Hi-C

Deciphering the 3D genome organization across species from Hi-C data

This paper introduces Chimaera, a CNN that predicts Hi-C maps from DNA sequences, revealing chromatin structure features and evolutionary relationships across species.

Three-Dimensional Epigenome Roadmap of Human B-cell Differentiation Uncovers Mechanisms of Humoral Immunity and Oncogenesis

This paper creates a 3D epigenomic roadmap of human B-cell differentiation, revealing regulatory mechanisms in immunity and cancer.

Direct measurement of sub-kilobase chromatin structure reveals that linker histone H1 broadly compacts chromatin, with differential impact amongst epigenetic states

The paper directly measures sub-kilobase chromatin structure using RICC-seq 2.0 and finds that linker histone H1 broadly compacts chromatin, with differential effects on gene expression and epigenetic states.

Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes

The paper models DNA replication in yeast to show replication-dependent spatial patterns and chromatin dynamics in the nucleus.

Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D

The paper introduces ec3D, a method to reconstruct 3D structures of ecDNA from Hi-C data, revealing spherical configurations and unique long-range interactions in cancer.

An integrated view of the structure and function of the human 4D nucleome

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

Extending cis-regulatory networks using chromatin-RNA interactions

The paper integrates enhancer-promoter interactions and RNA-DNA contacts to show RNA's role in modulating cis-regulatory networks during neural differentiation.

Cohesin constrains histone modification-driven chromatin dynamics

This study shows that mutations in Asxl1 and Stag2 cause dysregulation of histone modifications and chromatin structures, leading to aberrant gene upregulation and myelodysplastic syndromes.

Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts

The paper identifies trans-acting genetic variation that regulates 3D chromatin interactions through heterochromatin formation, showing how this mechanism coordinates chromatin state and gene expression changes.

Bacteriophage PAK_P3 genome structuration and dynamics during infection of Pseudomonas aeruginosa reveal specific interactions patterns

The paper investigates the 3D genome structuration and dynamics of bacteriophage PAK_P3 during infection of Pseudomonas aeruginosa, revealing specific interactions between phage and host genomes.

Deep learning predicts haematopoietic stem cell ageing from 3D chromatin images

This paper develops a deep learning model to predict haematopoietic stem cell ageing from 3D chromatin images, achieving an AUROC of 0.77 and identifying key chromatin features as predictive markers.

Telomere-to-telomere reference genome of the common five-lined skink, Plestiodon fasciatus (Squamata: Scincidae)

The paper presents the first telomere-to-telomere, chromosome-level reference genome for the common five-lined skink, providing a highly complete and annotated genome sequence.

Cohesin forms fountains at active enhancers in C. elegans

The paper identifies cohesin-dependent 3D chromatin structures called fountains around active enhancers in C. elegans, showing their role in repressing enhancer activity and linking genome architecture to behavior.

The physical chemistry of interphase loop extrusion

The paper develops a minimal model of cohesin loop extrusion based on biochemical and biophysical data, showing how regulatory protein dynamics influence genome folding.

Dps binds and protects DNA in starved Escherichia coli with minimal effect on chromosome accessibility, dynamics and organisation

This study shows Dps compacts the E. coli nucleoid and increases short-range DNA interactions without significantly affecting chromosome accessibility, dynamics, or organisation.

Organization principles of dynamic three-dimensional genome architecture associated with centromere clustering states

The paper investigates how centromere clustering states in Cryptococcus neoformans influence 3D genome architecture during the cell cycle, revealing unique organizational principles.

CiFi: Accurate long-read chromosome conformation capture with low-input requirements

CiFi improves Hi-C analysis by combining 3C with PacBio HiFi sequencing, enabling better coverage in repetitive regions and low-input samples.

Cohesin drives chromatin scanning during the RAD51-mediated homology search.

The paper shows cohesin-driven chromatin loop extrusion facilitates homology search during RAD51-mediated DNA repair in mammalian cells.

Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs

The paper identifies allele-specific chromatin structures in imprinted domains and shows their interaction with cis-acting long non-coding RNAs to regulate imprinted gene expression.

Exploring multi-level microbial interactions from individual 3D genomes to community networks

This study introduces FindMeta3D to analyze microbial 3D genomes and cross-domain interactions, revealing conserved chromatin patterns and infection-related hotspots with therapeutic implications.

Epigenetics is all you need: A Transformer to decode chromatin structural compartments from the epigenome

This paper introduces TECSAS, a Transformer model that predicts chromatin subcompartment annotations from epigenomic data, revealing the impact of long-range epigenomic context on chromatin organization.

Nucleosome condensate and linker DNA alter chromatin folding pathways and rates

This study maps chromatin folding pathways and rates using a coarse-grained model, showing that linker DNA length and nucleosome condensate affect stability and structure.

Three-dimensional genome architecture connects chromatin structure and function in a major wheat pathogen

This study reveals the 3D genome architecture of Zymoseptoria tritici, showing how chromatin structure and function are interconnected through nuclear organization and gene regulation.

Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes

This study shows that chromosome compartment assembly is essential for subtelomeric gene silencing in Trypanosoma brucei, with RAP1 and phosphoinositides regulating this process.

mfSuSiE enables multi-cell-type fine-mapping and multi-omic integration of chromatin accessibility QTLs in aging brain.

mfSuSiE improves fine-mapping of chromatin accessibility QTLs across multiple cell types and integrates multi-omic data in aging human brain samples.

LsrL modulates Lsr2-induced chromatin structure to tune biosynthetic gene cluster regulation in Streptomyces venezuelae

This study investigates how Lsr2 and LsrL regulate chromatin structure and biosynthetic gene clusters in Streptomyces venezuelae using multi-omics approaches.

(A)symmetry in the Allele-Specific Chromosomal Structural Dynamics during Embryogenesis

This study quantifies chromosomal structural dynamics during embryogenesis, revealing allele-symmetric and asymmetric patterns in higher-order structures and geometrical compaction.

Elevated CO2 Reshapes the 3D Chromatin Landscape of Arabidopsis thaliana

This study shows elevated CO2 causes broad 3D chromatin reorganization in Arabidopsis thaliana, with intergenerational persistence and involvement of RdDM and PcG pathways.

Puget predicts gene expression across cell types using sequence and 3D chromatin organization data

Puget predicts gene expression across cell types using sequence and Hi-C data, improving generalization to new biosamples and species.

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.