Fig. 3.

Analysis of transcriptional dynamics Hoxa1 and Nanog using single-molecule RNA FISH. (A) Expression of Hoxa1 and Nanog in differentiating ES cells. Hoxa1 is shown in red channel andNanog is seen in green channel. Nuclei are stained with DAPI. (B) The one-to-two bright foci per cell represent nascent nuclear transcripts, whereas transcripts outside nuclei are steady-state stable mRNAs. (C) Quantification of nascent transcripts of Nanog and Hoxa1. Hoxa1 shows rapid up-regulation, whereas Nanog undergoes a progressive decrease after 2 h of RA treatment. (Scale bars: A, 10 μm; B, 5 μm.)