Mechanics and Dynamics of X-Chromosome Pairing at X Inactivation

At the onset of X-chromosome inactivation, the vital process whereby female mammalian cells equalize X products with respect to males, the X chromosomes are colocalized along their Xic (X-inactivation center) regions. The mechanism inducing recognition and pairing of the X's remains, though, elusive. Starting from recent discoveries on the molecular factors and on the DNA sequences (the so-called “pairing sites”) involved, we dissect the mechanical basis of Xic colocalization by using a statistical physics model. We show that soluble DNA-specific binding molecules, such as those experimentally identified, can be indeed sufficient to induce the spontaneous colocalization of the homologous chromosomes but only when their concentration, or chemical affinity, rises above a threshold value as a consequence of a thermodynamic phase transition. We derive the likelihood of pairing and its probability distribution. Chromosome dynamics has two stages: an initial independent Brownian diffusion followed, after a characteristic time scale, by recognition and pairing. Finally, we investigate the effects of DNA deletion/insertions in the region of pairing sites and compare model predictions to available experimental data.
Author Summary Some important cellular processes involve homologous chromosome recognition and pairing. A prominent example is the colocalization of X chromosomes occurring at the onset of X chromosome inactivation, the vital process whereby female mammalian cells silence one of their two X chromosomes to equalize the dosage of X products with respect to males (having just one X). The crucial question on how the Xs recognize each other and come together is, however, still open. Starting from important recent experimental discoveries, we propose a quantitative model, from statistical mechanics, which elucidates the mechanical basis of such phenomena. We demonstrate that a set of soluble molecules binding specific DNA sequences are sufficient to induce recognition and colocalization. This is possible, however, only when their binding energy/concentration exceeds a threshold value, and this suggests how the cell could regulate colocalization. The pairing mechanism that we propose is grounded in general thermodynamic principles, so it could apply to other DNA pairing processes. While we also explore the kinetics of X colocalization, we compare our results to available experimental data and produce testable predictions.