Hi-C

Learning from Hi-C reveals nuclear dynamical reorganization in budding yeast across the cell cycle

This paper uses Hi-C data to infer 3D genome structure and chromatin dynamics in budding yeast without prior assumptions about nuclear organization.

scHiR learns joint cellular representations from paired single-cell transcriptome and 3D genome data

scHiR learns joint representations from paired scRNA-seq and scHi-C data, improving clustering and trajectory inference while recovering input signals.

MaaD-TAD: an all-atom model of the duplicated PRAMEF/HNRNPCL chromatin domain built from sequence homology

The paper introduces MaaD-TAD, an all-atom model of a duplicated chromatin domain, using sequence homology and cohesin placement to reconstruct DNA structure where Hi-C data are missing.

Epigenome-informed Polymer Modeling Reveals Chromosome Folding Landscapes across Distinct Genetic and Epigenetic Contexts

This study uses epigenome-informed polymer modeling to generate chromosomal conformational ensembles from epigenomic data, revealing how genetic and epigenetic contexts shape chromosome folding landscapes.

Decoding Cell-type Specific Gene Regulation with CellReg3D by Integrating DNA Large Language Models and 3D Genome Structure

CellReg3D integrates DNA language models and 3D genome structure to model cell-type-specific gene regulation, achieving state-of-the-art performance in predicting epigenetic marks and gene expression.

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.

A generative network model reveals hierarchical structural memory guiding post-mitotic 3D genome inheritance

The paper introduces HiCONA, a Bayesian framework that identifies mitotically preserved chromatin interactions guiding post-mitotic 3D genome reassembly and epigenetic memory.

scSTEC: Annotating Chromatin Subcompartments from Individual Single-Cell Hi-C Data via Direct Two-Dimensional Embedding and Chromosome-wise Consensus

scSTEC directly annotates chromatin subcompartments from individual single-cell Hi-C matrices without imputation or cross-cell sharing, achieving results comparable to scGHOST with greater interpretability.

Continuous Topological Accessibility (RFA) as a 3D-Aware GRN Filter: Anticorrelation with eQTL and No Prediction of ΔRNA

This paper introduces RFA, a 3D-aware GRN filter, and finds it anticorrelates with eQTL via local distance-decay but does not predict ΔRNA.

Diversity-generating retroelements enable phages to expand their host range in the human gut.

The paper tracks phage-host interactions in the human gut and finds that DGR-encoding phages interact with multiple bacterial species and show increased nucleotide diversity in their receptor-binding proteins.

Pre-existing genome architecture partitions viral takeover in the smallest free-living eukaryote

The paper tracks viral infection in Ostreococcus tauri, showing pre-existing genome architecture dictates viral positioning and transcriptional changes during infection.

Does a map-level insulation constraint improve sequence-based prediction of 3D genome folding? A Stage 1 Registered Report with a reverse-complement-equivariant state-space model (HiFold-Mamba)

The paper evaluates whether insulation-based losses improve sequence-based prediction of 3D genome folding using a reverse-complement-equivariant state-space model, finding improvements in boundary and loop prediction.

Osmotic Coupling of Mechanics and Epigenetics Regulates Chromatin Phase Organization

This study develops a model linking nuclear hydration to chromatin phase organization and mechanics, showing how osmotic and mechanical cues influence chromatin structure through water content and histone dynamics.

3D-genome impacts of TAD-boundary-disrupting ultra-rare structural variants identified in schizophrenia

The paper identifies and functionally characterizes TAD-boundary-disrupting ultra-rare structural variants in schizophrenia using CRISPR/Cas9 in iPSCs, showing cell-type-specific effects on 3D-genome organization and gene expression.

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.

Locus-specific spatial and transcriptional dynamics direct T cell lineage choice in the thymus

The paper investigates how spatial and transcriptional dynamics at Cd4 and Cd8 loci influence T cell lineage choice in the thymus, revealing locus-specific chromatin environments that drive differentiation.

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.

Evaluation of object detection neural networks to find topologically associated domains in bulk Hi-C data

This study evaluates YOLOv8 and Mask R-CNN for detecting TADs in bulk Hi-C data by converting Hi-C matrices into images and comparing their performance against reference TADs.

Abnormal nuclear organization impairs adipogenic lineage commitment and terminal maturation in Hutchinson-Gilford progeria syndrome (HGPS)

This study shows that HGPS disrupts adipogenic lineage maturation through chromatin reorganization defects, despite normal lineage commitment rates.

U-Chrom: a unified framework for single-cell and spatial 3D genome data

U-Chrom provides a unified framework for analyzing single-cell and spatial 3D genome data, showing consistent cell-type differences across assays.

Efficient and precise discovery of LTR-retrotransposon families using HiRepEat

The paper introduces HiRepEat, a method for efficiently discovering and clustering LTR-retrotransposon families across genomes, showing results on vertebrate and Drosophila genomes.

Ctcf deficiency in myofibers induces pathological genome reprogramming toward the spontaneous development of myopathy

This study shows that Ctcf deficiency in myofibers leads to genome reprogramming and myopathy by disrupting 3D genome structure and gene regulation.

Radiotherapy Reshapes the 3D Genome in Medulloblastoma Cells

This study examines how radiotherapy affects the 3D genome of medulloblastoma cells, identifying molecular and structural changes associated with radiation response.

Structural variants from donor-specific assemblies affect recurrent chromatin contact divergence in humans

The paper shows that structural variants from donor-specific assemblies influence chromatin contact divergence in humans, with many SVs linked to regulatory contexts and expression variation.

Robust V(D)J Recombination in the Absence of SA1/2-mediated Chromatin Loops

This study shows that SA1/2 are not essential for V(D)J recombination in G0/G1-arrested cells, but their absence disrupts chromatin loops and long-range Igh recombination, while Ig{kappa} recombination remains functional.

Capture-(Hi)C analysis with PostChicago: Integrative metaprofiling and quantitative comparison of chromatin interactions

PostChicago provides a workflow for analyzing and comparing chromatin interactions from Capture-(Hi)C data, including quality control and visualization of metaprofiles.

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.

Hyperosmotic stress induces rewiring of 3D chromatin interactions

One hour of 200 mM sorbitol collapses most chromatin loops in human cells while several hundred transient, cohesin-dependent, CTCF-independent loops form at active promoters, preceding anchor-gene activation.

Reversing aging-like 3D genome disorganization in a Drosophila interphase model

The paper investigates the reversal of aging-like 3D genome disorganization in Drosophila by restoring lamina-associated domain interactions.