Topology, structures, and energy landscapes of human chromosomes.
Chromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a maximum entropy approach to derive a least-biased effective energy landscape for the chromosome. Simulations of the ensemble of chromosome conformations based on the resulting information theoretic landscape not only accurately reproduce experimental contact probabilities, but also provide a picture of chromosome dynamics and topology. The topology of the simulated chromosomes is probed by computing the distribution of their knot invariants. The simulated chromosome structures are largely free of knots. Topologically associating domains are shown to be crucial for establishing these knotless structures. The simulated chromosome conformations exhibit a tendency to form fibril-like structures like those observed via light microscopy. The topologically associating domains of the interphase chromosome exhibit multistability with varying liquid crystalline ordering that may allow discrete unfolding events and the landscape is locally funneled toward "ideal" chromosome structures that represent hierarchical fibrils of fibrils.
Department of Chemistry, Center for Theoretical Biological Physics, and.
Bin
B
Zhang
Department of Chemistry, Center for Theoretical Biological Physics, and Department of Physics and Astronomy, Rice University, Houston, TX 77005 pwolynes@rice.edu.
Peter G
PG
Wolynes
D002454:Cell Differentiation; D002843:Chromatin / Q000737:chemistry; D002875:Chromosomes / Q000737:chemistry; D002877:Chromosomes, Human / Q000737:chemistry*; D004247:DNA / Q000737:chemistry; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D007399:Interphase / Q000235:genetics; D008958:Models, Molecular; D008968:Molecular Conformation; D011336:Probability; D013816:Thermodynamics
D002843:Chromatin; D004247:DNA
chromosome conformation capture; liquid crystal; maximum entropy; topologically associating domains