Figure 3.

Transcriptional responses to butyrate in human and mouse ES cells. Colored dots depict genes that are significantly upregulated (red) or downregulated (green) in response to butyrate in the hESC lines H1 (panels A–D) and BG02 (panel E) and the mESC line R1 (panel F). Panel A - Scatter plot depicting the transcriptional response of H1 cells cultured for 6 passages in butyrate versus H1 cells maintained in CM (see text for details). Panel B - reversion toward the original pattern of expression after returning butyrate treated H1 cells back to CM for 3 passages (“Reconditioned Medium”). Panel C – Scatter plot depicting the transcriptional response to butyrate in BG02 cells (black dots), with red and green dots identifying those genes that were butyrate-regulated in H1 cells, to highlight genes that were coordinately regulated in both hESC lines. Panels D–F contain scatter plots (in black) depicting average expression levels in mEpiSCs versus mESC (from Tesar et al., 2007 - identical for all three panels). Panels D and E overlay butyrate responsive homologous genes in H1 and BG02 cells, respectively. Colored dots indicate homologous genes in the hESC lines that were significantly upregulated (red) or downregulated (green) in response to butyrate. Panel F overlays butyrate responsive genes in mESCs. Colored dot overlays indicate genes in mESCs (R1 cells) that were significantly upregulated (red) or downregulated (green) in response to butyrate. Note that butyrate pulls the gene expression profile of hESCs toward mESCs (X axis) and away from mEpiSCs (Y axis), while pushing mESCs toward EpiSCs, thus the relative orientation of red and green dots between panels D and E versus F is reversed. T-tests indicate that these changes are highly significant (Panel D: t=-9.921, panel E: t=-4.88, panel F: t=11.139, all p<0.001, see Supplemental Experimental Procedures).