A new model for random X chromosome inactivation

Abstract

X chromosome inactivation (XCI) reduces the number of actively transcribed X chromosomes to one per diploid set of autosomes, allowing for dosage equality between the sexes. In eutherians, the inactive X chromosome in XX females is randomly selected. The mechanisms for determining both how many X chromosomes are present and which to inactivate are unknown. To understand these mechanisms, researchers have created X chromosome mutations and transgenes. Here, we introduce a new model of X chromosome inactivation that aims to account for the findings in recent studies, to promote a re-interpretation of existing data and to direct future experiments.

Fig. 1.

Three models of X chromosome inactivation. (A) The blocking factor model. (a) Diploid autosomes work together to create a single blocking factor (blue shape), which can bind to only one X chromosome, preventing it from inactivating. (b) Nicodemi and Prisco used computer simulations to show that if the autosomes produce a swarm of blocking factors (blue dots) that can bind to each other and to the X chromosome, then all of the blocking factor molecules will accumulate on a single X. (B) The two factor model. Autosomes produce blocking factors and X chromosomes produce transacting competence factors (red shape). Blocking factors bind to competence factors with a two to one stoichiometry and then bind to one X chromosome; the remaining competence factor binds to the other X, which inactivates. (C) The sensing and choice model. After cells start to differentiate, the two Xpr regions (yellow) pair and upregulate Xist (red) on both X chromosmes. The Tsix/Xite region (blue) pairs and chooses which chromosome to inactivate, and represses Xist on the other. The X chromosome that represses Xist remains active (green), and the other becomes inactive (red).

Fig. 2.

Stochastic model of X chromosome inactivation. (A) The various components of the stochastic model. (B,a) Prior to cell differentiation, the stochastic model proposes that the autosomes produce a trans-acting factor (purple stars) that induces Tsix expression on both X chromosomes (blue shape). (b) Tsix, when bound by autosomal trans-acting factors, represses Xist transcription (red shape). (c) After differentiation, an X-linked locus (yellow triangle) produces a trans-acting factor (red circles) that attempts to upregulate Xist. (d) Competition between Tsix- and Xist-promoting factors creates a probability for each X chromosome to inactivate. Cells that do not inactivate either X chromosome will continue to produce the factor that promotes Xist upregulation in subsequent cell cycles. Cells that inactivate both X chromosomes will either die, or reactivate one. The percentages shown here reflect the proportions of each XCI configuration observed 7 days after differentiation. Xa, active X chromosome; Xi, inactive X chromosome.

Fig. 3.

Part of the mouse X chromosome inactivation center and sequence replacements and deletions within it. Sequences used to replace portions of the XIC are shown above the diagram, which shows their relative locations. The effects of these replacements are listed in Table 3. Below the diagram, the dotted lines show XIC regions that have been deleted. The effects of these deletions are listed in Table 2.

Fig. 4.

A problem with the two factor model. After XCI, X^TsixΔCpG:X^TsixΔCpG ES cells make three cell populations: one with a single active X (Xa) chromosome and a single inactive X (Xi) chromosome; one with two Xa chromosomes; and one with two Xi chromosomes. (A) Cells with normal XCI result from blocking factor (BF) binding to one X chromosome and the competence factor (C) binding to the other. (B) Cells with two Xa chromosomes and two Xi chromosomes result from BF and C binding to the same X chromosome. However, it is not clear how having both BF and C bound to a single X chromosome results in these two different populations of cells.

Fig. 5.

The feedback model of X chromosome inactivation. (A) A description of the components required for the model. (B,a) The active X chromosomes produce a trans-acting signal, A, that saturates specific sites on the autosomes. (b) Once saturated, the autosomes produce a swarm of inactivation signals, I. These signals bind to each other and to XCI inhibitors on the X chromosomes. Once all of the XCI inhibitors on an X chromosome are sufficiently bound by I, the XCI initiator induces inactivation. (c) With only one active X chromosome producing A, the autosomes are no longer saturated with A and stop producing I.

Fig. 6.

Three different paths to X inactivation. (A) In a normal X chromosome, all of the XCI_repress loci must be turned off by I. (B) In a mutant X chromosome where some of the XCI_repress loci have been removed, only a small amount of I is required to initiate XCI. Because these chromosomes have a lower threshold to overcome before initiating XCI, there is a higher probability that they will inactivate. (C) In a mutant X chromosome where all of the XCI_repress loci have been removed, XCI will initiate without any I.