Figure 2

Insights into regulatory and gene expression kinetics. (A and B) Observable regulatory network dynamics at 24- and 6-hourly measures with Otx2 and Pou5f1 target containing profiles annotated and in bold, See Supplementary Fig. S2 for full figure. Transcriptomes at 24- (top) and 6-hourly (bottom) were subjected to DREM analysis of mouse TF/target gene interactions. Lines represent the median fold change (relative to time 0) of grouped TF target genes- representing activity of the TF itself, line colors are assigned by branch and are not comparable between panels. A p-value cutoff of 0.001 was applied to calculating divergent TF activity (splits). (C) Expression of the key transcription factors Pou5F1 (Oct4) and Otx2. Red and blue boxes correspond to the time points highlighted in part A. (D) Distribution of the number of genes and the time delay required to meet a maximum correlation (>0.8) between gene targets of Pou5f1 and Pou5f1 itself compared to 95% quantiles of 500 random gene selections. (E) Two k-means clusters of short-lived RNA (slRNA) genes displaying differential expression without changes at 24-hourly time points (adj. p < 0.0001).