ArticleGenome research2012
Physical tethering and volume exclusion determine higher-order genome organization in budding yeast.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers.
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Who cites it
140 citing papers in PubMed.
- Condensin accelerates long-range intra-chromosomal interactions.Nature communications · 2026Article
- Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes.Genome biology · 2025Article
- Organization principles of dynamic three-dimensional genome architecture associated with centromere clustering states.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Scale-free models of chromosome structure, dynamics, and mechanics.PNAS nexus · 2025Article
- Genome Mountaineering: Expanding Horizons of the 3D Genome for the Intrepid Evolutionary Adventurer.Genome biology and evolution · 2025Review
- Condensin Accelerates Long-Range Intra-Chromosomal Interactions.bioRxiv : the preprint server for biology · 2025Article
- Review
- Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets.Nature cell biology · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets.bioRxiv : the preprint server for biology · 2023Article
- The power of weak, transient interactions across biology: A paradigm of emergent behavior.Physica D. Nonlinear phenomena · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.Biophysical journal · 2023Article
- Evaluating the role of the nuclear microenvironment in gene function by population-based modeling.Nature structural & molecular biology · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.bioRxiv : the preprint server for biology · 2023Article
- Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.Epigenetics & chromatin · 2023Article
- Nuclear genome organization in fungi: from gene folding to Rabl chromosomes.FEMS microbiology reviews · 2023Article
- Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics.PLoS computational biology · 2023Article
- Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III.PLoS genetics · 2023Article
- Inference of 3D genome architecture by modeling overdispersion of Hi-C data.Bioinformatics (Oxford, England) · 2023Article
- Karyotype engineering reveals spatio-temporal control of replication firing and gene contacts.Cell genomics · 2022Article
80 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
In this paper we show that tethering of heterochromatic regions to nuclear landmarks and random encounters of chromosomes in the confined nuclear volume are sufficient to explain the higher-order organization of the budding yeast genome. We have quantitatively characterized the contact patterns and nuclear territories that emerge when chromosomes are allowed to behave as constrained but otherwise randomly configured flexible polymer chains in the nucleus. Remarkably, this constrained random encounter model explains in a statistical manner the experimental hallmarks of the S. cerevisiae genome organization, including (1) the folding patterns of individual chromosomes; (2) the highly enriched interactions between specific chromatin regions and chromosomes; (3) the emergence, shape, and position of gene territories; (4) the mean distances between pairs of telomeres; and (5) even the co-location of functionally related gene loci, including early replication start sites and tRNA genes. Therefore, most aspects of the yeast genome organization can be explained without calling on biochemically mediated chromatin interactions. Such interactions may modulate the pre-existing propensity for co-localization but seem not to be the cause for the observed higher-order organization. The fact that geometrical constraints alone yield a highly organized genome structure, on which different functional elements are specifically distributed, has strong implications for the folding principles of the genome and the evolution of its function.
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