Hi-C

Droplet Hi-C for Fast and Scalable Profiling of Chromatin Architecture in Single Cells

The paper introduces Droplet Hi-C, a method for single-cell chromatin conformation profiling, and demonstrates its application in analyzing gene regulatory programs and detecting genetic variations in cancer cells.

Discovery of dynamic changes in 3D chromatin architecture through polymer physics model

The paper develops a polymer physics model to simulate 3D chromatin architecture dynamics in developing lymphoid cells, revealing structural changes linked to gene regulation and cell fate.

The chromatin conformation landscape of Alzheimer's disease

The paper investigates chromatin conformation changes in Alzheimer's disease, finding loss of genomic loops and CTCF dysfunction linked to neurodegeneration.

scGHOST: Identifying single-cell 3D genome subcompartments

SCGHOST identifies single-cell 3D genome subcompartments using scHi-C data and provides insights into cell-to-cell variability in nuclear organization.

Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome

The paper maps 3D genome architecture in neuronal and non-neuronal cells, finding reduced compartmentalization and increased long-range polycomb interactions in neurons.

p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response

This study shows p53 rapidly changes 3D chromatin structure to regulate gene transcription, identifying 340 new direct target genes.

Predicting A/B compartments from histone modifications using deep learning

This paper introduces a deep learning model to predict A/B compartments from histone modifications, achieving high accuracy across cell types and showing the importance of specific histone marks.

Removing unwanted variation between samples in Hi-C experiments

The paper introduces BNBC, a normalization and batch correction method for Hi-C data, improving cross-sample comparisons and analyses.

Integrating Chromosome Conformation and DNA Repair in a Computational Framework to Assess Cell Radiosensitivity

The paper develops a computational framework integrating Hi-C data and DNA repair models to simulate radiation effects and assess cell radiosensitivity.

High resolution maps of chromatin reorganization through mouse meiosis reveal novel features of the 3D meiotic structure

The paper maps chromatin reorganization during mouse meiosis at high resolution, revealing novel features of 3D meiotic structure and the role of CTCF in loop anchoring.

DiffGR: Detecting differentially interacting genomic regions from Hi-C contact maps

DiffGR detects differentially interacting genomic regions between Hi-C contact maps by comparing TAD-level interactions in human and mouse datasets.

Mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two stage exit from mitosis

The paper shows mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two-stage process during mitotic exit.

Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness

This study evaluates 22 chromatin loop calling methods using Hi-C data, identifies their strengths and weaknesses, and introduces a new robustness score for performance assessment.

Increased Enhancer-Promoter Interactions during Developmental Enhancer Activation in Mammals

The paper examines 3D enhancer-promoter interactions during mammalian development, finding that most enhancers bypass neighboring genes and show tissue-specific conformations with increased interactions upon activation.

MED1 IDR acetylation reorganizes the transcription preinitiation complex, rewires 3D chromatin interactions and reprograms gene expression

This study shows that acetylation of MED1's IDR affects PIC assembly, chromatin organization, and gene expression in ER+ breast cancer cells.

Enhancer-promoter interactions are reconfigured through the formation of long-range multiway chromatin hubs as mouse ES cells exit pluripotency

The paper studies 3D genome structure changes in single mouse ES cells exiting pluripotency, finding reorganization of enhancer-promoter interactions through multiway chromatin hubs.

Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity and tumor-specific looping-mediated biological pathways

The paper uses Hi-C profiling in breast tissues to reveal 3D chromatin-regulated tumor heterogeneity and identifies CA2 as a driver of tamoxifen resistance through enhancer-promoter looping.

DNA replication and polymer chain duplication reshape the genome in space and time

The paper develops a computational framework to model DNA replication dynamics and their impact on chromosome organization, showing replication-dependent loop extrusion and sister chromatid interactions in yeast.

Chrom-pro: A User-Friendly Toolkit for De-novo Chromosome Assembly and Genomic Analysis

Chrom-pro is a toolkit for chromosome-level genome assembly and analysis that integrates SGS, TGS, and Hi-C data into an automated workflow, achieving high BUSCO scores and collinearity with reference genomes.

Chromatin packing domains persist after RAD21 depletion in 3D.

The paper shows that RAD21 depletion reduces but does not eliminate chromatin packing domains in electron microscopy, suggesting non-cohesin mechanisms largely control 3D structure.

Assessing the impact of Brd2 depletion on chromatin compartmentalization

This study reanalyzes Brd2 depletion effects on chromatin compartments using Micro-C data and cooltools, showing persistent but reduced compartment strength changes.

Discovery and characterization of chromosomal inversions in the arboviral vector mosquito Aedes aegypti

This study identifies chromosomal inversions in Aedes aegypti using Hi-C, revealing geographic distribution patterns and potential roles in host choice and disease transmission.

Chromatin structure and var2csa - a tango in regulation of var gene expression in the human malaria parasite Plasmodium falciparum?

The paper investigates how var2csa influences var gene expression in Plasmodium falciparum by analyzing chromatin structure changes after gene deletion.

Chromosome Structure I: Loop extrusion or boundary:boundary pairing?

This study tests two models for TAD boundary formation in flies and finds that boundary pairing, not loop extrusion, determines TAD endpoints.

Activity of MukBEF for chromosome management in E. coli and its inhibition by MatP

The paper investigates how MukBEF manages chromosome structure in E. coli and how MatP/matS inhibits its activity through unloading.

Multi-omic Analysis of Primary Human Kidney Tissues Identifies Medulla-Specific Gene Expression Patterns

The paper identifies medulla-specific gene expression patterns in adult human kidney tissues using multi-omic data and corrects misassignments in the GTEx database.

Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils

This study identifies Smc5/6's role in organizing transcription-induced positive DNA supercoils by initiating loop extrusion at cohesin-dependent boundaries.

LoopSage: An Energy-Based Monte Carlo approach for the Loop Extrusion Modelling of Chromatin

LoopSage simulates chromatin loop extrusion using a Monte Carlo method, showing significant correlation with ChIA-PET data and phase transitions in chromatin structure.

3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression

The paper introduces HAPI, a 3D genomics method, to identify enhancer hijacking in cancer cell lines, revealing novel oncogene activation mechanisms.

SATB2 organizes the 3D genome architecture of cognition in cortical neurons

The paper shows SATB2 influences 3D genome structure in cortical neurons, affecting gene expression and cognitive-related functions.