Hi-C

The paper refines the multiMDS approach to identify 3D chromatin relocalization regions using PRIM, avoiding 1D limitations and comparing four cell types.

This study profiles colorectal cancer specific enhancers and reveals their regulation network using HiChIP, Hi-C, and RNA-seq data, showing their role in cancer progression.

The paper identifies Alu sequences as key mediators of enhancer-promoter interactions through trans-acting R-loops formed by eRNAs, showing their functional and evolutionary significance.

DeTOKI identifies and characterizes chromatin topologically associating domains (TADs) in single cells using scHi-C data, revealing their dynamic yet regulated nature.

The paper examines dynamic chromatin changes in human CAR T cells during exhaustion, identifying regulatory networks and enhancer roles in exhaustion-associated genes.

This study investigates how SARS-CoV-2 alters host chromatin architecture and epigenome, revealing disruptions in 3D genome structure and transcriptional regulation of immune-related genes.

Si-C reconstructs biologically valid super-resolution 3D genome structures from sparse single-cell Hi-C data, revealing cell-to-cell variation and hyperfine chromatin features.

The paper shows that poised enhancers' chromatin and 3D features are conserved in vivo in mouse and chicken embryos, and they play essential roles in developmental gene induction.

The paper investigates how enhancer-promoter interactions and transcription are affected by acute loss of CTCF, cohesin, WAPL, and YY1, finding minimal effects on E-P interactions and gene expression despite 3D genome perturbations.

The paper uses population-based modeling of Hi-C data to analyze the nuclear microenvironment's role in gene function, revealing structural variability and functional heterogeneity.

This study shows that complete depletion of linker histone H1 in Arabidopsis disrupts correlations between chromatin compartmentalization, DNA methylation, and gene expression.

This paper introduces a novel adaptor-switching strategy, s3, that significantly improves usable reads per cell in single-cell genomics assays while maintaining high-throughput capabilities.

The paper identifies TAD cliques as repressive chromatin domains with distinct structural and functional features across cell types.

This study uses long-read metagenomics and Hi-C to assemble high-quality canine MAGs and identify prophages and plasmids.

The paper introduces a computational framework to reconstruct DNA extrusion scenarios from aggregate Hi-C data and demonstrates how DNA extrusion explains directional biases and dynamic promoter-enhancer interactions.

The paper analyzes epigenetic modifications and transcription features across human cell lines and tissues to uncover their interplay and generate new hypotheses.

The paper shows that TAD formation on the inactive X occurs before transcription during X-reactivation, independent of transcriptional activity.

This study examines how 3D chromatin organization in mouse liver changes throughout the circadian cycle, revealing dynamic domain assignments and promoter-specific chromatin contacts.

HiC-DC+ is a tool for Hi-C/HiChIP interaction calling and differential analysis, showing improved performance in HiChIP benchmarking and revealing 3D organization changes during cohesin perturbation and differentiation.

This study analyzes chromatin architecture in Xenopus tropicalis, revealing TAD formation dynamics and conserved CTCF-Rad21 orientation patterns across vertebrates.

This study identifies HMGB1 as an RNA-binding protein that coordinates chromatin folding and RNA homeostasis in senescence through interactions with other RBPs and regulation of SASP-related transcripts.

The paper examines genome architecture changes during medaka gastrulation, finding that CTCF loops form while CTCF binding sites remain fixed, and transcription precedes mature domain formation.

This study identifies RNA processing factors as regulators of cohesin localization and 3D genome structure through their interaction with cohesin and impact on domain boundaries.

This paper introduces diffBUM-HMM, a statistical model for detecting RNA flexibility changes in high-throughput structure probing data, showing higher sensitivity and fewer false positives than existing methods.

scGRNom predicts cell-type disease genes and regulatory networks from multi-omics data, revealing shared and disease-specific functions in schizophrenia and Alzheimer's Disease.

GRiNCH identifies and smooths topological units from sparse chromatin contact data, improving TAD detection and structural recovery across different sequencing depths.

MUNIn identifies long-range chromatin interactions across multiple samples by accounting for sequencing depth and heterogeneity, achieving lower false positives and higher power for shared peaks.

The paper uses scHi-C data and the RPR method to analyze changes in chromosomal architecture during early embryogenesis, revealing intermingling of paternal/maternal chromosomes and Rabl-like polarization.

scHiCTools provides a computational toolbox for analyzing single-cell Hi-C data, offering methods for smoothing, embedding, clustering, and visualization of chromatin organization.