Hi-C

Histo-LCM-Hi-C reveals the 3D chromatin conformation of spatially localized rare cells in tissues at high resolution

The paper introduces Histo-LCM-Hi-C to study 3D chromatin structure of rare tissue cells, showing distinct chromatin organization in liver Kupffer cells compared to whole liver and in vitro macrophages.

Persistent chromatin loops shape gene expression plasticity upon stimulation and restimulation of human neurons

The paper shows that persistent chromatin loops in human neurons influence gene expression plasticity during and after stimulation, with some loops maintaining repression or activation for up to five days.

Predicting chromatin conformation contact maps

The paper predicts missing chromatin conformation contact maps across cell types and assays, exploring how 3D genome architecture varies.

Brain Region-Specific Epigenomic Reorganization and Altered Cell States in Alzheimer's Disease

This study presents a single-cell multi-omic atlas of Alzheimer's disease brain regions, revealing region-specific epigenomic changes and altered cell states.

Recurrent enhancer-promoter interactions across samples

This study analyzes the recurrence of enhancer-promoter interactions across multiple Hi-C and HiChIP datasets, finding that most interactions are shared across samples and cell types.

First Genome-Wide Centromere Map of Trypanosoma cruzi Reveals Linear and 3D Compartment Boundaries and Spatial Clustering

The paper generates a high-quality genome assembly and centromere map for T. cruzi using Hi-C and ChIP-seq, revealing structural boundaries and 3D clustering of centromeres.

Dynamics and interplay of gene expression and chromosome organization across a predatory lifecycle

This study maps transcriptional activity and chromosome architecture in Bdellovibrio bacteriovorus across its predatory lifecycle stages using multi-omics approaches.

VECTOR: A Framework to Identify and Quantify Structural Changes in Chromatin using Hi-C Data

VECTOR quantifies chromatin structure from Hi-C data using Von Neumann entropy and graph spectral theory, outperforming existing tools in detecting structural changes across biological conditions.

Can Random Walking on a Hi-C Contact Matrix Lead to Data Quality Improvement? An Assessment

This study evaluates random walk methods for improving Hi-C data quality, finding no significant benefit for TAD identification despite parameter tuning challenges.

Chromatin landscape and enhancer-gene interactiondifferences between three cardiac cell types

The paper identifies cell-type-specific enhancer-gene interactions in cardiac cells and maps disease-associated SNPs to enhancers in endothelial cells.

HiC-SCA: A Spectral Clustering Method for Reliable A/B Compartment Assignment From Hi-C Data

HiC-SCA improves A/B compartment assignment from Hi-C data through spectral clustering with noise filtering and resolution selection, showing better consistency across datasets.

HiCDOC: chromatin compartment prediction and differential analysis from Hi-C data with replicates

HiCDOC predicts and differentially analyzes chromatin compartments from Hi-C data with replicates, identifying biologically relevant compartment changes supported by transcriptional differences.

Comprehensive Noise Reduction in Single-Cell Data with the RECODE Platform

The paper introduces iRECODE, a noise reduction method for single-cell data that improves accuracy and efficiency in handling technical and batch noise across various sequencing modalities.

Loop extrusion provides mechanical robustness to chromatin

This study develops a force-dependent model of chromatin loop extrusion and shows it alters DNA force-extension behavior non-monotonically, providing mechanical robustness to chromatin.

Genome assembly of five Tephritid species for the enhancement of the Sterile Insect Technique

The paper presents chromosome-level genome assemblies for five Tephritid species using long-read sequencing, short-read polishing, and Hi-C scaffolding.

Genome-Wide Annotation of Promoter-Enhancer Interactions via Chromatin Loops in the Hybrid Rat Diversity Panel

The paper identifies genome-wide promoter-enhancer interactions in rat brain using Hi-C data and CTCF binding sites, revealing regulatory elements linked to developmental processes.

Improved genome assembly of whale shark, the world's biggest fish: revealing "chromocline" in intragenomic heterogeneity

The paper presents an improved chromosome-level genome assembly of the whale shark, revealing a chromocline effect in substitution rates across chromosomes.

An RNA-mediated DNA melting mechanism for CRISPR-Cas9

This study identifies an RNA-mediated DNA melting mechanism in CRISPR-Cas9 using simulations and experiments, showing RNA bases intercalate to promote strand separation.

Single-molecule chromosome tracing reveals a diversity of megabase heterochromatin domains

The paper identifies three types of megabase-scale heterochromatin domains in C. elegans using single-molecule tracing and shows their developmental dynamics and structural differences.

Human Papillomavirus Genomes Associate with Active Host Chromatin during Persistent Viral Infection

This study shows HPV31 genomes associate with active host chromatin regions, linking viral persistence to transcriptional activity and integration sites in cervical cancers.

Ectomesenchymal identity emerges via relief of Twist1transcript destabilization

The paper identifies a vertebrate-specific regulatory mechanism for Twist1 expression in cranial neural crest cells, linking enhancer activity to transcript destabilization.

Cell type specific enrichment of somatic aneuploidy in the mammalian brain

The paper identifies cell type-specific aneuploidy in the adult mouse brain, finding a strong enrichment of chromosome 16 trisomy in non-neuronal cells.

MeCP2 binding and genome-lamina reorganization precede long gene activation during mouse corticogenesis

The paper identifies genome-lamina reorganization preceding long gene activation in mouse corticogenesis and links it to MeCP2 binding.

Multiple long-range cis interactions generate CTCF insulator-dependent viral chromatin domains in quiescent HSV-1 genomes

The paper investigates how HSV-1 CTCF insulators regulate chromatin organization and transcription through long-range cis interactions, showing that deletion of the CTRL2 insulator disrupts chromatin domains and alters transcriptional accessibility.

Diverse epigenomic mechanisms underpin transcriptional dysregulation in Polycomb-altered acute myeloid leukemia

This study investigates how PRC2 depletion in AML affects epigenomic and transcriptional changes, revealing altered chromatin accessibility, H3K27me3 levels, and gene expression patterns that impact cell phenotype and treatment response.

MIA-Jet: Multi-scale Identification Algorithm of Chromatin Jets

MIA-Jet detects chromatin jets in 3D genome data, revealing their dependence on cohesin and CTCF, and outperforms existing methods across multiple species and datasets.

The multiscale distribution of radiation-induced DNA damage and its impact on local genome structure

This study measures radiation-induced DNA damage distribution using END-seq and shows its correlation with 3D genome structure and chromatin features.

Age-Dependent Maturation and Rejuvenation of the Neural 3D Chromatin Interactome in Enriched Environments

The paper shows that environmental enrichment modulates age-related changes in the 3D chromatin interactome of mouse hippocampal neurons, inducing maturation in young mice and partial rejuvenation in old mice.

An integrated multi-tissue atlas of epigenomic landscapes and regulatory elements in the bovine genome

The paper constructs a bovine epigenomic atlas to annotate regulatory elements and decode the regulatory syntax of the cattle genome, aiding in fine-mapping GWAS loci for complex traits.

Finding ancestry-specific chromatin architecture in Alzheimer's disease

The paper identifies ancestry-specific chromatin architecture differences in Alzheimer's Disease using Hi-C and ATAC-seq data from African and European ancestry individuals.