ArticlePLoS computational biology2015
Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae.The EMBO journal · 2026Article
- High-throughput DNA repair monitoring in Saccharomyces cerevisiae suggests SSB- and DSB-induced chromatin reconfiguration.Scientific reports · 2025Article
- Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.Life science alliance · 2024Article
- Article
- Live-cell imaging of chromatin contacts opens a new window into chromatin dynamics.Epigenetics & chromatin · 2023Review
- Review
- Live-cell imaging probes to track chromatin modification dynamics.Microscopy (Oxford, England) · 2021Article
- The 3D nuclear conformation of the major histocompatibility complex changes upon cell activation both in porcine and human macrophages.BMC molecular and cell biology · 2021Article
- Zooming in on chromosome dynamics.Cell cycle (Georgetown, Tex.) · 2020Review
- Addressing the role of centromere sites in activation of ParB proteins for partition complex assembly.PloS one · 2020Article
- Challenges and guidelines toward 4D nucleome data and model standards.Nature genetics · 2018Review
- ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.PLoS computational biology · 2018Article
- Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration.Scientific reports · 2017Article
- Donor Preference Meets Heterochromatin: Moonlighting Activities of a Recombinational Enhancer in Saccharomyces cerevisiae.Genetics · 2016Article
- High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division.BMC cell biology · 2016Article
- Physical Modeling of Dynamic Coupling between Chromosomal Loci.Biophysical journal · 2016Article
- The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.Cell reports · 2015Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Inherently dynamic, chromosomes adopt many different conformations in response to DNA metabolism. Models of chromosome organization in the yeast nucleus obtained from genome-wide chromosome conformation data or biophysical simulations provide important insights into the average behavior but fail to reveal features from dynamic or transient events that are only visible in a fraction of cells at any given moment. We developed a method to determine chromosome conformation from relative positions of three fluorescently tagged DNA in living cells imaged in 3D. Cell type specific chromosome folding properties could be assigned based on positional combinations between three loci on yeast chromosome 3. We determined that the shorter left arm of chromosome 3 is extended in MATα cells, but can be crumpled in MATa cells. Furthermore, we implemented a new mathematical model that provides for the first time an estimate of the relative physical constraint of three linked loci related to cellular identity. Variations in this estimate allowed us to predict functional consequences from chromatin structural alterations in asf1 and recombination enhancer deletion mutant cells. The computational method is applicable to identify and characterize dynamic chromosome conformations in any cell type.
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