ATAC-seq

A Multimodal Spatial and Epigenomic Atlas of Human Adult Lung Topography

The paper creates a high-resolution multimodal lung atlas using single-nucleus RNA and chromatin data from 11 healthy adults, identifying 70 cell populations and 332,846 chromatin regions.

The fire ant social chromosome exerts a major influence on genome regulation

The paper investigates how a supergene in fire ants influences genome regulation through chromatin accessibility, enhancer activity, and gene expression.

Identification of causal genes and mechanisms by which genetic variation mediates juvenile idiopathic arthritis susceptibility using functional genomics and CRISPR-Cas9

This study identifies causal genes and mechanisms for juvenile idiopathic arthritis by integrating GWAS, PCHi-C, ATAC-seq, and CRISPRa/i in CD4+ T cells from JIA patients.

PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms

The paper shows PBX1 and PBX3 regulate SHH expression in the FEZ through opposite mechanisms, with PBX1 upregulating and PBX3 downregulating SHH via a shared cis-regulatory element.

Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex

The paper evaluates computational methods for predicting cell type-specific enhancers in the mouse cortex using in vivo validation data and finds that open chromatin and sequence models improve prediction accuracy.

The epigenetic regulator TRIM24 controls melanoma cell dedifferentiation and resistance to treatment in melanoma

This study identifies TRIM24 as an epigenetic regulator that promotes melanoma cell dedifferentiation and treatment resistance, with potential as a druggable target.

EYKTHYR reveals transcriptional regulators of spatial gene programs

EO_SCPLOWYKTHYRC_SCPLOW identifies spatial transcriptional regulators by integrating gene expression and chromatin accessibility in spatial multiome data, outperforming existing methods in mouse brain and tumor datasets.

Rescuing Ischemic Brain Injury by Rewiring Mitochondrial Electron Flow

This study shows that expressing alternative oxidase (AOX) reduces reverse electron transfer and oxidative stress in ischemia-reperfusion brain injury, preserving complex I function and providing neuroprotection.

Upstream open reading frame inactivation augments GATA4 translation and cardiomyocyte hypertrophy in mice

This study shows that inactivating a uORF in the Gata4 gene in mice leads to increased GATA4 translation and cardiac hypertrophy.

Machine-guided cell-fate engineering

The paper introduces a machine-learning pipeline, CellCartographer, to design TF pooled-screens for cell type conversion using chromatin accessibility data, achieving efficient differentiation of iPSCs into six cell types within 6 days.

Single-cell chromatin landscape and DNA methylation patterns reveal shared molecular programs in human tumor and non-tumor tissue CCR8+ Treg cells

The paper compares CCR8+ Treg cells in tumor and tumor-free tissues using chromatin accessibility and DNA methylation, finding high similarity suggesting tumor microenvironment activation of tissue Treg cells.

Myosin modulator Aficamten inhibits force in cardiac muscle by altering myosin's biochemical activity without changing thick filament structure

This paper shows Aficamten inhibits cardiac myosin ATPase without changing thick filament structure, unlike Mavacamten, leading to similar force reduction but different kinetic effects.

PATZ1 Reinstates a Growth-Permissive Chromatin Landscape in Adult Corticospinal Neurons After Injury

This study maps chromatin accessibility changes in mouse forebrain development and shows that PATZ1 can reverse epigenetic restrictions in adult neurons to enhance axon regeneration after injury.

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity

The paper identifies a spatiotemporal cancer cell trajectory in glioblastoma that explains tumor heterogeneity across regions and subclones.

Decoding Plasticity Regulators and Transition Trajectories in Glioblastoma with Single-cell Multiomics

This study uses single-cell multiomics to identify regulatory programs and plasticity regulators in glioblastoma, revealing MYT1L as a key repressor of malignant plasticity.

Let-7 restrains an oncogenic circuit in AT2 cells to prevent fibrogenic cell intermediates in pulmonary fibrosis

This study identifies let-7 as a regulator of AT2 cell differentiation and fibrosis prevention by controlling oncogenic networks and epigenetic changes.

Mechanism of formin-mediated filament nucleation from profilin-actin

This study investigates how formins nucleate actin filaments by analyzing the role of FH1 and FH2 domains in binding and transferring profilin-actin complexes.

Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at meiotic promoters in mice

The paper identifies NFYA as a factor that promotes accessible chromatin at meiotic gene promoters in pre-meiotic germ cells, enabling timely meiotic entry in mice.

Induction of Moderate DNA Damage Enhances Megakaryopoiesis and Platelet Production

The paper shows that low-dose PARP inhibitors or gamma-irradiation increase DNA damage in megakaryocytes and their progenitors, leading to higher megakaryopoiesis and platelet production in mice.

Transcription factor occupancy is affected by genetic variation in the white adipose tissue of C57BL6/j and 129S1/SvImJ mice

The paper investigates how genetic variation in two mouse strains affects chromatin accessibility and TF binding in adipose tissue, linking these changes to gene regulation and disease susceptibility.

Tet1 safeguards lineage allocation in intestinal stem cells

This study shows Tet1 buffers intestinal stem cell differentiation by reducing sensitivity to extrinsic signals, without altering chromatin accessibility.

Epidermal loss of PRMT5 leads to the emergence of an atypical basal keratinocyte-like cell population and defective skin stratification

This study shows that loss of PRMT5 in skin leads to defective stratification and an atypical keratinocyte population with senescence-like features.

Chromatin profiling data indicate regulatory mechanisms for differentiation during development in the acoel Hofstenia miamia

The paper uses ATAC-seq to analyze chromatin accessibility during embryonic development in Hofstenia miamia, identifying regulatory mechanisms and gene networks involved in differentiation.

EZH1 Q571R-mediated chromatin compaction and its oncogenic potential in thyroid cancer

This study shows that the EZH1Q571R mutation enhances chromatin compaction and PRC2 activity, leading to repression of tumor suppressor genes in follicular thyroid cancer.

Ischemic Injury Drives Tumor Growth via Accelerated Hematopoietic Aging

This study shows that peripheral ischemia accelerates hematopoietic aging, promoting tumor growth by skewing immune cell composition and enhancing immunosuppression.

Mitochondrial heterogeneity disrupts osteoclast differentiation and bone resorption by impairing respiratory complex I

This study shows mitochondrial heteroplasmy impairs osteoclast differentiation and bone resorption by disrupting respiratory complex I and autophagy, and identifies spermidine as a potential therapeutic agent.

Spatial profiling of chromatin accessibility reveals alteration of glial cells in Alzheimer's disease mouse brain

The paper uses spatial ATAC-seq to identify chromatin accessibility changes in glial cells of Alzheimer's disease mouse models, linking them to AD-related pathways and human risk genes.

Cell Type Specific Enhancers for Dorsolateral Prefrontal Cortex.

The paper identifies cell type-specific enhancers for the DLPFC in NHPs using single nucleus RNA-Seq and ATAC-Seq, validates them with AAV injections, and demonstrates functional expression in specific neuron types.

Compensatory Plasticity Defines a Vulnerable Neuronal State in Alzheimers Disease with Psychosis

The paper identifies transcriptional changes in upper-layer cortical pyramidal neurons in Alzheimer's disease with psychosis, linking them to network dysfunction and vulnerability.

Phase-separating MoSpa2 Complex Organizes Actin Nucleation Center for M.oryzae Plant Infection

This study identifies MoSpa2's role in organizing actin nucleation centers in Magnaporthe oryzae through phase separation, supporting polarized growth and host infection.