Figure 6. Linear model predicting the chromatin accessibility mechanisms and TFs contributing to PSC gene expression.

(A) Linear modeling analysis of all pituitary cells (“pan pituitary cell analysis”) infers the chromatin accessibility and TFs involved in stem cell-specific SOX2 expression. Left, top track shows the contribution of each peak to gene expression measured by −log(p value), and bottom tracks display the TF binding sites. Right, the individual contribution of each predicted TF to SOX2 expression is shown as −log(p values). See Figure S7E for SOX2 analysis in stem cells only.

(B) Pan pituitary cell analysis infers the chromatin accessibility and TFs involved in stem cell-specific GATA3 expression.

(C) Top, right: Linear modeling analysis infers GATA3 chromatin accessibility. Bottom: t-SNE showing GATA3 gene expression (left panels) and chromatin accessibility (middle and right panels) in all cells (top) versus PSCs (bottom). The top left panel indicates the identification of all cell type clusters.

(D) Linear modeling analysis of stem cells only infers the chromatin accessibility and TFs involved in the differential expression of GATA3 expression within the stem cell population. No TF is predicted to contribute to GATA3 expression in stem cells.

(E) Pan pituitary cell analysis infers the chromatin accessibility and TFs involved in stem cell-specific POMC expression. Boxed is MNX,1 the second highest identified TF that is predicted to contribute to POMC expression. See Figure S7 for POMC analysis in stem cells only.

(F) RNAscope mRNA in situ hybridization showing the colocalization of Mnx1 (red) and Tbx19 (blue) transcripts in wild-type CD-1 postnatal day 3 (P3) and adult (P56) female mouse pituitaries. Blue arrows highlight specific cells with colocalization. Scale bar, 25 μm. Shown are representative stainings from three to five biological replicates for each age.