Structure and Dynamics of Interphase Chromosomes

By Angelo Rosa, Ralf Everaers. PLoS Comput. Biol., 2008

480 citations recorded by the source corpus.

During interphase chromosomes decondense, but fluorescent in situ hybridization experiments reveal the existence of distinct territories occupied by individual chromosomes inside the nuclei of most eukaryotic cells. We use computer simulations to show that the existence and stability of territories is a kinetic effect that can be explained without invoking an underlying nuclear scaffold or protein-mediated interactions between DNA sequences. In particular, we show that the experimentally observed territory shapes and spatial distances between marked chromosome sites for human, Drosophila, and budding yeast chromosomes can be reproduced by a parameter-free minimal model of decondensing chromosomes. Our results suggest that the observed interphase structure and dynamics are due to generic polymer effects: confined Brownian motion conserving the local topological state of long chain molecules and segregation of mutually unentangled chains due to topological constraints.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/45c3c4839affda7cd8a6ab2c8d893873a2172ab9

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In Molecular Biology

Citations in the corpus

A Polymer Model with Epigenetic Recolouring Reveals a Pathway for the de novo Establishment and 3D organisation of Chromatin Domains (2016, methodology): “With this choice, the recolouring rate is ~ 0.1 s−1 and a simulation runtime of 106 Brownian times corresponds to 2.5-3 hours (see SI for more details on the mapping).”
Formation of Chromosomal Domains by Loop Extrusion (2015, background): “While polymer models have provided insight into multiple levels of chromosome organization (Baù et al., 2011; Lieberman-Aiden et al., 2009; Marko and Siggia, 1997; Naumova et al., 2013; Rosa and Everaers, 2008), relatively few have focused on TADs.”
Polymers with spatial or topological constraints: Theoretical and computational results (2011, background): “the discussions in [284, 85, 286, 287, 288]) chromosomes instead segregate into spatially distinct regions, or territories.”
Chromatin organization by an interplay of loop extrusion and compartmental segregation (2017, background): “A more realistic picture would start from mitotic chromosomes (55), where neither compartments nor TADs are observed (20, 62), which we leave for future investigations.”
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data (2013, background): “Other studies have used simulations of polymer rings to suggest that chromosomal territories can be formed owing to topological constraints that prevent mixing 87 of individual chromosomes 88–90 .”