Hi-C

Genetic elements promote retention of extrachromosomal DNA in cancer cells

A genome-wide plasmid screen, Retain-seq, identifies thousands of CpG-rich promoter-like human elements that tether episomes to mitotic chromosomes, shape ecDNA structure, and lose function when methylated.

Uncovering High-Resolution Organization of Genomic Loci using Experimentally Informed Polymer Model

This study introduces a polymer physics-based model integrating contact data and nucleosome positioning to reveal structural differences between active and inactive chromatin states in human genomic loci.

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture

This study reconstitutes gene-scale chromatin arrays with controlled histone modifications to show acetylation increases structural fluctuations and reduces nucleosome contact frequency.

Evo2HiC: a multimodal foundation model for integrative analysis of genome sequence and architecture

Evo2HiC improves prediction of 3D genome architecture and epigenomic signals by integrating DNA sequences and Hi-C data, achieving better accuracy and computational efficiency.

ChromPolymerDB: A High-Resolution Database of Single-Cell 3D Chromatin Structures for Functional Genomics

ChromPolymerDB reconstructs single-cell 3D chromatin structures from bulk Hi-C data and provides a database for analyzing chromatin conformation across 50 human cell types.

GAT-HiC: Efficient Reconstruction of 3D Chromosome Structure via Residual Graph Attention Neural Networks

GAT-HiC predicts 3D chromosome structure from Hi-C data using graph attention networks, showing generalization across different datasets and outperforming existing methods.

Pathway and gates for ATG2A-mediated lipid transport in autophagy

This study identifies the mechanism of ATG2A-mediated lipid transport in autophagy, revealing N-terminal helices as gates that regulate lipid transfer efficiency.

Universal dynamics of cohesin-mediated loop extrusion

The paper tracks TAD anchors in human cells to quantify cohesin-mediated loop extrusion dynamics and shows consistent extrusion rates across diverse genomic regions.

The Divergent 3D Genome Landscapes of Aging and Neurodegenerative mouse models

This study compares 3D genome changes in aging and neurodegenerative mouse models using Hi-C, finding shared early features and distinct later changes linked to DNA damage.

HIRA defines early replication initiation zones independently of their genome compartment

The paper shows HIRA regulates early replication initiation zones independently of chromatin accessibility, histone marks, and 3D compartment organisation.

The 3D nuclear position and compartmentalization of genes prime their response to mechano-confinement

The paper investigates how 3D nuclear positioning and compartmentalization of genes influence transcriptional responses to mechanical confinement using Hi-C and transcriptome analyses.

DiffHiChIP: Identifying differential chromatin contacts from HiChIP data

DiffHiChIP identifies differential chromatin contacts from HiChIP data by addressing limitations in existing methods through improved statistical modeling and distance correction.

Generating three-dimensional genome structures with a variational quantum algorithm

This paper proposes a variational quantum algorithm to model 3D genome structures from contact data and demonstrates its ability to generate ensembles of viable conformations.

NPM1 mislocalization mediated by RNA Pol I inhibition alters chromatin landscape

The paper shows RNA Pol I inhibition disrupts nucleolar structure, alters NPM1 localization, and changes chromatin landscape through histone modifications and DNA methylation.

Integrated multi-omic and functional evidence uncover substantial strain-specific divergence in zebrafish

The paper compares two zebrafish strains using multi-omic data to identify genetic and regulatory differences affecting circadian rhythms and immune response.

Spatial genome organization in nematodes with programmed DNA elimination

The paper investigates spatial genome organization during programmed DNA elimination in nematodes, showing conserved 3D genome reorganization across species.

Rapid canalization of chromosome conformation-transcription fingerprints during embryogenesis revealed by fully-automated cell identity decoding with CeSCALE

The paper develops CeSCALE to analyze lineage-resolved conformation-transcription relationships in C. elegans embryos, revealing robust inheritance of local chromatin features during development.

OLIVE Provides Rapid Visualization and Analysis of Chromatin Tracing Experiments

OLIVE provides a web-based tool for visualizing and analyzing chromatin tracing data, enabling interactive exploration and quantitative analysis of three-dimensional chromatin structures.

Development of a long-read high-throughput chromatin conformation capture method for evaluating both cis and trans interactions between integrated Hepatitis B Virus and host genomes.

The paper develops a long-read Hi-C method to study 3D interactions between integrated HBV DNA and host genomes, improving sensitivity and specificity for analyzing these interactions.

Mechanistic Genome Folding at Scale through the Differentiable Loop Extrusion Model

This paper introduces dLEM, a differentiable loop extrusion model that predicts genome folding mechanisms from contact maps and integrates with deep learning to infer extrusion parameters from genomic features.

Dynamics of microcompartment formation at the mitosis-to-G1 transition

The paper uses Region Capture Micro-C to study microcompartment formation during mitosis-to-G1 transition, finding they form in prometaphase and are influenced by chromatin compaction and loop extrusion.

Micro-C in Solanum Uncovers Conserved Genome Folding and Epigenetically Defined Loops with Bifunctional Enhancer-Silencer Activity

The paper generates a high-resolution Micro-C map of tomato, identifies two epigenetic classes of chromatin loops, and reveals their dual regulatory roles in gene expression.

METAHICT enables comprehensive genome-resolved microbiome analysis with metagenomic Hi-C

METAHICT improves metagenomic Hi-C analysis by integrating binning, reassembly, and downstream tools to recover high-quality MAGs and reduce contamination.

STAG2 cohesin cooperates with DREAM to maintain quiescence and suppress tumourigenesis in the urothelium

This study shows that STAG2 cohesin works with DREAM to maintain quiescence and prevent tumor formation in urothelial cells by regulating chromatin structure and cell cycle control.

Mapping the Telomeric 3D Interactome with Telomere-C Reveals Repetitive Element Hubs Associated with Telomere Maintenance

The paper introduces Telomere-C, a method to map telomeric 3D interactions, revealing ultra-long-range contacts and repetitive element hubs linked to telomere maintenance.

Loss of multi-level 3D genome organization during breast cancer progression

This study investigates how 3D genome organization changes during breast cancer progression using Hi-C and epigenomic data, revealing structural alterations linked to oncogenic gene activation.

Temporal Expression Prediction by Integrating Genome Dynamics via Spatio-temporal GNNs

The paper introduces spatio-temporal GNNs to predict mRNA and miRNA expression over time using Hi-C data, achieving high correlation and variance explanation.

Targeting the 3D genome by anthracyclines for chemotherapeutic effects

This study shows anthracycline drugs disrupt 3D chromatin structure by interfering with CTCF binding, altering gene regulation and clinical outcomes in AML.

Protamine lacunae preserve the paternal chromatin landscape in sperm

The paper uses Fiber-seq to study paternal chromatin repackaging in sperm, finding that protamine lacunae and nucleosome retention play distinct roles in epigenetic inheritance.

SLUR(M)-py: A SLURM Powered Pythonic Pipeline for Parallel Processing of 3D (Epi)genomic Profiles

SLUR(M)-py is a Python pipeline using SLURM for parallel processing of multi-omic epigenomic data, demonstrating improved speed and completeness over existing HPC pipelines.