Hi-C

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

DiffModeler uses diffusion models to accurately model protein complex structures from low-resolution cryo-EM maps, achieving high TM-Scores across various resolutions.

Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers

This study introduces SCA-seq to resolve spatial chromatin interactions at single-molecular resolution and demonstrates its application in analyzing epigenomic markers.

Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development

The paper investigates cross-TAD enhancer-promoter communication during limb development using ORCA and simulations, finding that boundary stacking enables such interactions and explains architectural stripes.

DiffDomain enables identification of structurally reorganized topologically associating domains

DiffDomain identifies structurally reorganized TADs using Hi-C and single-cell Hi-C data, outperforming existing methods in accuracy and detecting new TAD subtypes.

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

Chromosome-scale inshore hagfish genome places 1R before the cyclostome-gnathostome split and 2R in the gnathostome stem, and reveals two cyclostome-specific duplications (CR1, CR2).

Differences in Alu vs L1-rich chromosome bands underpin architectural reorganization of the inactive-X chromosome and SAHFs

The paper investigates how Alu and L1-rich chromosome bands influence the structural reorganization of the inactive X chromosome and SAHFs, showing resistance of Alu-rich regions to condensation.

A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development.

The paper identifies a critical noncoding superenhancer region essential for regulating anterior HOXA genes in craniofacial development, showing its deletion causes severe developmental defects in mice and a human patient.

mosGraphGen: a novel tool to generate multi-omics signaling graphs to facilitate integrative and interpretable graph AI model development

mosGraphGen generates multi-omics signaling graphs to enable integrative and interpretable graph AI model development by converting multi-omics data into biologically meaningful graphs.

Chromatin structure and 3D architecture define differential functions of PU.1 cis regulatory elements in human blood cell lineages

The paper identifies PU.1 cis-regulatory elements in human blood cell lineages and shows how chromatin structure and 3D architecture influence their function as enhancers or silencers.

Node Features of Chromosome Structure Network and Their Connections to Genome Annotation

The paper investigates network properties of chromosome structure networks derived from Hi-C data and their connections to genome annotations, finding that semi-local properties better characterize biological features than local or diffusive features.

A comprehensive evaluation of generalizabilityof deep-learning based Hi-C resolution improvement methods

This paper evaluates deep-learning methods for improving Hi-C resolution using experimentally generated datasets and finds they perform poorly on sparse data, with retraining offering limited improvement.

Identification of active transposable element candidates from ROH in a de novo assembled chromosome-scale genome of a Nishikigoi, an ornamental fish derived from Common carp (Cyprinus carpio)

The paper identifies active transposable element candidates in Nishikigoi using ROH islands and long-read sequencing, revealing unique genetic features and a novel approach for TE detection.

Machine Learning Unravels Inherent Structural Patterns in Escherichia Coli Hi-C Matrices and Predicts DNA Dynamics

This paper uses machine learning to analyze Hi-C data from E. Coli, revealing structural patterns and predicting DNA dynamics, showing that a subset of contact pairs suffices for accurate predictions.

Histone binding of ASF1 is required for fruiting body development, but not for genome stability in the filamentous fungus Sordaria macrospora

This study shows that ASF1 histone binding is essential for fertility in Sordaria macrospora, but not for genome stability, and identifies a chromosomal duplication linked to the mutant phenotype.

Protein search processes mediated by chromatin topology

The paper investigates how chromatin compaction affects protein search kinetics using models and experimental data, finding optimal compaction minimizes protein residence time.

Mitotic chromosomes harbor cell type and species-specific structural features within a universal looping architecture

The paper investigates mitotic chromosome architecture across species and cell types, finding species-specific loop sizes but no cell type differences, and links loop size to chromosome arm compaction.

Adhesome Receptor Clustering is Accompanied by the Colocalization of the Associated Genes in the Cell Nucleus

The paper shows that genes coding for adhesome receptor proteins are spatially co-localized and co-regulated in the nucleus, with transcription factors also co-localizing to reinforce extracellular matrix sensing.

Reference-guided automatic assembly of genomic tandem repeats with only HiFi and Hi-C data enables population-level analysis

TRFill improves genome assembly of tandem repeats using HiFi and Hi-C data, enhancing completeness and enabling population-level analysis of subtelomeric repeats.

Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression

Polymer Model Unveils Quantitative Association of Chromatin Conformation and Gene Regulation

The paper introduces a computational framework linking chromatin structure to gene regulation using polymer models and Hi-C data, showing how CTCF deletion affects gene expression in limb development.

Cell-type-specific 3D-genome organization and transcription regulation in the brain

The paper investigates 3D-genome organization and transcription regulation in distinct cell types of the mouse brain, finding cell-type-specific nuclear architecture and chromatin compartmentalization correlated with transcriptional activity and MeCP2 regulation.

Extensive remodelling of XIST regulatory networks during primate evolution

The paper examines how XIST regulatory networks evolve in primates, showing extensive diversification and the role of transposons and enhancers in different species.

Revisiting the Use of Structural Similarity Index in Hi-C

The paper shows that the structural similarity index from CHESS is unreliable due to noise in Hi-C data, warning against its biological interpretation.

Multiscale Bayesian Simulations Reveal Functional Chromatin Condensation of Gene Loci

This paper introduces Hi-C metainference, a Bayesian method to model chromatin organization, revealing that gene loci in mouse embryonic stem cells are dynamically condensed and organized as crumpled globules.

CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline

This study shows that CTCF-mediated 3D chromatin structure pre-establishes gene expression programs required for spermatogenesis by forming meiosis-specific super-enhancers and regulating chromatin loops.

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

This study examines how HPV integration affects host chromatin structure and gene regulation in cervical cancer, finding that integrations are enriched in active chromatin regions and induce local and long-range transcriptional upregulation within TADs.

Differential Roles of positive and negative supercoiling in organizing the E. coli genome

This study investigates how positive and negative supercoiling influence 3D genome organization in E. coli using Hi-C and ChIP-seq data, finding positive supercoiling enhances spatial contacts more than negative supercoiling.

Hi-C2B: Optimised detection of chromosomal contacts within synchronised meiotic S. cerevisiae cells

The paper introduces an optimized Hi-C protocol, Hi-C2B, for studying chromosomal contacts in synchronized meiotic S. cerevisiae cells, improving reproducibility and reducing noise.

The Hippo kinase LATS1 controls CTCF chromatin occupancy and the hormonal response of three-dimensionally grown breast cancer cells

This study shows that 3D culture of breast cancer cells alters chromatin structure and gene expression, with LATS1 kinase playing a key role in CTCF displacement and hormonal response.

Brd2 is dispensable for genome compartmentalization and replication timing

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