Hi-C

A Resolution-Agnostic Geometric Transformer for Chromosome Modeling Using Inertial Frame

This paper introduces InertialGenome, a transformer-based framework for resolution-agnostic chromosome 3D structure reconstruction, showing improved performance across multiple resolutions and experimental validation.

Rewiring of 3D Enhancer-Promoter Interactome Underlies Diabetic Endothelial Dysfunction

The paper identifies RBBP6-mediated degradation of JUNB as a mechanism causing 3D enhancer-promoter disruption and endothelial dysfunction in diabetes.

Haplotype-resolved reconstruction and functional interrogation of cancer karyotypes

This paper introduces refLinker, a method for haplotype-resolved analysis of cancer karyotypes, revealing transcriptional consequences of somatic Xi rearrangements.

Machine learning and multi-omic analysis reveal contrasting recombination landscape of A and C subgenomes of winter oilseed rape

The paper uses machine learning and multi-omic data to analyze recombination patterns in the A and C subgenomes of Brassica napus, finding distinct landscape features between them.

Pioneer factor IRF1 unlocks latent enhancers to rewire chromatin and immunometabolism in inflammatory macrophages

This study identifies IRF1 as a pioneer factor that remodels chromatin and drives metabolic reprogramming in inflammatory macrophages through enhancer activation and transcriptional control.

ARCH3D: A foundation model for global genome architecture

This paper introduces ARCH3D, a foundation model for global genome architecture that captures spatial structure and interchromosomal interactions using a novel masked locus modeling task.

3D-super-enhancers are condensate-associated cis-regulatory communities

The paper introduces BOUQUET, an algorithm that identifies 3D-super-enhancers as protein-rich cis-regulatory communities associated with co-activator condensates in mammalian cells.

Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis

The paper identifies 3D regulatory hubs involved in sex determination using spatial auto-correlation analysis in mouse embryos.

SMCHD1 loss re-wires MYOD1 enhancer nexuses and chromatin accessibility landscapes in muscle cells

This study shows that SMCHD1 loss disrupts enhancer organization and chromatin accessibility in muscle cells, leading to altered MYOD1 regulation and potential FSHD pathology.

Global re-organisation of genome architecture at the transition to gametogenesis

This study reveals a unique 3D genome architecture in premeiotic gonadal germ cells, linked to epigenetic reprogramming and loss of TADs, alongside DNA demethylation.

Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies

This study uses FFPE-compatible Hi-C to detect enhancer-hijacking rearrangements in lymphoid cancers, identifying clinically relevant drivers missed by standard methods.

Replication Timing Uncovers a Two-Compartment Nuclear Architecture of Interphase Euchromatin in Maize

The paper uses Hi-C and 3D FISH to show maize euchromatin has two distinct interphase subcompartments, early-S and middle-S, defined by replication timing and chromatin organization.

Eco-evolutionary dynamics of active virus-host interactions in a freshwater lake: revealed through metaHi-C

The paper uses metaHi-C to identify active phage-host interactions in a freshwater microbial community, revealing ecological patterns and evolutionary dynamics.

Enhanced Hi-C Capture Analysis reveals complex regulatory architecture at the PICALM-EED locus for Alzheimer Disease

This study uses eHiCA to identify regulatory interactions at the PICALM-EED locus, showing distinct chromatin interactions for SNPs within a segregating haplotype.

Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation

The paper identifies 'fountains' as enhancer-specific chromosome organization elements emerging during zygotic genome activation in zebrafish and mouse.

Modeling nascent transcription from chromatin landscape and structure

The paper introduces CLASTER, a deep learning model that predicts nascent transcription levels from chromatin landscape and 3D structure data, achieving high correlation with experimental measurements.

DNA supercoiling links transcription and chromatin architecture during human stem cell differentiation

This study maps DNA supercoiling and chromatin interactions during human stem cell differentiation, showing that gene activation increases negative supercoiling and correlates with enhanced DNA contacts.

scDIAGRAM: Detecting Chromatin Compartments from Individual Single-Cell Hi-C Matrix without Imputation or Reference Features

scDIAGRAM detects chromatin compartments in single-cell Hi-C data without imputation or reference features, showing accuracy in simulated and real datasets.

Repeat expansions in C9orf72 rewire the 3D chromatin landscape in ALS

This study shows that C9orf72 repeat expansions alter chromatin loops in neurons, linking RNA-DNA interactions to gene dysregulation in ALS.

NSD3 stabilizes nuclear compartmentalization and promotes megabase-scale chromatin interactions

The paper identifies NSD3 as a factor that stabilizes nuclear compartmentalization and promotes long-range chromatin interactions in both fusion-positive and fusion-negative cells.

PEhub resolves the hierarchical regulatory architecture of multi-way enhancer hubs in the human brain

PEhub identifies multi-way enhancer hubs in human brain regions using HiChIP data, revealing their hierarchical organization and association with transcriptional output and genetic risk.

HiCInterpolate: 4D Spatiotemporal Interpolation of Hi-C Data for Genome Architecture Analysis.

HiCInterpolate interpolates Hi-C contact matrices between timestamps to generate high-resolution 3D genome structures, preserving key chromatin features.

Noncanonical loops regulated by EMF1 and cohesin-associated factors shape the distinct 3D genome architecture in plants

The paper identifies noncanonical loops in Arabidopsis regulated by EMF1 and PDS5s, showing distinct chromatin organization compared to mammals.

Formation of homolog pairing-induced domains in early Drosophila embryo genome

The paper uses Hi-C data to reconstruct 3D genome structures in Drosophila embryos and identifies pairing-induced domains formed by specific homologous interactions.

esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions

This study investigates the roles of esBAF and INO80C in shaping 3D genome organization in mouse embryonic stem cells, finding they influence subcompartment identity and enhancer-promoter interactions.

The Drosophila ZAD zinc finger protein Mulberry shapes the organization of the regulatory genome in the early embryo

This study identifies Mulberry as a looping factor in Drosophila embryos that shapes genome organization through nuclear condensates and long-range regulatory interactions.

Boosting the detection of enhancer-promoter loops via novel normalization methods for chromatin interaction data

Raichu improves enhancer-promoter loop detection in Hi-C data by enhancing sensitivity and recovering missed loops compared to ICE normalization.

HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets

HiChIA-Rep quantifies similarity between chromatin interaction datasets by integrating 1D and 2D signals, distinguishing replicates and factors better than existing tools.

An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia

The paper presents an integrated single-cell and epigenomic resource for exploring basal ganglia datasets across species, enabling multi-omics and comparative analysis.

Unique territorial and compartmental organization of chromosomes in the holocentric silkworm

The paper discovers a novel chromatin folding structure, compartment S, in the silkworm Bombyx mori using Hi-C, showing unique loop extrusion and contact patterns.