ATAC-seq

Integrative genomic and transcriptomic analyses uncover regulatory landscape of symbiotic nitrogen fixation in soybean natural population

The paper integrates genomic and transcriptomic data from a soybean diversity panel to identify regulatory elements and genes involved in symbiotic nitrogen fixation, revealing key circadian clock genes and eQTLs.

Wnt activation in mature dermal adipocytes leads to lipodystrophy and skin fibrosis via ATGL-dependent lipolysis.

This study shows that Wnt activation in mature dermal adipocytes causes lipodystrophy and skin fibrosis, which can be reversed by stopping Wnt activation.

Mitochondrial fission controls astrocyte morphogenesis and organization in the cortex

This study shows that mitochondrial fission is essential for astrocyte morphogenesis and organization in the cortex, with Drp1 loss causing morphological and functional deficits.

Identification of transporters essential for survival of Leishmania promastigotes in the digestive tract of sand flies

The paper identifies 34 transporter genes essential for Leishmania promastigote survival in sand flies, with V-ATPase subunits critical for parasite differentiation and life cycle progression.

Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons

The paper introduces Projection-TAGs, a tool for multiplex projection tracing and multi-modal profiling of projection neurons in mice.

Heat shock induces alternative polyadenylation through dynamic DNA methylation-regulated chromatin looping

The paper shows heat shock induces alternative polyadenylation by dynamically regulating DNA methylation and chromatin looping at the DNAJB6 gene.

Single-nucleus analysis reveals oxidative stress in Down syndrome basal forebrain neurons at birth

The paper uses single-nucleus sequencing to identify oxidative stress and metabolic changes in Down syndrome basal forebrain neurons at birth.

Divergence between transcriptomes and chromatin accessibility during differentiation from a bipotential progenitor cell population to erythroblasts and megakaryocytes

The paper compares transcriptomes and chromatin accessibility in MEP, ERY, and MEG cells to reveal divergence in gene regulation during differentiation.

Persistent Activation of Endothelial Cells is Linked to Thrombosis and Inflammation in Cerebral Cavernous Malformation Disease

This paper identifies JUNB as a key driver of chronic brain vascular inflammation in CCM disease through multi-omic analysis of endothelial cell activation.

Lineage memory shapes viral resistance barriers in human skin

The paper shows that viral resistance in human skin cells is inherited through cellular lineages and preserved across generations.

The human transcription factor occupancy landscape viewed using high-resolution in situ base-conversion strand-specific single-molecule chromatin accessibility mapping

The paper introduces a high-resolution single-molecule chromatin accessibility mapping method to quantify transcription factor occupancy and co-accessibility in human cell lines.

Chromatin accessibility differences between the hybrids of nasuta-albomicans complex of Drosophila

The paper examines chromatin accessibility differences in hybrids of Drosophila species to explore how chromosomal rearrangements influence epigenetic divergence and reproductive isolation.

Nuclear Receptor Transcription factors promote axon regeneration in the Adult Corticospinal Tract

This study identifies NR2F1 and NR2F6 as nuclear receptor transcription factors that promote axon regeneration in the corticospinal tract through chromatin remodeling, enhancer redeployment, and translational reprogramming.

Integrative Multi-Omics Analysis of IFNγ-induced Macrophages and Atherosclerotic Plaques Reveals Macrophage-dependent STAT1-Driven Transcription in Atherosclerosis

This study identifies STAT1-dependent genes in IFNγ-treated macrophages and links them to atherosclerosis through multi-omics analysis in human and mouse models.

FOXM1 Inhibition Promotes Polyploidization and Metabolic Maturation in Human iPSC-Derived Hepatocytes by Modulating the Wnt/β-Catenin Pathway

This study shows that FOXM1 inhibition promotes terminal differentiation of human iPSC-derived hepatocytes by enhancing polyploidization and metabolic maturation through the Wnt/β-catenin pathway.

Distinct topologically associated domains underlie the regulatory logic in lymphatic endothelial cells contributing to proper cell differentiation

This study identifies cell type-specific topologically associated domains in lymphatic endothelial cells and defines regulatory networks contributing to their differentiation.

Single-cell omics reveal distinct gene regulatory dynamics underpinning embryonic and extraembryonic lineage functions during pig blastocyst development

The paper analyzes single-cell transcriptomic and epigenomic data from porcine blastocysts to identify gene regulatory dynamics in embryonic and extra-embryonic lineages during development.

Endothelial Cells retain inflammatory memory through chromatin remodeling

This study shows that endothelial cells retain inflammatory memory through chromatin remodeling, with JunB playing a key role in epigenetic priming after sepsis.

The mycomembrane differentially and heterogeneously restricts antibiotic permeation

This paper shows that the mycomembrane of Mycobacterium tuberculosis and M. smegmatis differentially and heterogeneously restricts antibiotic permeation using the PAC-MAN method.

Environmentally-relevant doses of bisphenol A and S exposure in utero disrupt germ cell programming across generations resolved by single nucleus multi-omics

This study shows that prenatal exposure to BPA or BPS at environmentally relevant doses disrupts germ cell programming across generations, affecting sperm counts and transcriptional and epigenetic changes in mice.

Indistinguishable mitochondrial phenotypes after exposure of healthy myoblasts to myalgic encephalomyelitis or control serum

This study replicates a previous experiment and finds no significant differences in mitochondrial phenotypes of myoblasts exposed to ME or control serum.

Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma

The paper analyzes multiomic data from primary and metastatic esophageal adenocarcinoma tumors to identify cell states and their spatial interactions, linking them to clinical outcomes.

TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation

The paper introduces TAC-C, a method combining ATAC-seq and Hi-C to study chromatin interactions in crops, revealing SPL-mediated photosynthesis regulation and chromatin loop structures.

Tbx1 stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus

The paper investigates the role of Tbx1 in cardiopharyngeal mesoderm differentiation and morphogenesis, finding it stabilizes transcriptional profiles and regulates a conserved gene module.

ASXL1 truncating mutations drive leukemic resistance to T cell attack

This study identifies ASXL1 truncating mutations as a driver of leukemic resistance to T cell attack and proposes EZH2 inhibition as a therapeutic strategy to overcome this resistance.

Non-consensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning

The paper shows that GC content increases around transcription factor binding sites across cell lines and proposes that this reflects a scanning mechanism for DNA binding.

TFBSFootprinter: a multiomics tool for prediction of transcription factor binding sites in vertebrate species

TFBSFootprinter predicts transcription factor binding sites across 124 vertebrate species using multiomic data, outperforming existing tools in accuracy.

Identification of candidate causal cis-regulatory variants underlying electrocardiographic QT interval GWAS loci

The paper identifies candidate causal cis-regulatory variants at electrocardiographic QT interval GWAS loci by integrating open chromatin data and expression quantitative trait loci.

Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease

This study uses spatiotemporal single-cell analysis to track T cell clonal dynamics and phenotypic plasticity in GVHD, revealing links between TCR features, clonal expansion, and disease severity.

Clonal lineage tracing and parallel multiomics profiling reveal transcriptional diversification induced by ARID1A deficiency

This study uses an integrated platform to show that ARID1A deficiency increases transcriptomic and epigenetic heterogeneity in cancer cells through stochastic and constrained chromatin changes.