Self-Assembly and DNA Binding of the Blocking Factor in X Chromosome Inactivation

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Abstract
X chromosome inactivation (XCI) is the phenomenon occurring in female mammals whereby dosage compensation of X-linked genes is obtained by transcriptional silencing of one of their two X chromosomes, randomly chosen during early embryo development. The earliest steps of random X-inactivation, involving counting of the X chromosomes and choice of the active and inactive X, are still not understood. To explain “counting and choice,” the longstanding hypothesis is that a molecular complex, a “blocking factor” (BF), exists. The BF is present in a single copy and can randomly bind to just one X per cell which is protected from inactivation, as the second X is inactivated by default. In such a picture, the missing crucial step is to explain how the molecular complex is self-assembled, why only one is formed, and how it binds only one X. We answer these questions within the framework of a schematic Statistical Physics model, investigated by Monte Carlo computer simulations. We show that a single complex is assembled as a result of a thermodynamic process relying on a phase transition occurring in the system which spontaneously breaks the symmetry between the X's. We discuss, then, the BF interaction with X chromosomes. The thermodynamics of the mechanism that directs the two chromosomes to opposite fates could be, thus, clarified. The insights on the self-assembling and X binding properties of the BF are used to derive a quantitative scenario of biological implications describing current experimental evidences on “counting and choice.” In mammals, female cells silence one of their two X chromosomes to equalize X products with respect to males. The mechanism whereby cells count their X's and randomly choose the one to inactivate is, though, one of the most mysterious aspects of X chromosome inactivation (XCI). The longstanding hypothesis is that a molecular complex, a “blocking factor” (BF), exists: the BF is present in a single copy and can randomly bind to just one X per cell which is protected from inactivation, as the second X is inactivated by default. We add here a missing crucial step to such a picture: we explain, on a thermodynamic ground, why only one complex is formed in the cell, how it is self-assembled and how it selectively binds DNA recognition sequences. Such a process, leading to the spontaneous breaking of the binding symmetry of two equivalent targets, results from collective behavior at a molecular level whose general features are independent from the ultimate biochemical molecular details. It embodies, thus, a new general stochastic regulatory mechanism which could be relevant to a broad class of cell processes involving a random switch.