Hi-C

Mapping genomic loci prioritises genes and implicates synaptic biology in schizophrenia

A genome-wide association study of 69,369 schizophrenia cases and 236,642 controls identifies 270 risk loci, prioritizes 130 genes, and links common and rare risk variants to neuronal synaptic biology.

The RNA-RNA interactome between a phage and its satellite virus reveals a small RNA differentially regulates gene expression across both genomes

KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin

This paper reveals the 3D chromatin structure of KSHV during latency and reactivation, showing similar TAD organization and reorganization of regulatory units.

MYC overexpression leads to increased chromatin interactions at superenhancers and c-Myc binding sites

This study investigates how MYC overexpression affects chromatin interactions and c-Myc binding in cancer cells, revealing its role in stabilizing enhancer-promoter interactions and driving oncogene expression.

Somatic structural variant formation is guided by and influences genome architecture

This study investigates how 3D chromatin architecture influences and is influenced by somatic structural variants in cancer, showing an interplay between chromatin structure and SV formation.

The complete sequence of a human genome

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

NOMe-HiC: joint profiling of genetic variants, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

NOMe-HiC jointly profiles genetic variants, DNA methylation, chromatin accessibility, and 3D genome structure from the same DNA molecule, showing high concordance with mono-omic assays and revealing coordinated chromatin accessibility in spatially proximal regions.

Transcriptomics, Regulatory Syntax, and Enhancer Identification in Heterogenous Populations of Mesoderm-Induced ESCs at Single-Cell Resolution

This study uses bulk and single-cell assays to analyze gene expression, histone modifications, and chromatin features in ESCs transitioning to mesoderm lineages, identifying cis-regulatory elements and transcription factors involved in lineage specification.

Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion

The paper investigates how H1 depletion affects gene expression, H1 variant distribution, and genome 3D conformation in breast cancer cells.

Stripenn detects architectural stripes from chromatin conformation data using computer vision

Stripenn detects and quantifies architectural stripes from chromatin conformation data using computer vision, outperforming existing methods in biological applications.

A maximum-entropy model to predict 3D structural ensembles of chromatins from pairwise distances: Applications to Interphase Chromosomes and Structural Variants

This paper introduces a computational method to predict 3D chromatin structures from pairwise distances and applies it to analyze chromosome organization and structural variants.

THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data

THUNDER is a deconvolution method that infers cell type proportions from bulk Hi-C data, outperforming existing methods in accuracy.

Polymer physics and machine learning reveal a combinatorial code linking chromatin 3D architecture to 1D epigenetics

The paper uses machine learning and polymer physics to infer 3D chromatin architecture from Hi-C data and shows how 1D epigenetic patterns encode this structure through combinatorial binding site arrangements.

The chromatin organization of a chlorarachniophyte nucleomorph genome

This study maps open chromatin, transcription, and 3D organization of the nucleomorph genome in Bigelowiella natans, revealing its highly accessible and transcribed state with strong nucleosome positioning and telomeric chromosome interactions.

NSD2 E1099K drives relapse in pediatric acute lymphoblastic leukemia by disrupting 3D chromatin organization

This study shows NSD2 E1099K mutation disrupts 3D chromatin organization in B-ALL, leading to drug resistance and clonal evolution through compartmentalization changes.

Euchromatin activity enhances segregation and compaction of heterochromatin in the cell nucleus

This study models nuclear chromatin organization using active Zimm chains to show how euchromatin activity drives heterochromatin segregation and compaction through hydrodynamic interactions and crosslinking.

monaLisa: an R/Bioconductor package for identifying regulatory motifs

monaLisa identifies transcription factors from experimental data by integrating with Bioconductor packages for motif analysis.

Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions

This paper introduces CTCC, a method using cryomilling to map chromatin interactions, showing it can generate global contact maps similar to Hi-C but with enhanced signal for stable inter-chromosomal contacts.

Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes and gene regulation

This study quantifies how transposable elements contribute to 3D genome structure and gene regulation across species and cell types, showing their role in shaping chromatin organization and gene expression.

HiC-LDNet: A general and robust deep learning framework for accurate chromatin loop detection in genome-wide contact maps

HiC-LDNet is a deep learning framework for chromatin loop detection in Hi-C data, achieving high accuracy in both bulk and sparse single-cell Hi-C maps.

Strong interactions between highly-dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin

The paper develops a dynamical model of Drosophila nuclei to study how LAD-NE interactions and TAD dynamics shape chromatin structure.

Multivalent binding proteins can drive collapse and reswelling of chromatin in confinement

This study shows that multivalent binding proteins can cause chromatin to collapse and reswell in confined spaces, with reswelling dependent on protein concentration and confinement strength.

Multiple parameters shape the 3D chromatin structure of single nuclei

This study shows that multiple factors influence the 3D chromatin structure of single nuclei during Drosophila embryonic development.

Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification

The paper introduces LOOPbit, a method to detect chromatin loops from Hi-C data by classifying CTCF-CTCF interactions, achieving higher enhancer-promoter loop detection than existing tools.

Higher-order chromatin organization defines Progesterone Receptor and PAX2 binding to regulate estradiol-primed endometrial cancer gene expression

The paper identifies progestin control regions (PgCRs) where PR and PAX2 bind to regulate gene expression in endometrial cancer cells.

Epigenetic dysregulation from chromosomal transit in micronuclei

This study shows that chromosomal transit through micronuclei causes epigenetic dysregulation in cancer cells, leading to long-term chromatin accessibility abnormalities.

Precise Transcript Reconstruction with End-Guided Assembly

Bookend improves transcript assembly by using 5' and 3' end information from RNA-seq data, achieving accurate transcriptome reconstruction in single cells and model organisms.

HiCzin: Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression

HiCzin normalizes metagenomic Hi-C data and detects spurious contacts using zero-inflated negative binomial regression, improving bias correction and contig clustering.

Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C

This paper presents a chromosome-level genome assembly for Telopea speciosissima using long-reads, linked-reads, and Hi-C data, along with new tools for genome curation and size estimation.

Single Molecule Analysis of CENP-A Chromatin by High-Speed Atomic Force Microscopy

The paper uses high-speed atomic force microscopy to analyze single-molecule dynamics of CENP-A nucleosomes and shows how CENP-C affects their mobility and chromatin accessibility.