Hi-C

A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships

The paper creates a high-density chromatin interaction network across species by integrating 3C experiments, showing improved prediction of coexpression and eQTL for long-range and trans chromatin contacts.

Combined promoter-capture Hi-C and Hi-C analysis reveals a fine-tuned regulation of 3D chromatin architecture in colorectal cancer

The paper combines promoter-capture Hi-C and Hi-C data to analyze 3D chromatin architecture in colorectal cancer, identifying dysregulated genes and histone modifications associated with tumor-suppressive programs.

Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution

The paper introduces liCHi-C, a low-input Hi-C method, to map promoter-enhancer interactions in clinical samples and identify disease-relevant regulatory elements and structural variants.

Falign: An effective alignment tool for long noisy 3C data

Falign improves alignment of fragmented long noisy 3C data by addressing fragment boundary issues and increasing data utilization.

Intuitive interpretation of heterochromatin and euchromatin through rapid Hi-C analysis

This paper introduces a rapid method to classify heterochromatin and euchromatin using Hi-C data, providing intuitive visual interpretation of contact frequencies.

Topoisomerases I and II facilitate condensin DC translocation to organize and repress X chromosomes in C. elegans

This study shows that topoisomerases I and II regulate condensin DC translocation on the X chromosome in C. elegans, with TOP-2 affecting long-range movement and TOP-1 affecting short-range movement, both essential for gene repression.

Deep generative modeling and clustering of single cell Hi-C data

This paper introduces scDEC-Hi-C, a deep generative framework for analyzing single cell Hi-C data, showing improved clustering and imputation over existing methods.

Structural basis for preservation of a subset of Topologically Associating Domains in Interphase Chromosomes upon cohesin depletion

The paper shows that some Topologically Associating Domains (TADs) persist without cohesin, supported by Hi-C data, polymer simulations, and 3D structural analysis in mouse and human cells.

Mitotic chromosomes scale to nucleo-cytoplasmic ratio and cell size in Xenopus

This study shows mitotic chromosomes scale with cell size and nucleo-cytoplasmic ratio in Xenopus, distinct from other subcellular structures, through mechanisms involving condensin I and importin pathways.

The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer

PENGUIN reconstructs protein interactions at enhancer-promoter regions and identifies cancer-associated SNPs in prostate cancer cell lines.

Remodeling and compaction of the inactive X is regulated by Xist during female B cell activation

This study shows that Xist regulates Xi compaction and TAD boundaries in B cells, impacting XCI maintenance and X-linked gene expression.

High-resolution promoter interaction analysis implicates genes involved in the activation of Type 3 Innate Lymphoid Cells in autoimmune disease risk

The paper maps promoter interactions in human ILC3s using PCHi-C and links GWAS risk variants to target genes, identifying new autoimmune disease risk genes.

The chromatin factor ROW cooperates with BEAF-32 in regulating long-range inducible genes

The paper shows that ROW cooperates with BEAF-32 to regulate long-range transcription through chromatin loops at TAD boundaries.

An Associative Memory Hamiltonian Model for DNA and Nucleosomes

This paper introduces a computational model called WEChroM to simulate DNA and nucleosome mechanics, showing it can reproduce DNA structure, supercoiling behavior, and nucleosome unwrapping.

High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)

The paper generates genome assemblies and linkage maps for Leptidea species to study structural rearrangements, finding extensive fissions, fusions, and polymorphisms, with LINEs and LTR elements enriched at fusion breakpoints.

Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus

The paper investigates epigenomic and 3D chromatin conformation changes in human frontal cortex and hippocampus development using sn-m3C-seq, finding distinct chromatin conformations in neurons and glial cells and linking risk variants to regulatory regions.

Three-dimensional genome re-wiring in loci with Human Accelerated Regions

The paper identifies human-specific 3D genome re-wiring in conserved loci, linking accelerated evolution to regulatory rewiring in neural progenitor cells.

Comparison and critical assessment of single-cell Hi-C protocols

This study compares two single-cell Hi-C protocols, showing that whole-genome amplification introduces more artifacts and noise than PCR-based amplification.

Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi

Fast-Higashi improves scHi-C analysis by jointly identifying cell identities and chromatin meta-interactions with tensor decomposition and a novel algorithm, enhancing rare cell type detection and developmental trajectory reconstruction.

Three-dimensional chromatin re-organization during muscle stem cell aging

This study examines how 3D chromatin organization changes in muscle stem cells during aging, revealing static global structures and rewired local contacts linked to transcription factor binding and gene expression changes.

ParticleChromo3D: A Particle Swarm Optimization Algorithm for Chromosome and Genome 3D Structure Prediction from Hi-C Data

ParticleChromo3D uses particle swarm optimization to reconstruct 3D chromosome and genome structures from Hi-C data, showing higher accuracy than existing methods.

Deciphering Multi-way Interactions in the Human Genome

The paper maps multi-way chromatin contacts using long reads and identifies cell type-specific transcription clusters by integrating contacts with chromatin accessibility and gene expression.

Probabilistic 3D-modelling of genomes and genomic domains by integrating high-throughput imaging and Hi-C using machine learning

The paper introduces pTADbit, a machine learning method that improves 3D genome modeling using Hi-C data and microscopy distances, achieving higher accuracy and faster computation.

Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells

The paper uses targeted chromatin interaction profiling to identify causal genes at type 2 diabetes GWAS loci with higher sensitivity and resolution than genome-wide methods.

Transcriptional units form the elementary constraining building blocks of the bacterial chromosome

The paper shows that transcriptional units form discrete 3D domains that constrain bacterial chromosome organization at a fine scale.

Catch me if you can: Capturing extracellular DNA transformation in mixed cultures via Hi-C sequencing

This study demonstrates that microorganisms in activated sludge can acquire synthetic plasmids via transformation under kanamycin pressure, using Hi-C sequencing to identify transformants.

PHi-C2: interpreting Hi-C data as the dynamic 3D genome state

PHi-C2 converts Hi-C data into dynamic 3D genome models using polymer modeling and provides an optimized algorithm and Colab workflow for analysis.

Structural Reorganization and Relaxation Dynamics of Axially Stressed Chromosomes

This study uses a coarse-grained polymer model to simulate mitotic chromosome mechanics, finding they are ten times stiffer than interphase chromosomes and exhibit viscoelastic behavior.

CTCF and cohesin promote focal detachment of DNA from the nuclear lamina

The paper investigates the role of CTCF and cohesin in LAD positioning, finding they reinforce borders but do not position LADs, and mediate fine-tuning of nuclear lamina interactions.

Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture

The paper develops a stochastic model of histone dynamics at the replication fork, showing that differential diffusivity explains histone inheritance patterns and predicts epigenomic patterns observed in experiments.