ATAC-seq

Deconvolution of the mechanisms of T cell drug response in multiple myeloma induction therapy

This study investigates the molecular effects of RVd therapy on T cells using TEA-seq, revealing how individual and sequential drug administration impacts T cell function and states.

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.

Epigenetic characterization and manipulation of rare circadian neuron subtypes

El-INTACT nuclear purification gives clean ATAC-seq from ~120 Drosophila clock neurons and 16 PDF neurons, revealing cell-type-specific Clk enhancers; disrupting two renders flies arrhythmic.

SIM2s coordinates programmed mitophagy with respiratory chain supercomplex remodeling during mammary epithelial differentiation

Human-specific retrotransposons encode the regulatory logic of two lineages in a bipotent neural crest and central nervous system precursor

The paper identifies human-specific retrotransposons as regulatory elements in bipotent neural crest and central nervous system precursors, showing their association with gene expression and transcription factor motifs.

Distinct RNA-RNA spatial interaction sub-networks of transcription factors in hepatic cells

The paper uses RIC-seq and integrates multi-omics data to classify transcription factors into two clusters based on RNA-RNA spatial interactions and their genomic and clinical features.

A putative cis-regulatory element near Shox2 in the jerboa genome (Jaculus jaculus) is not sufficient to alter mouse limb bone lengths

The paper tests a putative cis-regulatory element near Shox2 in jerboas to see if it affects mouse limb bone length, finding no detectable phenotype.

Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

Integration of cell-specific gene expression and chromatin accessibility facilitates localization of neurodegenerative risk in microglia

The paper integrates cell-specific gene expression and chromatin accessibility to identify neurodegenerative disease risk loci specific to microglia.

Predictive control of human pancreatic cell fate using a digital model of in vitro differentiation

The paper develops a predictive digital model of human pancreatic cell differentiation using single-cell multiomic data to identify regulators and validate their roles in islet fate specification.

Genome-scale perturbation signatures from primary human CD4+ T cells improve genetics-based prioritization of immune drug targets

The paper introduces IGNITE, a framework that combines genetic data with functional genomics to prioritize immune drug targets, showing improved performance over genetic methods alone.

FetchPA: a guided, end-to-end solution for local ATAC-Seq data processing and analyses

FetchPA provides an end-to-end ATAC-Seq analysis pipeline for users without bioinformatics expertise, enabling local and public data processing and differential accessibility analysis.

Ryder: Epigenome normalization using a two-tier model and internal reference regions

Ryder normalizes epigenomic bigWig tracks against stable internal reference regions such as invariant CTCF sites, correcting background and signal separately, recovering expected perturbation effects that depth-only normalization obscured.

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.

Single-cell transcriptomic and epigenomic analysis reveals X-linked sex differences in aging mouse hypothalamus

The paper analyzes single-nucleus multi-omics data from mouse hypothalamus to reveal sex-specific aging differences, particularly on the X chromosome.

Variant-to-gene mapping in ocular cell types identifies candidate effector genes for primary open-angle glaucoma

This study maps POAG risk variants to candidate effector genes in ocular cell types, identifying ARHGEF12 as a potential target.

Epigenetic perturbation unravels diverse origins, state conversions and de-differentiation of cortical astrocytes

This study investigates the role of DOT1L in astrogenesis, identifying its role in maintaining astrocyte states and revealing multiple origins and state conversions of cortical astrocytes.

ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility

This study compares ATAC-seq and MNase-seq in budding yeast, showing they detect distinct chromatin states and functional roles in gene regulation.

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.

Nuclear βactin dependent chromatin accessibility governs stem cell pluripotency and extracellular matrix gene programs to maintain cellular biomechanics for cell lineage decisions

This study shows nuclear βactin regulates chromatin accessibility and ECM mechanics to maintain pluripotency and lineage decisions in mESCs.

CHD8 orchestrates chromatin landscapes during early female neuronal differentiation

This study investigates CHD8's role in female neuronal differentiation using multi-omics analysis, revealing its impact on chromatin structure and gene regulation in mouse models.

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.

A single-nucleus multiomic and spatial atlas of gene regulation in human spermatogenesis

This study creates a single-nucleus multiomic and spatial atlas of human spermatogenesis, linking gene regulatory networks to infertility-associated genetic variation and disease perturbations.

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.

Motif-based model of transcription predicts effects of sequence variants in AR enhancers and reveals distinct functions for AR-associated transcription factors

The paper develops a motif-based model to predict sequence variant effects in AR enhancers and identifies functional classes of transcription factors, validated against mutagenesis data and GWAS risk alleles.

Cell cycle control of chromatin creates a therapeutic window for epigenetic therapy in tumors

This paper shows that extending G1 phase in cancer cells creates a therapeutic window for epigenetic drugs, with LSD1 inhibition and CDK4/6 inhibition working synergistically to induce differentiation and improve survival in AML models.

Minimizing time in culture: A prototypic autologous manufacturing workflow for monoclonal iPSC lines within seven weeks

This study develops a time-efficient, standardizable workflow for generating monoclonal iPSC lines from human skin biopsies within seven weeks, with low variability and genomic integrity.

The Notch signaling pathway is a master regulator of CD8+ T cell exhaustion and differentiation during chronic infection

This study shows that Notch signaling regulates CD8+ T cell exhaustion and differentiation during chronic infection by promoting the transition from progenitor to effector-like cells and preventing terminal exhaustion.