Hi-C

This study identifies factors influencing Sleeping Beauty transposition, showing chromatin context, cargo size, and transcriptional activity affect efficiency and reintegration patterns.

The paper tracks phage-host interactions in the human gut and finds that DGR-encoding phages interact with multiple bacterial species and show increased nucleotide diversity in their receptor-binding proteins.

The paper tracks viral infection in Ostreococcus tauri, showing pre-existing genome architecture dictates viral positioning and transcriptional changes during infection.

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.

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

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.

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.

This paper introduces DropHiChew and loop velocity to study DNA movement dynamics, enabling accurate trajectory estimation with shallow sequencing.

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.

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.

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

U-Chrom provides a unified framework for analyzing single-cell and spatial 3D genome data, showing consistent cell-type differences across assays.

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

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

This study shows that SA1/2 are not essential for V(D)J recombination in G0/G1-arrested cells, but their absence disrupts chromatin loops and long-range Igh recombination, while Ig{kappa} recombination remains functional.

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.

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.

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.

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

This study uses Hi-C in mouse embryonic stem cells to show A/B compartment strength increases during S-phase, challenging previous views on cell-cycle dynamics.

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.

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

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.

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.

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

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

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

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

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.