Figure 3.

Dynamic and heterogeneous XCI states in female cells. (A) Fraction of maternal expression for autosomal genes in each condition of cells. Fraction of maternal expression was calculated using maternal allelic reads divided by the sum of maternal and paternal allelic reads. (B) Activity of maternal and paternal X Chromosomes in each condition. The indexes of the activity of Chr Xs in female cells range from 1 (one active X Chromosome) to 2 (two active X Chromosomes). Each type of female cell was divided into three different XCI groups: (1) uninitiated-XCI (1.8< activity of Chr Xs ≤2); (2) ongoing-XCI (1.2< activity of Chr Xs ≤1.8); and (3) completed-XCI (1≤ activity of Chr Xs ≤1.2). (C) The percentage of cells in each XCI group for each condition. Because it is not possible to determine whether the uninitiated-XCI cells are going to inactivate the maternal or paternal X Chromosome, Student's t-test was only applied to the cells of the initiated (ongoing and completed) XCI group. (D–H) Chromosome-wide expression ratio of inactive X Chromosome compared to active X Chromosome. The ratio was calculated using the number of allelic reads of inactive X Chromosome divided by that of active X Chromosome based on a moving window of an average of 10 genes. Red, green, and magenta lines denote the female cells in uninitiated-, ongoing-, and completed-XCI groups, respectively.