Hi-C

Finding ancestry-specific chromatin architecture in Alzheimer's disease

The paper identifies ancestry-specific chromatin architecture differences in Alzheimer's Disease using Hi-C and ATAC-seq data from African and European ancestry individuals.

The challenge of chromatin model comparison and validation a project from the first international 4D Nucleome Hackathon

The paper describes a project from the 4D Nucleome Hackathon aimed at developing a workflow for comparing and validating chromatin models, identifying challenges in model comparison and software development.

Pore-C sequencing identifies episome-driven chromosome conformation perturbations differentiating pneumococcal epigenetic variants

The paper uses Hi-C and Pore-C sequencing to compare chromosomal conformation in pneumococcal variants, finding that episomal elements drive differential contact patterns through stochastic replication and excision.

Specialised super-enhancer networks in stem cells and neurons

The paper compares super-enhancer networks in embryonic stem cells and dopaminergic neurons, revealing their structural differences and functional roles in transcriptional regulation.

Form Follows Function: A New Paradigm of Pancreatic Cancer Progression

This paper identifies geometric and spatial patterns in pancreatic cancer that correlate with aggressive behavior and develops an AI tool to improve clinical evaluation and treatment planning.

Deciphering ESR1-driven transcription in human endometrial stromal cells via transcriptome, cistrome, and integration with chromatin landscape

This study investigates ESR1 and estrogen-driven transcription in human endometrial stromal cells using transcriptome, cistrome, and chromatin landscape data to identify gene regulation and its implications in decidualization and endometrial cancer.

Disentangling spatial organization and splicing of rare intron classes in the human genome

The paper investigates how spatial organization and splicing of rare intron classes are related in human cells, finding that intron identity, not position, primarily determines splicing efficiency.

MLL2 facilitates long-range gene regulation through LINE1 elements

This study shows MLL2 regulates gene expression through LINE1 elements in mouse ESCs, not by opposing Polycomb repression at bivalent promoters.

Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts

The paper uses synthetic enhancer engineering in mESCs to show that enhancer clusters increase transcriptionally productive enhancer-gene contacts through enhanced RNA Polymerase II pause release.

Condensins-mediated mitotic folding persists as a structural echo in interphase chromatin

The paper investigates how condensins shape chromatin contacts in interphase nuclei using Hi-C data from mouse embryonic stem cells, showing structural memory of mitotic folding.

Genetic and Epigenetic Reprogramming of Transposable Elements Drives ecDNA-Mediated Metastatic Prostate Cancer

The paper identifies a subgroup of mCRPC characterized by LINE1 repeat DNA elements flanking the AR gene, which drive AR overexpression and confer resistance to androgen signaling inhibitors.

Joint decomposition of Hi-C maps reveals salient features of genome architecture across tissues and development

The paper introduces a framework to jointly decompose Hi-C maps across tissues and development, revealing distinct nuclear architecture patterns and improving gene expression prediction.

Chromosome-level genome assembly of autotetraploid Selenicereus megalanthus and gaining genomic insights into the evolution of trait patterning in diploid and polyploid pitaya species

Exploration of oncogenic cooperation between germline variation and somatic mutation in prostate cancer progression

This study identifies PTPRK as a gene modulated by TMPRSS2::ERG fusion and a regulatory SNP, showing its role in prostate cancer progression and potential as a biomarker.

Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy

The paper develops a dynamic barrier model to explain genome folding features using biophysically measured CTCF and cohesin dynamics, showing that barrier bound times influence ChIP-seq, Hi-C, and chromosome morphology.

PARP1 Regulates 3D Structure and Function of Super-Enhancers and Hormone-Control Regions in Breast Cancer Cells

This paper shows PARP1 regulates 3D chromatin structure and gene expression at super-enhancers and hormone-control regions in breast cancer cells through chromatin looping and compartment organization.

Static Three-Dimensional Structures Determine Fast Dynamics Between Distal Loci Pairs in Interphase Chromosomes

The paper develops a theory to predict chromatin dynamics using static 3D structures, showing that fast enhancer-promoter dynamics and scaling relationships are determined by chromatin organization.

scHiCcompare: an R package for differential analysis of single-cell Hi-C data

The paper introduces scHiCcompare, an R package for differential analysis of single-cell Hi-C data, improving detection of chromatin interactions across various conditions.

Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing

Hi-reComb estimates recombination maps from bulk gamete Hi-C data, showing accurate results in fish sperm and enabling structural variant analysis.

A comprehensive data repository of environmental toxicants exposed mouse epigenomes from the TaRGET II Consortium

The paper introduces a data repository containing epigenomic data from mice exposed to various environmental toxicants, enabling research on disease susceptibility.

Novel Spatial-Structural-Zero-Aware Dissimilarity Measures for Subtype Discovery Using Single Cell Hi-C Data

This study introduces szKendall, a dissimilarity measure for scHi-C data that accounts for structural zeros, improving cell clustering performance.

Complex genetic variation in nearly complete human genomes

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

The 3D genome of pediatric B-cell precursor acute lymphoblastic leukemia

This study maps the 3D chromatin landscape of pediatric B-cell precursor acute lymphoblastic leukemia using Micro-C, revealing how genetic aberrations reshape chromatin structure and gene regulation.

Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer

This study identifies NKX2-1-driven epigenetic and 3D chromatin remodeling as key to neuroendocrine prostate cancer progression and reveals CBP/p300 inhibitors as potential therapeutic targets.

Master transcription factor binding sites constitute the core of early replication control elements

The paper identifies subERCEs as master transcription factor binding sites that drive early replication timing and transcription in mESCs, functioning as both enhancers and structural chromatin organizers.

Liebenberg syndrome severity arises from variations in Pitx1 locus topology and ectopically transcribing cells

This study shows that variations in enhancer-promoter interactions at the Pitx1 locus lead to pathogenic activation in variable cell proportions, defining phenotypic severity in Liebenberg syndrome.

Hierarchical prediction and perturbation of chromatin organization reveal how loop domains mediate higher-order architectures

HiCGen predicts and perturbs chromatin organization, revealing loop domains' role in higher-order structures like TADs and compartments.

Structural insights into transcriptional regulation by the helicase RECQL5

This study determines the structure of RECQL5-bound Pol II elongation complexes using cryo-EM, revealing how RECQL5 stabilizes Pol II and modulates its translocation state to reduce transcription stress.

Loopsim: Enrichment Analysis of ChromosomeConformation Capture with Fast EmpiricalDistribution Simulation

Loopsim performs enrichment analysis on Hi-C loop profiles by simulating empirical null distributions to assess statistical significance of loop features.

Quantifying Conformational Heterogeneity of 3D Genome Organization in Fruit Fly

The paper quantifies cell-to-cell conformational heterogeneity of 3D chromatin structures in fruit fly using a new metric and compares models based on different Hi-C data types.