ATAC-seq

Mechanistic dissection of the CHD4 enhancers reveals cooperative functions among the homotypic ZNF410 clustered motifs

The paper investigates how ZNF410 regulates the CHD4 gene through enhancer regions, showing additive contributions from two enhancers and cooperative binding of ZNF410 to clustered motifs.

Analysis of regulatory network modules in hundreds of human stem cell lines reveals complex epigenetic and genetic factors contribute to pluripotency state differences between subpopulations

The paper identifies regulatory network modules in human stem cells, showing epigenetic and genetic factors influence pluripotency state differences.

Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provides Insights into Type 2 Diabetes Genetics

This study investigates how human pancreatic islet cells respond to ER and cytokine stress and identifies T2D-associated genetic variants that modulate these responses.

Loss of Ezh2 in the medial ganglionic eminence alters interneuron fate, cell morphology and gene expression profiles

This study shows that loss of Ezh2 in the medial ganglionic eminence (MGE) leads to changes in interneuron fate, morphology, and gene expression.

Matrix-rigidity cooperates with biochemical cues in M2 macrophage activation through increased nuclear deformation and chromatin accessibility

This study shows matrix rigidity enhances M2 macrophage activation by altering nuclear mechanics and chromatin accessibility through cooperation with biochemical signals like IL4/13.

Identification of a core transcriptional program driving the human renalmesenchymal-to-epithelial transition

The paper identifies a core transcriptional program driving the human renal mesenchymal-to-epithelial transition using human renal organoids and multi-ome profiling.

Chromatin states contribute to coordinated allelic transcriptional bursting to drive iPSC reprogramming

The paper investigates how chromatin states influence coordinated allelic transcriptional bursting during iPSC reprogramming and finds that chromatin accessibility correlates with allelic coordination.

Multi-omic Analysis of Primary Human Kidney Tissues Identifies Medulla-Specific Gene Expression Patterns

The paper identifies medulla-specific gene expression patterns in adult human kidney tissues using multi-omic data and corrects misassignments in the GTEx database.

Single-cell multi-omics reveals insights into differentiation of rare cell types in mucinous colorectal cancer

The paper uses single-cell multi-omics to study EEC differentiation in mucinous colorectal cancer, identifies STAT3 as a regulator, and discovers a rare cancer cell type with neuron-like features.

An epigenetic barrier sets the timing of human neuronal maturation

Chromatin regulators including EZH2, EHMT1/2, and DOT1L establish an epigenetic barrier in human neural progenitors that poises maturation genes and sets the protracted pace of cortical neuron maturation.

High-throughput single-cell, single-mitochondrial DNA assay using hydrogel droplet microfluidics

This paper introduces a high-throughput method for single-cell, single-mtDNA analysis using agarose-based droplet microfluidics, achieving high mtDNA retention and enabling scalable analysis.

scPerturb: Harmonized Single-Cell Perturbation Data

The paper harmonizes single-cell perturbation datasets and introduces E-statistics for analyzing perturbation effects across diverse data sources.

Stepwise recruitment of Hsc70 by DNAJB1 produces ordered arrays primed for bursts of amyloid fibre disassembly

This study shows DNAJB1 recruits Hsc70 in two steps to amyloid fibers, forming ordered arrays that enable efficient disaggregation, while a mutant disrupts this organization.

Cross-omic Transcription Factors meta-analysis: an insight on TFs accessibility and expression correlation

This paper investigates the correlation between transcription factor expression and motif information in functional genomic regions to understand TF dynamics across cell types.

Aging Differentially Alters the Transcriptome and Landscape of Chromatin Accessibility in the Male and Female Mouse Hippocampus

This study examines how aging affects the transcriptome and chromatin accessibility in male and female mouse hippocampus, identifying sex-specific changes in gene expression, alternative splicing, and chromatin features.

Epigenetic reprogramming driving successful and failed repair in acute kidney injury

This study maps epigenetic changes during AKI repair in mice and humans, identifying CREB5 as a regulator of both successful and failed tubular repair.

Changes in microglia chromatin accessibility in aged female mice.

This study identifies age-related changes in chromatin accessibility in female microglia, showing more gains than losses in accessibility, enriched in immune-related genes and intergenic regions.

OPA1 protects intervertebral disc and knee joint health in aged mice by maintaining the structure and metabolic functions of mitochondria

This study shows that OPA1 maintains mitochondrial structure and metabolic functions in NP cells and chondrocytes, preventing age-related degeneration in mouse intervertebral discs and knee joints.

Epigenetic reprogramming shapes the cellular landscape of schwannoma

This study identifies two molecular groups in schwannomas driven by epigenetic reprogramming and shows ionizing radiation can reprogram neural crest to immune-enriched schwannomas.

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

Chromosome-scale inshore hagfish genome places 1R before the cyclostome-gnathostome split and 2R in the gnathostome stem, and reveals two cyclostome-specific duplications (CR1, CR2).

Discriminative histone imputation using chromatin accessibility

This paper introduces dHICA, a deep learning framework that predicts histone modifications using chromatin accessibility and DNA sequences, outperforming existing methods and enabling downstream applications.

BATF controls IFN I production via DC-SCRIPT in plasmacytoid dendritic cells

The paper shows BATF suppresses IFN I production in pDCs via DC-SCRIPT, revealing a negative feedback loop in antiviral immunity.

Increased chromatin accessibility mediated by nuclear factor I drives transition to androgen receptor splice variant dependence in castration-resistant prostate cancer

This study shows that ARv7 drives AR activity in castration-resistant prostate cancer through increased chromatin accessibility mediated by NFI factors.

Evidence for compensatory evolution within pleiotropic regulatory elements

The paper investigates how pleiotropy affects the evolution of cis-regulatory elements, finding that more pleiotropic elements show greater conservation in function despite lower sequence conservation.

SMARTdb: An Integrated Database for Exploring Single-cell Multi-omics Data of Reproductive Medicine

SMARTdb provides a platform for exploring single-cell multi-omics data in reproductive biology, revealing conserved gene expression patterns and epigenetic regulation across species.

The chromatin landscape of healthy and injured cell types in the human kidney

The paper defines the chromatin landscape of healthy and injured kidney cells using multi-omics data, identifying regulatory elements and transcription factor networks involved in injury response.

HDACs repress runaway stress and cell identity to promote reprogramming in root regeneration

This study identifies HDACs HDA9 and HDA19 as critical for reprogramming plant root regeneration by repressing old identities and stress responses, followed by cell division rate modulation.

Substrate Specificities of DDX1: A Human DEAD-box protein

This study identifies the nucleotide substrates and RNA structures that stimulate DDX1 ATPase activity, showing DDX1 hydrolyzes only ATP and deoxy-ATP in the presence of RNA.

Evolution of plant cell-type-specific cis-regulatory elements

The paper constructs a single-cell chromatin accessibility atlas in rice and compares it across grass species to study the evolution of cell-type-specific cis-regulatory elements.

Unraveling wheat endosperm development: epigenetic regulation and novel regulators for enhanced yield and quality

This study identifies novel regulators of starch and seed storage protein biosynthesis in wheat endosperm, revealing their role in grain yield and quality through epigenetic and transcriptional mechanisms.