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. Author manuscript; available in PMC: 2021 Jun 4.
Published in final edited form as: Cell Stem Cell. 2020 May 26;26(6):938–950.e6. doi: 10.1016/j.stem.2020.04.020

Figure 4. Sequence features implement signaling-based combinatorial control of gene expression.

Figure 4.

(A) Expected and observed normalized GFP expression of enhancer reporter assays for genes chosen for validation. Expected expression was computed under a linear model where effects are assumed to be linearly additive. Asterisks denote result of paired t-tests on log expression. * is significant at p < 0.2, ** at p < 0.1.

(B, C) Mean expression of GFP reporters in enhancer reporter assay (left) and scRNA-seq (right) showing combinatorial effects. Expression in enhancer reporter assay is normalized to the −/− condition. (B) Assay results for Evx1, which is most highly expressed in RA-/Wnt+, (C) Assay results for Pbx1, which is most highly expressed in RA+/Wnt-

(D) Expected and observed normalized GFP expression of reporters containing sequence features from the enhancer, the native promoter, or both for Cdx1 and Lefty1. Expected expression was computed under a linear model where effects are assumed to be linearly additive. Asterisks denote result of paired t-tests. * is significant at p < 0.2, *** at p < 0.05.

(E, F) Mean expression of GFP reporters in enhancer reporter assay (left) and scRNA-seq (right) showing combinatorial effects. Expression in enhancer reporter assay is normalized to the −/− condition. (B) Assay results for Cdx1, which is most highly expressed in RA-/Wnt+, (C) Assay results for Lefty1, which is most highly expressed in RA+/Tgfβ+/Bmp- See also Figure S4