-omic human neural organoid cell atlas of the posterior brain

The paper creates a multi-omic atlas of human neural organoids modeling the posterior brain and identifies morphogen conditions that expand organoid models.

Epigenetic Reprogramming Alters Intestinal Stem Cell Fate in Pouchitis

This study shows that inflammation in pouchitis alters intestinal stem cell fate through epigenetic changes, which can be reversed by JAK/STAT therapies.

Catalytic activity of KMT5B promotes cilia tuft formation without affecting chromatin accessibility of ciliary genes

The paper shows that KMT5B promotes cilia tuft formation independently of chromatin accessibility changes at ciliary genes.

Multi-omic latent variable data integration reveals multicellular structure pathways associated with resistance to tuberculin skin test (TST)/interferon gamma release assay (IGRA) conversion in Uganda

The paper integrates multi-omic data to identify latent factors associated with resistance to TB conversion, revealing pathways related to multicellular structure and cell-cell interactions.

Contextualizing gene expression with feature rich graph neural networks

This paper introduces OGL, a deep learning method that integrates multi-omics data to predict gene expression and uncover regulatory interactions across cell lines and tissues.

SUV39H1 Preserves Cancer Stem Cell Chromatin State and Properties in Glioblastoma

This paper shows SUV39H1 is critical for maintaining glioblastoma stem cell properties and progression, and targeting it enhances chemotherapy effectiveness.