ArticleNature protocols2018
Computational 3D genome modeling using Chrom3D.
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 38 papers.
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Who cites it
38 citing papers in PubMed.
- Senescent cells cluster CTCF on nuclear speckles to instruct an alternative splicing program.Nature aging · 2026Article
- The pangenome ofiScience · 2026Article
- Dynamic changes in Lamin B1 and heterochromatin coincide with chromatin condensation during human erythropoiesis.Genome biology · 2026Article
- Loss of multilevel 3D genome organization during breast cancer progression.Genome research · 2026Article
- Design Space and Declarative Grammar for 3D Genomic Data Visualization.IEEE transactions on visualization and computer graphics · 2026Article
- SMCHD1 maintains heterochromatin, genome compartments and epigenome landscape in human myoblasts.Nature communications · 2025Article
- The Role of Lamins in Genome Organisation: A Modelling Perspective.Sub-cellular biochemistry · 2025Review
- Multiscale molecular modeling of chromatin with MultiMM: From nucleosomes to the whole genome.Computational and structural biotechnology journal · 2024Article
- Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization.Nature communications · 2024Article
- Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription.Genome research · 2024Article
- Near telomere-to-telomere genome of the model plant Physcomitrium patens.Nature plants · 2024Article
- DiffDomain enables identification of structurally reorganized topologically associating domains.Nature communications · 2024Article
- Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of chromosomes.Journal of molecular cell biology · 2023Review
- Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.Epigenetics & chromatin · 2023Article
- The interplay of 3D genome organization with UV-induced DNA damage and repair.The Journal of biological chemistry · 2023Article
- Drosophila Models Reveal Properties of Mutant Lamins That Give Rise to Distinct Diseases.Cells · 2023Article
- Article
- Review
- Uncovering the Principles of Genome Folding by 3D Chromatin Modeling.Cold Spring Harbor perspectives in biology · 2022Review
- Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains.Nature neuroscience · 2022Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chrom3D is a computational platform for 3D genome modeling that simulates the spatial positioning of chromosome domains relative to each other and relative to the nuclear periphery. In Chrom3D, chromosomes are modeled as chains of contiguous beads, in which each bead represents a genomic domain. In this protocol, a bead represents a topologically associated domain (TAD) mapped from ensemble Hi-C data. Chrom3D takes as input data significant pairwise TAD-TAD interactions determined from a Hi-C contact matrix, and TAD interactions with the nuclear periphery, determined by ChIP-sequencing of nuclear lamins to define lamina-associated domains (LADs). Chrom3D is based on Monte Carlo simulations initiated from a starting random bead configuration. During the optimization process, TAD-TAD interactions constrain bead positions relative to each other, whereas LAD information constrains the corresponding bead toward the nuclear periphery. Optimization can be repeated many times to generate an ensemble of 3D genome models. Analyses of the models enable estimations of the radial positioning of genomic sites in the nucleus across cells in a population. Chrom3D provides opportunities to reveal spatial relationships between TADs and LADs. More generally, predictions from Chrom3D models can be experimentally tested in the laboratory. We describe the entire Chrom3D protocol for modeling a 3D diploid human genome, from the creation of input files to the final rendering of 3D genome structures. The procedure takes ∼18 h. Chrom3D is freely available on GitHub.
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