Hi-C

Reference-Guided De Novo Retrieval of 3D Chromatin Organizational Features with Representation Learning

The paper introduces C-Fetch, a framework that retrieves 3D chromatin features using reference examples, showing improved enrichment for biologically relevant contacts compared to existing methods.

Local chromatin, 3D genome folding and transposon cargo shape Sleeping Beauty transposition

This study identifies factors influencing Sleeping Beauty transposition, showing chromatin context, cargo size, and transcriptional activity affect efficiency and reintegration patterns.

Localized Chromatin Rewiring Shapes Rhythmic Transcription within a Stable 3D Genome in Rice

The paper identifies localized chromatin rewiring in rice's stable 3D genome that coordinates rhythmic transcription across the circadian cycle.

A molecular framework of chromatin extrusion in plants

This study identifies PDS5A as a key regulator of chromatin loop extrusion and TAD-like domains in Arabidopsis, revealing a promoter- and motif-based mechanism for loop anchoring and transcriptional control.

Evolution of CTCF underlies the establishment of loop extrusion as a predominant chromatin folding mechanism in vertebrates

The paper investigates the evolution of CTCF's role in chromatin organization across species, finding that vertebrate CTCF enables loop extrusion but requires additional factors for full genome architecture.

Disrupted chromatin architecture blocks B lymphopoiesis in Down syndrome

The paper develops ChromE-seq to study 3D chromatin architecture in fetal hematopoiesis, finding that T21 disrupts B-lineage development by altering chromatin connectivity and regulatory circuits.

WNT/β-catenin increases 3D chromatin mobility and reorganisation during posterior cell state transitions

EWS::WT1 Isoform-Dependent Regulation of Neogenes in Desmoplastic Small Round Cell Tumors

This study identifies DSRCT-specific neogenes regulated by the EWS::WT1 fusion protein and shows their potential as biomarkers and therapeutic targets in desmoplastic small round cell tumors.

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

Distinct RNA-RNA spatial interaction sub-networks of transcription factors in hepatic cells

The paper uses RIC-seq and integrates multi-omics data to classify transcription factors into two clusters based on RNA-RNA spatial interactions and their genomic and clinical features.

Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

Repeat element-anchored enhancer-promoter interactions (REEPIs) shape the regulatory landscape of hormone-resistant breast cancer

The paper identifies repeat element-anchored enhancer-promoter interactions (REEPIs) in hormone-resistant breast cancer and links them to transcriptional adaptation and regulatory reprogramming.

Polycomb establishes TAD-scale H3K27me3 mega-domains to safeguard neuronal identity

The paper identifies Polycomb repressive complexes (PRCs) as establishing TAD-scale H3K27me3 domains in mature neurons to maintain identity by silencing alternative lineage genes.

Cooperative CTCF-nucleosome oligomerization stabilizes chromatin loop anchors

CTCF dimerization on stacked nucleosomes is resolved by cryo-EM through a ZnF6-7-8 interface. Disrupting it in mouse stem cells weakens CTCF-cohesin loops more than insulation and impairs germline differentiation.

Looplook: Integrating multiomics refinement and graph clustering for target assignment and functional inference of chromatin regulatory networks

Looplook integrates 3D chromatin topology with functional genomics to improve CRE-target gene assignment and functional inference in chromatin regulatory networks.

KAT3 Shuttling Between Neuronal Identity and Activity-Dependent Plasticity Programs Drives Large-Scale Chromatin Remodeling

The paper shows that KAT3 cofactors move between neuronal identity and activity-dependent plasticity programs, causing chromatin remodeling in hippocampal neurons.

Genomic indicators of gene function: A systematic assessment of the human genome

The paper assesses genomic indicators of gene function in the human genome, finding that transcriptional activity and evolutionary conservation are strongest predictors of functional regions.

WAVE2 and REST/NRSF Regulate Clustered Gene Expression by Maintaining Heterochromatin Organization

This study shows WAVE2 and REST/NRSF regulate clustered gene expression by maintaining heterochromatin organization through chromatin dynamics and spatial reorganization.

BioMaster: Multi-agent System for Automated Bioinformatics Analysis Workflow

BioMaster automates complex bioinformatics workflows using a multi-agent system, improving accuracy, efficiency, and scalability across tasks like RNA-seq and Hi-C processing.

The CTCF Paralog BORIS Contributes to the Ovarian Cancer Transcriptional Program by Relaxing CTCF-mediated 3D Genome Organization

This study shows that BORIS, a CTCF paralog, promotes ovarian cancer by altering 3D genome organization and transcriptional programs through chromatin remodeling.

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.

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.

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.

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 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.

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.

A Chromatin-Structure-Guided Framework for Predictive and Interpretable Regulatory Genomics

CHROME improves regulatory genomics predictions by integrating physically validated chromatin interactions into graph models, enhancing accuracy and interpretability for ChIP-seq, eQTL, and variant pathogenicity.