Hi-C

This study shows that Brd2 depletion does not alter genome replication timing or A/B compartmentalization in mouse embryonic stem cells.

The paper identifies Stonewall as a protein that positions chromatin at the nuclear periphery in Drosophila, linking this positioning to gene repression and germline stem cell fate.

This study shows that vaccinia virus infection causes coordinated changes in host chromatin structure, accessibility, and gene expression over time.

This study investigates how the HCHC complex affects genome organization in Neurospora crassa by altering histone acetylation and cytosine methylation, leading to changes in heterochromatic region compaction and interactions.

This study shows that inhibiting β-catenin/CBP interaction with ICG-001 alters 3D chromatin structure in pancreatic cancer, affecting insulin signaling and promoting tumor growth.

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

The paper introduces a novel algorithm to improve Hi-C contact matrices by inferring linear genomes from Hi-C data using genome graphs, resulting in more accurate structural representations.

The paper uses polymer simulations to model chromatin dynamics and shows that productive interactions depend on contact frequency, capture radius, and duration, not just average contact matrices.

The paper develops HiDENSEC to analyze Hi-C data in heterogeneous cancer samples, identifying chromosomal rearrangements and their impact on melanoma progression.

This paper introduces two 3C-derived methods, Tri-4C and Tri-HiC, for ultrafine mapping of chromatin interactions at 100 basepair resolution, revealing regulatory genome architecture and enhancer-promoter loops.

A de novo yeast neochromosome carrying all 275 tRNA genes was built and characterized; it imposes a growth burden, with genome doubling and deletions in haploids possibly reflecting compensation.

hipFG harmonizes and integrates diverse functional genomics data into standardized, searchable datasets for analysis workflows.

This study shows FoxA1/2 reprogram the epigenome of NKX2-1-negative lung adenocarcinoma to drive a gastric lineage switch through DNA demethylation and regulatory element activation.

The paper uses TSA-seq to map genomic regions near nucleoli and pericentric heterochromatin in human cell lines, revealing variable heterochromatin localization and complex nuclear organization.

The paper identifies ProA and ProB repeat sequences as sequence determinants of chromatin compartments, showing their role in genome organization and cancer progression.

This paper evaluates and classifies bacterial chromosome structure reconstruction tools using 3C/Hi-C and microscopy data, highlighting challenges and future directions.

The paper resolves the haplotypes of arbuscular mycorrhizal fungi and identifies two nuclear populations involved in host interactions.

The paper uses high-resolution CTCF MNase HiChIP data to analyze chromatin loop structures and introduces FactorFinder, finding that fully extruded CTCF-CTCF loops are rare and that chromatin state affects cohesin extrusion dynamics.

The paper studies allopolyploidization in weeping willow, showing how sex chromosomes evolve and revert after hybridization between two dioecious species.

This paper introduces EVRC, an algorithm for reconstructing chromosome 3D structures using co-clustering coefficients and error-vector resultant, showing high similarity to real structures in simulations and Hi-C data.

OpenNucleome enables GPU-accelerated molecular dynamics simulations of the human nucleus to model structural organization and dynamic processes, revealing mechanisms of genomic anchoring and nuclear zoning.

This study investigates how chromatin-associated RNA interacts with 3D genome organization in human cells, revealing a feedback loop between RNA distribution and chromatin structure.

This study identifies AD-specific DNA methylation signatures and chromosomal epigenome erosion in LOAD brain cells and shows their conservation in induced neurons.

The paper investigates how the Hox gene Ubx is restricted to hindwings in butterflies by analyzing chromatin structures and CRISPR perturbations, revealing silencing and insulating sequences.

The paper identifies how the 2μ plasmid in yeast binds to inactive chromosomal regions through nucleosome signals and RNA Pol II depletion, revealing a stable and rapid tethering mechanism.

The paper introduces cudaMMC, a GPU-accelerated Monte Carlo method for chromatin 3D modeling, showing faster performance and better model scores than previous methods.

The paper investigates allele-specific enhancer-promoter interactions in an imprinted domain during mouse neural commitment, finding that biallelic interactions occur but only maternal ones are productive.

The paper uses deep learning to assess how sequence changes affect chromatin organization, finding that repetitive elements and noncoding RNA genes significantly influence 3D genome structure.

This study identifies a mutation in SMCHD1 that enhances gene silencing and disrupts developmental processes, revealing distinct roles of SMCHD1 in chromatin structure and gene regulation.

The paper introduces a computational method to identify trans-chromosomal interactions and finds that genes regulated by the same factor co-localize to form RNA factories.