ATAC-seq

Visualizing the Epigenetic Landscape of Aging and Cellular Reprogramming: Optimized ATAC-see for Cells and Tissues

The paper optimizes ATAC-see for high-throughput chromatin accessibility imaging in aging and reprogramming, revealing age-related chromatin changes and reprogramming-induced remodeling.

Elevated mitochondrial metabolism in Down syndrome iPSCs reduces commitment to neuroectoderm

This study shows that increased mitochondrial metabolism in Down syndrome iPSCs impairs neuroectoderm commitment by reducing ciliation, and this effect can be reversed by inhibiting mitochondrial calcium uptake.

Multi-omics analysis reveals chromatin and transcriptomic remodeling in hippocampal CA1 following adolescent social isolation

Two weeks of post-weaning isolation in male mice altered expression of 106 CA1 genes, enriched for myelination, while chromatin accessibility shifted only at nominal significance and tracked expression weakly.

XChrom: a cross-cell chromatin accessibility prediction model integrating genomic sequence and cellular context

XChrom predicts chromatin accessibility across cells and genomic regions using genomic sequence and cell identity, outperforming existing methods and enabling cross-species analysis.

Tandem repeat variation shapes immune cell type-specific gene expression

The paper identifies immune cell type-specific gene expression regulated by tandem repeats using multi-omics data from large cohorts.

CDH1 loss remodels gene expression and lineage identity in human mammary epithelial cells

This study shows that CDH1 loss in human mammary epithelial cells remodels gene expression and lineage identity toward a luminal progenitor-like state, contributing to ILC oncogenesis.

Unpacking Chromatin Accessibility with Fiber-seq

This paper introduces Fiber-seq, a method for detecting chromatin accessibility on individual DNA fibers, and provides guidelines for its proper use and analysis.

Integration of ATAC and RNA-sequencing identifies chromatin and transcriptomic signatures in classical and non-classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation

The paper integrates ATAC-seq and RNA-seq data from zebrafish osteoblasts to identify chromatin and transcriptomic signatures and mechanisms of entpd5a regulation.

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection

A multi-omics resource of B cell activation reveals genetic mechanisms for immune-mediated diseases

This study profiles B cell activation states using multi-omics data to identify genetic mechanisms underlying immune-mediated diseases.

Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods

The paper investigates how genomic changes in coleoid cephalopods shape 3D genome architecture and regulatory landscapes, revealing species-specific chromatin loops and their role in neural development.

Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types

The paper introduces optimized fluorescence-activated nuclei sorting (FANS) protocols to isolate cell-type-specific nuclei from human and mouse brain tissue for multi-omic analysis.

Signaling by a tyrosine-sulfated peptide balances growth and osmotic stress response in rice

Overexpressing rice peptide OsPSY8 lengthens roots but lowers osmotic stress survival, while knockout raises it; OsWRKY24 represses the OsPSY8 promoter and is induced by PEG.

Genome-wide discovery of cis-regulatory elements in a large genome

The paper develops resources to identify cis-regulatory elements in the Parhyale hawaiensis genome using ATAC-seq and sequence conservation analysis.

EWS::WT1 Isoform-Dependent Regulation of Neogenes in Desmoplastic Small Round Cell Tumors

This study identifies DSRCT-specific neogenes regulated by the EWS::WT1 fusion protein and shows their potential as biomarkers and therapeutic targets in desmoplastic small round cell tumors.

HDAC inhibitor treatment restores transcriptome, chromatin accessibility and memory deficits in a mouse model for Down syndrome

Controlling for DNA dosage with Whole Genome Sequencing improves ATAC-seq peak calling

This paper improves ATAC-seq peak calling by integrating whole-genome sequencing data to control for DNA dosage biases, enhancing peak accuracy and relevance to gene regulation.

Increased chromatin accessibility following 1α,25-dihydroxyvitamin D3 treatment in human endometrial stromal cells

This study examines how 1,25-dihydroxyvitamin D3 affects chromatin accessibility in human endometrial stromal cells using ATAC-seq, revealing increased signal intensity and pre-accessible chromatin environments for transcription.

Regulation of immune signal integration and memory by inflammation-induced chromosome conformation

This study shows that inflammation-induced changes in 3D genome conformation regulate immune signal integration and transcriptional memory in macrophages.

Paclitaxel induces NM2-dependent cellular contraction through GEF-H1 dissociation from microtubules and RhoA/ROCK activation in cancer cells

This study shows paclitaxel induces cancer cell contraction via GEF-H1 dissociation from microtubules and RhoA/ROCK activation, with tubulin acetylation regulating this process.

Reversibility of Nuclear and 3D Genomic Changes in Non-Cancerous Fibroblasts After Constricted Migration

This study shows that non-cancerous fibroblasts experience reversible nuclear and 3D genomic changes after constricted migration, unlike stable changes in cancer cells.

Functional screening of ZIP8 naturally occurring variants identifies pathogenic mutations and trafficking defects

The paper functionally screens ZIP8 variants to identify pathogenic mutations and trafficking defects using a combined experimental and computational approach.

Flexible use of conserved motif vocabularies constrains genome access in cell type evolution

The paper shows that conserved motif vocabularies constrain genome access in cell type evolution across species.

GenoME: a MoE-based generative model for individualized, multimodal prediction and perturbation of genomic profiles

GenoME predicts genomic profiles and perturbations using ATAC-seq and DNA sequence, generalizing to new cell types and identifying enhancer-promoter connections.

Cyclin C nuclear release and mitochondrial dysfunction define molecular signatures of MED13L Syndrome

The paper identifies mitochondrial dysfunction and cyclin C mislocalization as consistent features of MED13L syndrome, linking them to clinical severity and suggesting potential biomarkers.

Purinergic receptor activation rectifies autism-associated endothelial dysfunction

This study shows that purinergic receptor activation can correct endothelial dysfunction linked to autism in a mouse model by restoring bioenergetic function and cerebrovascular reactivity.

Conserved Neuronal-like and Secretory Programs Define the Spatial Architecture of Gastroenteropancreatic Neuroendocrine Tumors

This study identifies conserved neuronal-like and secretory programs in GEP-NETs and links them to spatial microenvironmental niches and metastatic potential.

mmVelo: A deep generative model for estimating cell state-dependent dynamics across multiple modalities

mmVelo estimates cell state-dependent dynamics across multiple modalities using deep generative modeling, validated on mouse and human data.

Targeted ATAC-see (tATAC-see): A Visual Assay for Target-Specific Chromatin Profiling

tATAC-see captures target-specific chromatin states using a visual assay, showing dynamic remodeling in aging models and LAD resistance.

Expression status transition of NOTCH1 accompanies chromatin remodeling in human early retinal progenitor cells

The paper examines NOTCH1 expression changes in human retinal progenitor cells and links them to chromatin remodeling using single-cell RNA-seq and ATAC-seq data.