ArticleProceedings of the National Academy of Sciences of the United States of America2016
Population-based 3D genome structure analysis reveals driving forces in spatial genome organization.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers.
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Who cites it
124 citing papers in PubMed.
- Mega-enhancers compartmentalize transcriptionally active long genes in the brain.Nature cell biology · 2026Article
- Nuclear mNature chemical biology · 2026Article
- GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery-center axis.Nature protocols · 2026Review
- Generating three-dimensional genome structures with a variational quantum algorithm.Briefings in bioinformatics · 2025Article
- From Rabl-like Architecture to Chromosome Territories: A Conserved Developmental Transition in Animal Genomes.Molecular biology and evolution · 2025Article
- 3D genome organization shapes DNA damage susceptibility to platinum-based drugs.Nucleic acids research · 2025Article
- Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution.Nature communications · 2025Article
- Unveiling the role of chromosome structure morphology on gene function through chromosome conformation analysis.Genome biology · 2025Article
- Deciphering single-cell genomic architecture: insights into cellular heterogeneity and regulatory dynamics.Genomics & informatics · 2025Review
- 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
- Motif distribution in genomes gives insights into gene clustering and co-regulation.Nucleic acids research · 2025Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.International journal of molecular sciences · 2024Article
- Hi-C-guided many-polymer model to decipher 3D genome organization.Biophysical journal · 2024Article
- Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations.bioRxiv : the preprint server for biology · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.Nucleic acids research · 2024Article
- Interplay between epigenome and 3D chromatin structure.BMB reports · 2023Review
- Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.Molecular cell · 2023Review
64 more citing papers are in PubMed but not listed here.
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13 authors.
Funding
Abstract
Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm the presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization.
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