Hi-C

Epigenome Alterations and 3D Chromatin Architecture Remodeling in Inflammatory Macrophage Activation under Diabetic Conditions

This study investigates how diabetic conditions alter the 3D chromatin architecture and epigenome of macrophages, revealing disease-associated rewiring of the 3D epigenome and potential therapeutic targets.

Human FACT complex coordinates cohesin and transcription on chromatin

This study shows that the FACT complex regulates cohesin dynamics on chromatin, facilitating loop extrusion and preventing cohesin accumulation in transcribed regions.

WNT/β-catenin increases 3D chromatin mobility and reorganisation during posterior cell state transitions

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.

Fetal signatures in the 3D genome of iPSC-derived neurons and their implications for disease modeling

This study compares chromatin architecture in iPSC-derived neurons to fetal and mature neurons, finding iPSC-derived neurons resemble fetal neurons and have distinct chromatin features.

3D Reconstruction of Dinoflagellate Chromosomes from Hi-C Data Challenges the Cholesteric Liquid Crystal Hypothesis

This study uses Hi-C data to challenge the Cholesteric Liquid Crystal model of dinoflagellate chromosomes by showing no evidence of cholesteric discs and demonstrating transcription occurs throughout chromosomes.

Hi-C data from the filamentous fungus Podospora anserina and associated 3D models to visualize the spatial organization of its chromosomes

The paper presents Hi-C data and 3D models for Podospora anserina to study its chromosomal spatial organization and aid multi-omics integration.

Euchromatin forms condensed domains with short active regions on the surface

The paper develops a simulation framework to infer nucleosome-resolution chromatin structures from RCMC data, revealing euchromatin as condensed domains with accessible promoter/enhancer regions.

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

FourC: identifying significant and differential contacts in 1D chromatin conformation data

FourC identifies significant and differential contacts in 4C-seq data using a Bayesian model and Gaussian processes to address duplication and model spatial patterns.

Chromatin architecture dictates epigenetic memory

The paper develops a theory linking chromatin architecture to epigenetic memory stability and predicts compartment fusion over cell generations.

Regulatory-scale stripe analysis from single-cell Hi-C with scStripe

scStripe detects and quantifies chromatin stripes in single-cell Hi-C data, resolving cell-type-specific regulatory features and capturing genome-wide variation.

Cell Cycle-Dependent Chromatin Motion: A Role for DNA Content Doubling Over Cohesion

The paper uses Hi-D to track chromatin motion in live human cells and finds that DNA content doubling, not cohesin, reduces chromatin mobility during the cell cycle.

High-order enhancer hubs buffer allelic regulatory variation through kinetic compensation

The paper develops Nanopore-HiChIP to map enhancer hubs and shows they buffer allelic regulatory variation through kinetic compensation, preserving balanced transcriptional output.

State-Dependent 3D Enhancer Architecture Resolves a Shared Schizophrenia and Multiple Sclerosis Ketone and Lactate Sensing Logic Gate

The paper identifies a 3D enhancer hub at 12q24.31 that regulates HCAR2 and explains shared genetic mechanisms in schizophrenia and multiple sclerosis.

ssJSD: A fusion of sparsity and spatial information for HiC single-cell clustering

ssJSD improves scHiC clustering by integrating spatial interaction patterns and sparsity patterns to better distinguish cell types.

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.

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.

DiffDomain-Spectrum identifies structurally reorganized TADs from sparse aggregated single-cell Hi-C contact maps

DiffDomain-Spectrum identifies reorganized TADs from sparse aggregated scHi-C maps by analyzing eigenvalue spectra and comparing to a null model, showing higher sensitivity than existing methods.

Repeat element-anchored enhancer-promoter interactions (REEPIs) shape the regulatory landscape of hormone-resistant breast cancer

The paper identifies repeat element-anchored enhancer-promoter interactions (REEPIs) in hormone-resistant breast cancer and links them to transcriptional adaptation and regulatory reprogramming.

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.

Polycomb establishes TAD-scale H3K27me3 mega-domains to safeguard neuronal identity

The paper identifies Polycomb repressive complexes (PRCs) as establishing TAD-scale H3K27me3 domains in mature neurons to maintain identity by silencing alternative lineage genes.

Cooperative CTCF-nucleosome oligomerization stabilizes chromatin loop anchors

CTCF dimerization on stacked nucleosomes is resolved by cryo-EM through a ZnF6-7-8 interface. Disrupting it in mouse stem cells weakens CTCF-cohesin loops more than insulation and impairs germline differentiation.

Looplook: Integrating multiomics refinement and graph clustering for target assignment and functional inference of chromatin regulatory networks

Looplook integrates 3D chromatin topology with functional genomics to improve CRE-target gene assignment and functional inference in chromatin regulatory networks.

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.

Overcoming artificial structures in resolution-enhanced Hi-C data by signal decomposition and multi-scale attention

This paper introduces SHARP, a method to enhance Hi-C data resolution while avoiding artificial structures by decomposing signals and using multi-scale attention.

DUCK-Net: Automated deep learning segmentation of Ductular Reaction in murine liver injury captures multicellular niche dynamics from H&E morphology

This paper introduces DUCK-Net, a deep learning model for automated segmentation of Ductular Reactions in murine liver injury, showing high accuracy and correlation with spatial transcriptomic data.

Conformational asymmetry of replicated human chromosomes

The paper reveals a genome-wide asymmetry in sister chromatid alignment due to replication fork asymmetry, maintained by cohesive cohesins.

Differential analysis of image-based chromatin tracing data with Dory

Dory identifies differential spatial patterns in chromatin tracing data by analyzing structural differences between groups, linking changes to gene regulation.

HiC-LEGO: Biologically Guided High-Resolution 3D Genome Reconstruction Preserves Chromatin Organization at Kilobase Resolution

HiC-LEGO reconstructs high-resolution 3D genomes from Hi-C data, preserving chromatin organization and regulatory interactions at kilobase resolution.