ArticleNature protocols2018
Producing genome structure populations with the dynamic and automated PGS software.
Article in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Mega-enhancers compartmentalize transcriptionally active long genes in the brain.Nature cell biology · 2026Article
- One chromatin, many structures: From ensemble contact maps to single-cell 3D organization.Biophysical journal · 2026Article
- GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery-center axis.Nature protocols · 2026Review
- One Chromatin, Many Structures: From Ensemble Contact Maps to Single-Cell 3D Organization.bioRxiv : the preprint server for biology · 2026Article
- PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures.Journal of molecular biology · 2025Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- 3D genome organization shapes DNA damage susceptibility to platinum-based drugs.Nucleic acids research · 2025Article
- Unveiling the role of chromosome structure morphology on gene function through chromosome conformation analysis.Genome biology · 2025Article
- Visualization of chromosomal reorganization induced by heterologous fusions in the mammalian nucleus.Nature communications · 2025Article
- Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations.Bioinformatics (Oxford, England) · 2025Article
- Hi-C-guided many-polymer model to decipher 3D genome organization.Biophysical journal · 2024Article
- Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.Nucleic acids research · 2024Article
- Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.Molecular cell · 2023Review
- Evaluating the role of the nuclear microenvironment in gene function by population-based modeling.Nature structural & molecular biology · 2023Article
- Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data.Current opinion in cell biology · 2023Review
- Predicting scale-dependent chromatin polymer properties from systematic coarse-graining.Nature communications · 2023Article
- Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.Epigenetics & chromatin · 2023Article
- A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants.Nature communications · 2023Article
- Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations.Nature methods · 2022Article
- Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains.Biophysical journal · 2022Article
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Authors and funding
6 authors.
Funding
Abstract
Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genome's organization in space and time. We provide a user-friendly software package, called PGS, which runs on local machines (for practice runs) and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix, along with information about genome segmentation, and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and provides tools to extract and analyze the 3D coordinates of specific domains. Basic Linux command-line knowledge is sufficient for using this software. A typical running time of the pipeline is ∼3 d with 300 cores on a computer cluster to generate a population of 1,000 diploid genome structures at topological-associated domain (TAD)-level resolution.
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