Hi-C

Heat Shock Factor 1 forms nuclear condensates and restructures the yeast genome before activating target genes

This paper shows that Hsf1 forms condensates and restructures the yeast genome before activating HSR genes in response to ethanol stress, with different kinetics compared to thermal stress.

Promoter- and Enhancer-Dependent Cohesin Loading Initiates Chromosome Looping to Fold Tcrb Loci for Long-Range Recombination

The paper shows that cohesin loading from Vβ promoters or enhancers initiates loop extrusion across the Tcrb locus, enabling long-range recombination.

GrapHiC: An integrative graph based approach for imputing missing Hi-C reads

GrapHiC improves Hi-C read imputation by integrating Hi-C and ChIP-seq data in a graph framework, enhancing performance on sparse and cross-cell-type inputs.

Dissecting Regulatory Non-Coding Heart Disease GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Pathophysiological Relevance to Heart Failure

The paper identifies causal genes in heart disease GWAS loci by integrating Hi-C, chromatin accessibility, and transcriptomic data, revealing regulatory relationships in cardiac fibroblasts.

Heterogeneity in chromatin structure drives core regulatory pathways in B-cell Acute Lymphoblastic Leukemia

This study identifies how chromatin structure heterogeneity in B-ALL correlates with transcriptional subtypes and developmental stages, revealing its role in disease progression.

PneumoBrowse 2: An integrated visual platform for curated genome annotation and multiomics data analysis of Streptococcus pneumoniae

PneumoBrowse 2 provides an updated integrated platform for genome annotation and multi-omics data analysis of Streptococcus pneumoniae, enhancing research into its biology and potential treatments.

Multiscale Molecular Modelling of Chromatin with MultiMM: From Nucleosomes to the Whole Genome

The paper introduces MultiMM, a 3D chromatin simulation model that generates genome-wide structures from nucleosome data using energy minimization.

mRNA expression is co-regulated by non-nucleolar RNA polymerase I

The paper shows that RNA polymerase I co-regulates chromatin domains and mRNA synthesis with RNA polymerase II, affecting genome connectivity and gene expression.

Divergent 3D genome organization in livers of cave and surface morphs of Astyanax mexicanus as a potential driver of unique metabolic adaptations in cave environment.

This study examines 3D genome organization in livers of cave and surface morphs of Astyanax mexicanus, linking structural changes to metabolic adaptations.

HiCrayon reveals distinct layers of multi-state 3D chromatin organization

HiCrayon co-visualizes 3D chromatin conformation with 1D genomic data to reveal new insights into chromatin organization.

Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations

The paper uses polymer physics models to simulate and analyze the 3D structure of the LTN1 gene region, comparing results with Hi-C data to predict structural features for microscopy experiments.

Genome wide clustering on integrated chromatin states and Micro-C contacts reveals chromatin interaction signatures

The paper integrates chromatin states and Micro-C contacts to identify chromatin interaction signatures across cell types, revealing dynamic patterns of chromatin conformation.

Single-allele chromatin folding is organized by recurrent motifs that are reweighted across cell types and states

The paper shows that chromatin folding is organized by recurrent motifs that are reweighted across cell types and states, revealing a structured framework for chromatin variability.

Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance

This study identifies enhancer-promoter hubs in cancer types and shows their role in oncogenesis and drug resistance through topological and transcriptional changes.

Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments

This study identifies ZNF274's role in anchoring lineage-specific gene clusters within repressive perinucleolar compartments, revealing its impact on chromatin structure and gene regulation.

HiCMC: High-Efficiency Contact Matrix Compressor

HiCMC compresses Hi-C data more efficiently than existing methods by modeling chromosome structures, improving compression rates across multiple cell lines and resolutions.

The DNA loop release factor WAPL suppresses Epstein-Barr virus latent membrane protein expression to maintain the highly restricted latency I program

This study shows that WAPL suppresses LMP1 and LMP2A expression in EBV latency I by altering DNA looping and histone marks, preventing the transition to latency II.

Fast Low-Input Efficient Hi-C

The paper introduces FLIE Hi-C, a streamlined Hi-C method that reduces time, reagent use, and input material while maintaining data quality.

Micro-C reveals MORC/ApiAP2-mediated links between distant, functionally related genes in the human malaria parasite

The paper uses Micro-C to map DNA-DNA contacts in Plasmodium falciparum, revealing heterochromatic and euchromatic structures mediated by MORC/ApiAP2 and other factors.

HIRA-dependent provision of histone H3.3 in active chromatin ensures genome compartmentalisation

This study shows that HIRA-dependent histone H3.3 deposition maintains 3D genome compartmentalisation in active chromatin, independent of histone PTMs.

The long-range gene regulatory landscape of cerebellar granule neuron progenitors

The paper identifies long-range gene regulatory interactions in cerebellar granule neuron progenitors using pcHi-C, ATAC-seq, and ChIP-seq, revealing co-regulation by Atoh1 and CHD7.

Mechanism of homology search expansion during recombinational DNA break repair

This paper investigates the mechanism of homology search expansion during DNA break repair, revealing how chromatin structure, NPF stiffening, and resection drive genome-wide search.

Large-scale manipulation of radial positioning does not affect most aspects of genome organization

The paper manipulates nuclear radial positioning using Prm1 expression and finds that genome organization remains largely robust to this change.

Y chromosome-coded HSATII repeats may contribute to higher incidence of cancer in men

The paper investigates how Y chromosome-coded HSATII repeats may contribute to higher cancer incidence in men by analyzing their chromatin interactions and triplex formation.

Genome Restructuring around Innate Immune Genes in Monocytes in Alcohol-associated Hepatitis

The paper uses Hi-C and scRNA-seq to analyze chromatin structure and gene expression in monocytes from alcohol-associated hepatitis patients, finding altered genome organization affecting immune gene expression.

Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes

This paper introduces HapHiC, a reference-independent allele-aware scaffolding tool that improves chromosome assignment and contig ordering, and applies it to construct a haplotype-resolved allotriploid genome.

Spatial 3D genome organization controls the activity of bivalent chromatin during human neurogenesis

This study shows that spatial genome organization in human neurogenesis affects bivalent chromatin activity by relocating genes from the nuclear lamina to speckles, increasing transcription and resolving chromatin states.

EPInformer: A Scalable Deep Learning Framework for Gene Expression Prediction by Integrating Promoter-enhancer Sequences with Multimodal Epigenomic Data

EPInformer predicts gene expression by integrating promoter-enhancer sequences, epigenomic signals, and chromatin contacts, outperforming existing models in cross-chromosome validation and CRISPR experiments.

scHiCyclePred: a deep learning framework for predicting cell cycle phases from single-cell Hi-C data using multi-scale interaction information

scHiCyclePred predicts cell cycle phases from single-cell Hi-C data using multi-scale interaction features, outperforming existing methods.

Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning

The paper introduces a deep learning framework, AkitaR, to study how chromatin-associated RNAs influence genome folding in HFFc6 cells, identifying known and novel RNAs involved in chromatin architecture.