Figure 6.

X Chromosome Status of Female Naive Human ESCs

(A) CpG methylation of X-linked promoter CpG islands (CGIs) (n = 463) in naive and primed human ESCs. Male control lines are indicated in red.

(B) CpG methylation levels of non-CGI promoter regions (n = 357) or randomly chosen 2 kb bins (n = 1,000) along the X chromosome in naive and primed human ESCs. The 2 kb bins do not overlap any CGIs or non-CGI promoters. Male control lines are indicated in red.

(C) Phase and fluorescence images of MECP2^{GFP-OFF/Tom-ON} primed cells in hESM, and after conversion to the naive state in 5i/L/A and 4i/L/A.

(D) Histograms reporting the levels of MECP2-GFP and MECP-tdTomato in MECP2^{GFP-OFF/Tom-ON}-primed cells in hESM, and after conversion to the naive state in 5i/L/A and 4i/L/A. Note that the maximum intensity of MECP2-GFP is significantly weaker than MECP2-tdTomato.

(E) Flow cytometric analysis showing the distribution of MECP2-GFP and MECP-tdTomato in MECP2^{GFP-OFF/Tom-ON}-primed cells in hESM, after conversion to the naive state in 5i/L/A and 4i/L/A, and upon differentiation into neural precursors via a re-primed intermediate step.

(F) Allele-specific gene expression analysis using SNPs located within transcribed regions of X-linked genes in single-color MECP2^{GFP-ON/Tom-OFF}- or MECP2^{GFP-OFF/Tom-ON}-primed cells in hESM (top) and double-color naive cells maintained in 5i/L/A or 4i/L/A for ten passages (bottom). Red asterisks mark genes reported to escape X inactivation (see Supplemental Experimental Procedures).

See also Figures S6 and S7.