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. Author manuscript; available in PMC: 2011 Sep 3.
Published in final edited form as: Cell Stem Cell. 2010 Aug 19;7(3):329–342. doi: 10.1016/j.stem.2010.06.024

Figure 3. The XIST RNA- coated chromosome is inactive in female hiPSCs.

Figure 3

(A) NANOG immunostaining (red) combined with RNA FISH for ATRX nascent transcripts (green) in the Dapi-stained STEMCCA-hiPSC line 19. A pinpoint of ATRX marks the site of nascent transcription and occurs from only one X chromosome.

(B) The graph depicts the quantification of NANOG-positive cells with monoallelic, biallelic, or no ATRX expression for various STEMCCA-hiPSC lines at the indicated passage. Fibroblast origin is given as in Fig 2C.

(C) As in (A) for MIP-hiPSC line 1.

(D) As in (B) for various MIP-hiPSC lines.

(E) FISH for XIST RNA (red) and ATRX transcripts (green) in STEMCCA-hiPSC line G at passage 8 with Dapi staining the nucleus. The XIST RNA cloud signal does not overlap with the single ATRX signal.

(F) As in (E) for MIP-hiPSC line 5 at passage 3 with XIST RNA in green and ATRX transcripts in red.

(G) Immunostaining for H3K18ac (green) and FISH for XIST RNA (red) in STEMCCA-hiPSC line E at passage 8. Exclusion of the histone mark can be seen at the site of XIST RNA accumulation and was found in 96% of cells in the population indicating silencing of the entire XIST RNA-coated X in hiPSCs. Scale bar = 5um.

(H) As in (G), except that Xi exclusion of H3K4 me3 was analyzed. Exclusion of this histone mark was found in 92% of hiPSCs. See Fig S3 for additional data.