ATAC-seq

Integrated genomic analysis and CRISPRi implicates EGFR in Alzheimer's disease risk

The paper identifies EGFR as a potential therapeutic target in Alzheimer's disease by linking a risk variant to increased EGFR expression in brain cell types through genomic analysis and CRISPRi validation.

Glis3 is a modifier of cyst progression in autosomal dominant polycystic kidney disease

This study investigates Glis3's role in ADPKD, finding that its dual inactivation with Pkd1 worsens kidney disease, affecting metabolism and circadian function.

Single-cell multiomics reveals epigenetic rewiring of splenic memory B cells during murine malaria reinfection

The paper uses single-cell multiomics to study B cell changes in mice during malaria reinfection, finding shifts in memory B cell composition and epigenetic programs linked to rapid antibody production.

Conservation of cis-regulatory codes over half a billion years of evolution

The paper shows that cis-regulatory codes in retinal cell classes are highly conserved across vertebrates despite extensive enhancer turnover.

Mechanoepigenetic Targeting of Histone Methyltransferase EZH2 Increases Potential of Scalable Manufacturing in Human Derived Primary Mesenchymal Stromal Cells

This paper identifies a mechano-epigenetic pathway involving EZH2 that drives phenotypic drift in human MSCs during expansion and shows that EZH2 inhibition preserves stemness and therapeutic potency.

Transcriptional Dynamics and Chromatin Accessibility in the Regulation of Shade-Responsive Genes in Arabidopsis

This study investigates how chromatin accessibility and PIF7 binding regulate shade-responsive gene expression in Arabidopsis under short and prolonged shade exposure.

Spatially distinct chromatin compaction states predict neoadjuvant chemotherapy resistance in Triple Negative Breast Cancer

The paper uses FLIM to measure chromatin compaction in TNBC tissues and finds that spatial chromatin states predict resistance to neoadjuvant chemotherapy.

Maternal protein restriction alters chromatin accessibility in neuroprogenitors of the fetal hypothalamus of rats.

This study identifies altered chromatin accessibility in fetal rat hypothalamic neuroprogenitors due to maternal protein restriction, affecting gene regulation and developmental pathways.

OTX2 controls chromatin accessibility to direct somatic versus germline differentiation

This study shows OTX2 controls chromatin accessibility to promote somatic differentiation over germline fate in embryonic cells.

Glutamine deficiency enhances nuclear localization of TCA cycle enzymes and epigenetic modifications, impairing myogenesis

This study shows that glutamine deficiency reduces MPC proliferation by altering TCA cycle enzyme localization and epigenetic modifications, impairing myogenesis.

The regenerative potential of adult Nestin+ cerebellar astroglia is limited compared to in neonates

This study shows adult Nestin+ cerebellar astroglia have limited regenerative potential compared to neonatal cells, with ATAC-seq revealing developmental gene silencing as a key factor.

Identifying a gene signature of metastatic potential by linking pre-metastatic state to ultimate metastatic fate

This study identifies a gene signature of metastatic potential by linking pre-metastatic states to metastatic outcomes in mouse pancreatic cancer and validates its relevance in human tumors.

MEF2C controls segment-specific gene regulatory networks that direct heart tube morphogenesis

This study identifies MEF2C-dependent gene regulatory networks in specific heart segments and shows their role in heart tube morphogenesis using multi-omics data and deep learning.

The Regulatory Logic of Planarian Stem Cell Differentiation

The paper integrates single cell transcriptomics and chromatin accessibility data to uncover the regulatory logic of planarian stem cell differentiation, validating predictions with TF knockdown experiments.

Chrom-Sig: de-noising 1-dimensional genomic profiles by signal processing methods

Chrom-Sig de-noises 1-dimensional genomic coverage tracks using signal processing to separate signal from noise, validated across multiple datasets.

CountASAP: A Lightweight, Easy to Use Python Package for Processing ASAPseq Data

CountASAP converts ASAPseq FASTQ data into count matrices for downstream analysis.

WAD: a wavelet-based linear programming method using L1-minimal reconstruction loss for accessible chromatin data deconvolution

WAD deconvolves bulk accessible chromatin data to estimate cell-type proportions using wavelet-based denoising and L1-minimal linear programming, achieving lower error and higher concordance than existing methods.

A conserved transcriptional backbone and rewiring of gene-regulatory networks in activated human CD4⁺ T cells

The paper identifies a conserved set of transcription factors in human CD4+ T cell subtypes and shows subtype-specific rewiring of gene regulatory networks during activation and differentiation.

Goldilocks conundrum explains cryoinjury in slow-cooled amphibian embryonic cells

This study shows that cell size affects cryopreservation outcomes in amphibian embryonic cells, with optimal cryoprotectant conditions varying by cell size.

Domestication shaped the chromatin landscape of grain amaranth

The paper examines how domestication affects the chromatin landscape in grain amaranth, finding that 2.5% of chromatin regions switch states during domestication, associated with selective sweeps.

A Nextflow pipeline for molecular quantitative trait loci mapping in small sample size datasets with an application in Atlantic salmon

The paper introduces nf-RASQUAL, a Nextflow pipeline for molQTL mapping in small datasets, applied to Atlantic salmon to identify expression and chromatin accessibility QTLs.

Epigenomic and transcriptomic germ-free ageing atlas reveals sterile inflammation as an intrinsic ageing feature

This study presents a single-cell epigenomic and transcriptomic atlas of aged mice under germ-free conditions, revealing sterile inflammation as an intrinsic ageing feature.

ATP increases murine neuroblastoma cell size through a PANX1- and macropinocytosis-dependent mechanism

This study shows ATP increases murine neuroblastoma cell size via PANX1-dependent macropinocytosis, with PANX1 internalization and lipid interactions involved.

Decoding the pituitary gonadotrope regulatory architecture governing the preovulatory surge in vivo

The paper identifies a biphasic gene regulatory network in rat pituitary gonadotropes that controls the preovulatory hormone surge, showing FSH surge is driven by dynamic Fshb transcription rather than Lhb upregulation.

RUNX2 promotes epigenetic WNT signaling in inflamed intestinal epithelial cells

This study identifies RUNX2 as a regulator of WNT signaling in UC by analyzing snRNA-seq and snATAC-seq data from UC patient-derived colonoids.

A Multimodal Atlas Reveals the Anatomical Distribution of Medium Spiny Neuron Subtypes and a Novel RGS6+ Population in the Primate Striatum

The paper builds a multimodal atlas of medium spiny neurons in the primate striatum, identifying new subtypes and linking them to disease associations.

Pathway and gates for ATG2A-mediated lipid transport in autophagy

This study identifies the mechanism of ATG2A-mediated lipid transport in autophagy, revealing N-terminal helices as gates that regulate lipid transfer efficiency.

Dysregulation of transcription networks regulating oligodendrogenesis in age-related decline in CNS remyelination

The paper identifies age-related dysregulation of transcription networks in oligodendrocyte differentiation using single-nucleus RNA and ATAC sequencing in mice, with parallels in MS lesions.

Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge

The paper develops a general AI model that integrates diverse genomic modalities and knowledge, showing strong performance across cell types and tissues.

Single-nucleus multi-omics identifies shared and distinct pathways in Pick's and Alzheimer's disease

This study uses single-nucleus multi-omics to identify shared and distinct regulatory pathways in Pick's and Alzheimer's disease, revealing disease-specific enhancers and TF binding patterns.