Hi-C

LungCancer3D: A Comprehensive Database for Integrating Lung Cancer Chromatin Architecture with Other Multi-omics

LungCancer3D integrates HiC with multi-omics data to visualize lung cancer chromatin architecture and gene regulation mechanisms.

Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation from mouse embryonic stem cells

The paper develops a molecular dynamics model to study how epigenetic-structural changes in X chromosomes drive Xic pairing during early differentiation of mouse embryonic stem cells.

Hi-C Resolution Enhancement with Genome Sequence Data

This paper develops deep-learning methods to enhance Hi-C data resolution using genome sequence information and provides open-source code.

RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis

The paper shows RNA polymerase II is necessary for spatial chromatin reorganization after mitosis, as demonstrated by Hi-C and in silico modeling.

Large structural variations in the haplotype-resolved African cassava genome.

The paper assembles and resolves two haplotypes of a cassava line using multiple sequencing technologies, revealing over 5,000 large structural variants.

SSIM can robustly identify changes in 3D genome conformation maps

The paper confirms that SSIM depends on Hi-C matrix properties and provides improved methods for identifying differential 3D genome conformation.

qc3C: reference-free quality control for Hi-C sequencing data

The paper introduces a reference-free quality control method for Hi-C sequencing data, demonstrating its accuracy on simulated and real datasets.

Multiscale and integrative single-cell Hi-C analysis with Higashi

Higashi improves scHi-C data analysis by enhancing quality and extracting 3D genome features, revealing cell-to-cell variability and new gene regulation connections in human prefrontal cortex cells.

SMILE: Mutual Information Learning for Integration of Single Cell Omics Data

SMILE integrates single-cell omics data by learning discriminative representations through mutual information maximization, effectively removing batch effects and aligning diverse data types.

Building regulatory landscapes: enhancer recruits cohesin to create contact domains, engage CTCF sites and activate distant genes

This study shows enhancers recruit cohesin to form chromatin domains, engage CTCF sites, and activate distant genes, with transcription factors and mediator required for all distances but cohesin specifically for long-range activation.

A genome-wide analysis identifies DIDO3 binding at active chromatin and topological boundaries in mouse stem cells

This study identifies DIDO3 binding at active chromatin and topological boundaries in mouse stem cells, linking it to chromatin organization and transcriptional regulation.

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

The paper integrates single-cell RNA-seq, ATAC-seq, and Hi-C data to study nuclear configuration and gene expression changes during stem cell differentiation and X inactivation, revealing discrete structural changes and delayed chromatin compaction.

Low membrane fluidity triggers lipid phase separation and protein segregation in vivo

The paper shows that low membrane fluidity in bacteria triggers lipid phase separation and protein segregation without disrupting membrane function.

HPRep: Quantifying reproducibility in HiChIP and PLAC-seq datasets

HPRep quantifies reproducibility in HiChIP and PLAC-seq data by using a stratified and weighted correlation metric, outperforming existing Hi-C-based measures.

Prediction of the 4D Chromosome Structure From Time-Series Hi-C Data

This paper introduces 4DMax, a method that predicts dynamic chromosome structures from time-series Hi-C data, effectively interpolating chromatin positions and recovering structural features at unobserved time points.

CRISPR screens identify gene targets and drug repositioning opportunities at breast cancer risk loci

Hi-C Contacts Encode Heterogeneity in Sub-diffusive Motion of E. coli Chromosomal Loci

The paper uses Hi-C data to show that E. coli chromosome loci exhibit coordinate-dependent sub-diffusive motion, driven by Hi-C-guided long-range interactions.

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

The paper presents a high-quality Arabidopsis thaliana genome assembly using long-read sequencing and Hi-C data, resolving previously missing regions and centromeres.

β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture

This study shows that β-actin levels influence chromatin remodeling activities and 3D genome architecture in mouse embryonic fibroblasts.

DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity

This study shows DNA hypomethylation disrupts replication timing precision and 3D genome organisation in colorectal cancer DNMT1 and DNMT3B knockout cells.

Genomic and transcriptomic analyses reveal a tandem amplification unit of 11 genes and mutations of mismatch repair genes in methotrexate-resistant HT-29 cells

Systematic evaluation of chromosome conformation capture assays

This study evaluates 3C-based assays to understand how experimental parameters affect chromatin interaction detection and quantification, leading to the development of Hi-C 3.0.

Seeing the forest through the trees: Identifying functional interactions from Hi-C

This paper reviews methods for identifying functional interactions from Hi-C data by classifying approaches into three categories: domain discovery, statistical significance detection, and epigenomic integration.

The contribution of cohesin to chromatid organisation is critical during chromosome segregation

The paper shows cohesin maintains chromatid organisation during anaphase in yeast, despite being thought to be removed by separase cleavage.

Integrative Genome Modeling Platform reveals essentialityof rare contact events in 3D genome organizations

The paper develops a multi-modal data integration approach to improve genome structure modeling and shows that rare contact events are essential for predicting nuclear architecture.

Loops, TADs, Compartments, and Territories are Elastic and Robust to Dramatic Nuclear Volume Swelling

The paper investigates how genome structure responds to nuclear swelling, finding that global topology remains elastic and robust despite dramatic volume changes.

Restriction enzyme selection dictates detection range sensitivity in chromatin conformation capture-based variant-to-gene mapping approaches

The paper compares PCC and PCHiC methods using different restriction enzymes to assess their sensitivity in detecting promoter interactions and their association with regulatory features and genetic variation.

Minimalistic 3D Chromatin Models: Sparse Interactions in Single Cells Drive the Chromatin Fold and Form Many-Body Units

This paper introduces a minimalistic 3D chromatin polymer model that uses sparse interactions to generate single-cell chromatin conformations consistent with experimental data and reveals insights into chromatin structure and function.

DEVELOPMENTAL AND EVOLUTIONARY COMPARATIVE ANALYSIS OF A HOXD REGULATORY LANDSCAPE IN MAMMALS AND BIRDS

The paper compares Hoxd gene regulation in mammalian vibrissae and avian feather primordia with trunk elongation in mice and chickens, showing lineage-specific enhancer usage and functional divergence in conserved CREs.

Assessing chromatin relocalization in 3D using the patient rule induction method

The paper refines the multiMDS approach to identify 3D chromatin relocalization regions using PRIM, avoiding 1D limitations and comparing four cell types.