Location of three X-linked genes with respect to the Xist RNA domain during X inactivation. (A) 3D analysis of Xist RNA FISH (green) combined with DNA FISH to detect the location of X-linked genes (Lamp2, MeCP2, G6pdx, Pgk1, Chic1, Jarid1c, and the Xic locus; red) on female ES cells undergoing differentiation (days 2 and 4) and MEFs. Different profiles of X-linked gene location outside, at the outer edge, at the edge, at the inner edge, or inside the Xist RNA domain are shown following Amira reconstruction. (B) Distribution of the different locations of X-linked genes with respect to the Xist RNA domain before, during, and after X inactivation in differentiated ES cells at days 2 and 4, and in MEFs (n > 30). Genes showing a statistical difference in position distributions are indicated with red asterisks.