Hi-C

3D-genome impacts of TAD-boundary-disrupting ultra-rare structural variants identified in schizophrenia

The paper identifies and functionally characterizes TAD-boundary-disrupting ultra-rare structural variants in schizophrenia using CRISPR/Cas9 in iPSCs, showing cell-type-specific effects on 3D-genome organization and gene expression.

Localized Chromatin Rewiring Shapes Rhythmic Transcription within a Stable 3D Genome in Rice

The paper identifies localized chromatin rewiring in rice's stable 3D genome that coordinates rhythmic transcription across the circadian cycle.

Locus-specific spatial and transcriptional dynamics direct T cell lineage choice in the thymus

The paper investigates how spatial and transcriptional dynamics at Cd4 and Cd8 loci influence T cell lineage choice in the thymus, revealing locus-specific chromatin environments that drive differentiation.

A molecular framework of chromatin extrusion in plants

This study identifies PDS5A as a key regulator of chromatin loop extrusion and TAD-like domains in Arabidopsis, revealing a promoter- and motif-based mechanism for loop anchoring and transcriptional control.

Evolution of CTCF underlies the establishment of loop extrusion as a predominant chromatin folding mechanism in vertebrates

The paper investigates the evolution of CTCF's role in chromatin organization across species, finding that vertebrate CTCF enables loop extrusion but requires additional factors for full genome architecture.

Evaluation of object detection neural networks to find topologically associated domains in bulk Hi-C data

This study evaluates YOLOv8 and Mask R-CNN for detecting TADs in bulk Hi-C data by converting Hi-C matrices into images and comparing their performance against reference TADs.

Abnormal nuclear organization impairs adipogenic lineage commitment and terminal maturation in Hutchinson-Gilford progeria syndrome (HGPS)

This study shows that HGPS disrupts adipogenic lineage maturation through chromatin reorganization defects, despite normal lineage commitment rates.

Ctcf deficiency in myofibers induces pathological genome reprogramming toward the spontaneous development of myopathy

This study shows that Ctcf deficiency in myofibers leads to genome reprogramming and myopathy by disrupting 3D genome structure and gene regulation.

Radiotherapy Reshapes the 3D Genome in Medulloblastoma Cells

This study examines how radiotherapy affects the 3D genome of medulloblastoma cells, identifying molecular and structural changes associated with radiation response.

Disrupted chromatin architecture blocks B lymphopoiesis in Down syndrome

The paper develops ChromE-seq to study 3D chromatin architecture in fetal hematopoiesis, finding that T21 disrupts B-lineage development by altering chromatin connectivity and regulatory circuits.

Hyperosmotic stress induces rewiring of 3D chromatin interactions

One hour of 200 mM sorbitol collapses most chromatin loops in human cells while several hundred transient, cohesin-dependent, CTCF-independent loops form at active promoters, preceding anchor-gene activation.

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.

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.

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.

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.

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.

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.

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.

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.

Multiscale spatial analysis implicates chromosomal metaloops in gene patterning across the Drosophila brain

The paper identifies chromosomal metaloops in Drosophila brains and shows their role in organizing gene expression patterns through metadomains.

KAT3 Shuttling Between Neuronal Identity and Activity-Dependent Plasticity Programs Drives Large-Scale Chromatin Remodeling

The paper shows that KAT3 cofactors move between neuronal identity and activity-dependent plasticity programs, causing chromatin remodeling in hippocampal neurons.

Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3

This study shows that SUMOylation loss in Drosophila disrupts PRC1 condensates, causing 3D genome rewiring and gene misregulation without affecting H3K27me3 levels.

Genomic indicators of gene function: A systematic assessment of the human genome

The paper assesses genomic indicators of gene function in the human genome, finding that transcriptional activity and evolutionary conservation are strongest predictors of functional regions.

The linker histone H1.4 condenses chromatin in maturing postmitotic neurons

Epitope-tagged knockin mice show histone H1.4 protein accumulates in postmitotic neurons, shifts toward B-compartment heterochromatin with maturation, and H1f2/H1f4 loss impairs cerebellar granule neuron chromatin compaction.

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

The paper performs single-cell multiomics analysis of the human retina to identify regulatory elements and develop predictors for non-coding risk variants.