Hi-C

3D Epigenome Evolution Underlies Divergent Gene Regulatory Programs in Primate Neural Development

The paper maps 3D genome organization, chromatin accessibility, and gene expression in primate neural stem cells to identify human-specific epigenetic signatures and their role in gene regulation.

Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms

The paper investigates how TAD boundary width influences insulation between adjacent TADs, showing that wider boundaries reduce inter-TAD contacts and enhance insulation.

Non-coding structural variants identify a commonly affected regulatory region steering FOXG1 transcription in early neurodevelopment

The paper identifies a regulatory region affecting FOXG1 transcription in neurodevelopment through structural variants and chromatin analysis.

In silico nanoscope to study the interplay of genome organization and transcription regulation

The paper develops a multiscale modeling pipeline to simulate chromatin organization and transcription regulation in mouse embryonic stem cells, revealing how sequence-regulated accessibility facilitates enhancer-promoter communication.

Detection of rare plasmid hosts using a targeted Hi-C approach

This study develops Hi-C+ to detect rare plasmid hosts in soil, achieving a 0.001% detection limit and genus-level identification.

The NAT10 acetyltransferase modulates DNA damage-related factors and global 3D-genome architecture

This study shows NAT10 depletion affects DNA repair proteins and 3D-genome structure but not histone modifications.

Novel AI-powered computational method using tensor decomposition for identification of common optimal bin sizes when integrating multiple Hi-C datasets

This paper introduces a tensor decomposition method to automatically determine common optimal bin sizes for integrating multiple Hi-C datasets without manual parameter tuning.

Developmental regulation of Drosophila dosage compensation in a 3D genome context

The paper investigates how dosage compensation in Drosophila is regulated during development by analyzing 3D genome structures and histone modifications across sexes and tissues.

B cell stimulation changes the structure and higher-order organization of the inactive X chromosome

This study investigates how B cell stimulation affects the structure and organization of the inactive X chromosome, revealing dynamic changes in TAD boundaries and Xi compaction.

Characterizing trajectory-like chromatin architectures with Fun2

The paper introduces Fun2, a reinforcement learning-based algorithm to characterize trajectory-like chromatin architectures, including fountains and stripes, with improved adaptability and accuracy.

Replisomes restrict SMC-mediated DNA-loop extrusion in vivo

This study shows that replisomes block SMC-mediated DNA-loop extrusion in Bacillus subtilis by restricting SMC translocation, with occasional bypass events observed.

Understanding the Transfer and Persistence of Antimicrobial Resistance in Aquaculture Using a Model Teleost Gut System

This study uses an Atlantic salmon gut model to show that antimicrobial resistance plasmids persist and transfer among microbes even after antibiotic treatment stops.

Non-catalytic role for MLL2 in controlling chromatin organisation and mobility during priming of pluripotent cells for differentiation

This study shows MLL2 stabilizes 3D chromatin loops during pluripotent cell differentiation without requiring its enzymatic activity.

ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization

ChromaFactor deconvolves single-molecule chromatin organization data using non-negative matrix factorization to identify key functional components and their molecular contributions.

Conformational analysis of chromosome structures reveals vital role of chromosome morphology in gene function

The paper introduces a dimensionality reduction method to classify single-cell chromosome structures into conformational clusters, revealing that distinct morphologies influence gene function through subnuclear positioning.

Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences

The paper benchmarks Hi-C for virus-host linkage detection using synthetic communities and applies optimized protocols to soil samples, revealing new interactions and establishing performance metrics.

Long-range genomic loci stochastically assemble into hierarchical chromosome structures

The paper identifies long-range chromosomal loops spanning over 100 Mb and shows they form via multivalent binding, independent of known nuclear structures, suggesting a distributed mechanism for chromosome organization.

Unveiling Nucleosome Dynamics: A Comparative Study Using All-Atom and Coarse-Grained Simulations Enhanced by Principal Component Analysis

This study compares all-atom and coarse-grained simulations of nucleosome dynamics using the SIRAH force field, revealing similar structural parameters but distinct conformational sampling and breathing motion in coarse-grained models.

Hi-C sequencing data from cortex of laboratory rats

The paper presents a Hi-C dataset from rat frontal cortex to study strain-specific chromatin architecture and its impact on gene expression and neurological traits.

UV-induced reorganization of 3D genome mediates DNA damage response

This study investigates how UV radiation induces reorganization of the 3D genome and its role in DNA damage response and repair.

Structural Basis of Differential Gene Expression at eQTLs Loci from High-Resolution Ensemble Models of 3D Single-Cell Chromatin Conformations

The paper develops a method to analyze Hi-C and eQTL data to understand how 3D chromatin structures influence gene regulation through non-random interactions and ensemble modeling.

Joint analysis of RNA-DNA and DNA-DNA interactomes reveals their strong association

The paper jointly analyzes RNA-DNA and DNA-DNA interactomes across human and mouse cell lines, showing their close relationship is tissue-specific and conserved.

Shared and distinct molecular effects of regulatory genetic variants provide insight into mechanisms of distal enhancer-promoter communication

The paper identifies trimodal QTLs that jointly affect enhancer accessibility, promoter contacts, and gene expression in monocytes, revealing genetic links between enhancer activity and chromatin boundaries.

Multiplexed spatial mapping of chromatin features, transcriptome, and proteins in tissues

The paper introduces spatial-Mux-seq, a multi-modal spatial technology that profiles five modalities in tissues, revealing new insights into cell types, gene regulation, and epigenetic gradients in mouse embryos and brains.

A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition

New insights into the cis-regulation of the CFTR gene in pancreatic cells

The paper identifies tissue-specific cis-regulatory elements (CREs) for the CFTR gene in pancreatic and intestinal cells using 3D genomic analysis and functional assays.

Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor

This study shows that reduced TBX5 dosage affects 3D chromatin organization in human cardiomyocytes, with cell-to-cell variation and partial protection by CTCF co-occupancy.

GEM-Finder: dissecting GWAS variants via long-range interacting cis-regulatory elements with differentiation-specific genes

GEM-Finder identifies disease-associated CREs by integrating transcriptomic, epigenomic, and chromatin interaction data during endothelial differentiation, revealing 7.6 times more associations than conventional methods.

ScHiCAtt: Enhancing Single-Cell Hi-C Resolution Using Attention-Based Models

ScHiCAtt improves single-cell Hi-C resolution using attention mechanisms, outperforming existing methods across different organisms and downsampling conditions.

Response eQTLs, chromatin accessibility, and 3D chromatin structure in chondrocytes provide mechanistic insight into osteoarthritis risk

The paper identifies OA risk genes by integrating eQTLs, chromatin accessibility, and 3D chromatin structure in human chondrocytes, revealing 13 putative risk genes, 10 of which are novel.