Hi-C

The linker histone H1.4 condenses chromatin in maturing postmitotic neurons

Epitope-tagged knockin mice show histone H1.4 protein accumulates in postmitotic neurons, shifts toward B-compartment heterochromatin with maturation, and H1f2/H1f4 loss impairs cerebellar granule neuron chromatin compaction.

Comparative epigenomics across the barley pangenome links structural variation to regulatory genome function

The paper links structural variation to regulatory genome function in barley by analyzing epigenomic data across multiple genotypes and developmental contexts.

Mu-seq reveals previously undetected long-range contact patterns in the Escherichia coli nucleoid

Mu-seq maps long-range DNA-DNA contacts in E. coli without crosslinking, revealing new interaction patterns not detectable by Hi-C.

Multidimensional variation and population stratification across 8000 complete human centromeres

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

The paper performs single-cell multiomics analysis of the human retina to identify regulatory elements and develop predictors for non-coding risk variants.

Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation

The paper maps 3D genome organization and DNA methylation across 86,689 single nuclei from 16 human tissues, revealing cell-type-specific variations and discrepancies between methylation and chromatin structure.

Epigenetic and 3D genome reprogramming during the aging of human hippocampus

This study examines age-related changes in the human hippocampus using multi-omics data, revealing cell-type loss and epigenetic reprogramming linked to cognitive decline.

HiC2Self: self-supervised denoising for bulk and single-cell Hi-C contact maps

HiC2Self denoises Hi-C contact maps using self-supervised learning, reconstructing 3D chromatin structures from low-coverage data across bulk and single-cell samples.

Evolution of regulatory chromatin contacts: insights from duplicated genes

The paper studies the evolution of regulatory chromatin contacts in duplicated genes using Hi-C data, finding faster divergence in chromatin contacts compared to expression patterns.

Comparative analyses reveal rapid turnover and emergence of transitory 3D genome architectures in the fungal kingdom

This study compares 3D genome architectures across 55 fungal species, identifying novel configurations and challenging existing classifications.

DNA Sequence and Histone Variant H2A.Z Jointly Govern Nucleosome Unwrapping Pathways

The paper shows DNA sequence and H2A.Z histone variant jointly determine nucleosome unwrapping directionality through simulations and NMR data.

An Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain

The paper constructs an integrative single-cell epigenomic atlas of the adult mouse brain, mapping chromatin states and gene regulatory programs across 100 cell subclasses.

Architectural chromatin interactions provide a framework for context-dependent gene regulation

The paper develops an integrative framework to classify and interpret promoter-centric chromatin interactions by combining Hi-C, ChIA-PET, and functional genomic data, identifying a distinct class of architectural promoter-enhancer interactions with context-dependent regulatory roles.

Reversible chromatin remodeling enables Prosopis cineraria survival under recurrent heat extremes.

This study identifies reversible chromatin remodeling in Prosopis cineraria that enables survival under recurrent heat stress through epigenetic activation of heat-protective genes and metabolic buffering.

scWeave: A deep learning model that bidirectionally translates between gene expression and chromatin structure at single cell resolution

scWeave translates between gene expression and chromatin structure at single-cell resolution using deep learning, improving cross-modality inference across multiple datasets.

Foundation model reveals the shared organization of transcription and topologically associating domains

The paper develops a foundation model to analyze TADs and their impact on transcription, finding that TADs enhance co-regulation and this effect declines with aging and changes in cancer cells.

Reference Regulatory Element-Guided Gene Expression Analysis for Mechanistic Inference of Gene Regulatory Networks

This paper introduces REGA, a framework that uses reference regulatory elements to infer gene regulatory networks from expression data, showing improved performance across multiple benchmarks and applications.

TFIIIC regulates SMC complex binding and 3D DNA contacts between tRNA genes

This study shows TFIIIC regulates SMC complex binding and 3D DNA contacts between tRNA genes independently of RNA Pol III.

Cross-platform Hi-C meta-analysis identifies functional insulators that actively block enhancer-promoter interactions

The paper identifies functional insulators (FINs) through Hi-C meta-analysis, showing they block enhancer-promoter interactions and are distinct from TAD boundaries.

Recognition in Confinement: The Dynamics of Homologous Gene Pairing

This study extends Helical Coherence Theory to model homologous DNA pairing under confinement, showing that optimal confinement accelerates pairing while avoiding tangling and metastable states.

Explainable AI identifies recombination and chromatin environment as key predictors of subgenome evolution in maize and Brassica

The paper uses machine learning to identify recombination rate and chromatin environment as key factors influencing subgenome divergence in polyploid species like maize and Brassica.

The Metaphase Chromatin Unit: A Novel Unit of Higher-Order Chromosome Organization in Human Mitotic Cells

The paper identifies a quantitative unit of mitotic chromosome organization, the Metaphase Chromatin Unit (MCU), by analyzing metaphase lengths and DNA content across human chromosomes.

Modeling the spatial organization of replicated chromosomes in yeast reveals a loose asymmetric cohesion between sister chromatids

The paper models the spatial organization of replicated chromosomes in yeast, finding that cohesion between sister chromatids is asymmetric and loosely aligned.

CAD-C: An engineered nuclease enables repair-free in situ proximity ligation and nucleosome-resolution chromosome walks in human cells

This paper introduces CAD-C, a new chromatin conformation capture method that improves resolution and efficiency over existing techniques like Micro-C and Hi-C.

The Encyclopedia of DNA Elements

The paper presents ENCODE, a comprehensive reference map of the genomic basis of gene regulation, including regulatory elements, transcripts, and their interactions in human and mouse genomes.

OpenCafeMol with 3SPN.2 DNA model: GPU Acceleration for Long-Time Coarse-Grained Chromatin Simulations

The paper extends a GPU-accelerated molecular dynamics simulator to support DNA models and improves efficiency for simulating chromatin interactions over long timescales.

Molecular basis for the regulation of retroviral nucleosomal integration by chromatin compaction

This study investigates how chromatin compaction affects retroviral integration by analyzing the interaction between intasomes and nucleosomes, revealing distinct strategies in HIV-1 and PFV.

Multi-layered regulatory networks driving human dopaminergic neuron differentiation

The paper integrates multi-omics data to identify regulatory networks driving human dopaminergic neuron differentiation and highlights key transcription factors and enhancer-associated regulators.

A Goldilocks zone of DNA flexibility defines stable yet plastic nucleosomes, tuned by histone chemistry

The paper quantifies force-induced nucleosome unwrapping using a coarse-grained model, showing DNA flexibility and histone chemistry determine nucleosome stability and plasticity.

State-Dependent Transcriptomic Collapse of the Brain's Lactate and Ketone Thermodynamic Sensors in Schizophrenia

The paper identifies structural genomic variances in the HCAR2/HCAR1 locus that disrupt thermodynamic sensing in schizophrenia, linking metabolic dysfunction to clinical symptoms.