Figure 7.

Figure 7.

Genes with opposing temporal expression dynamics are marked by differential promoter motif utilization and TSS distribution. Published CAGE data from (30,31) was processed to generate a differential expression and promoter behaviour matrix for 4-somite, 14-somite and prim-5, three stages of zebrafish segmentation with differing ratios of rapid to slowly cycling cells, as demonstrated by Fucci imaging (A) and fluorophore pixel ratios (B). (A) Relative expression analysis of consensus clusters with a TPM > 5 in at least one time stage was performed. Genes where expression changes in the same direction by >1.5 fold in each sequential time stage were selected for further analysis and divided into gene where expression is lost over time (n = 93) and gained over time (n = 434) (4 somite → 14 somite [11–16 h post fertilization]→ Prim 5 [24hpf]). (B) Bar graph showing ratio of green / red fluorophore pixel density from imaged Fucci embryos at 4 and 14 somite and Prim 5 stages. (C) Heatmap visualizing the log₂ odds ratio of selected promoter motif occurrence for genes with expression lost, or gained over time versus genes with no temporal dynamics (n = 7762) (*P< 0.05, **P< 0.01, ***P< 0.001, Fisher's exact test). (D) Consensus cluster interquantile width (IQW) in genes with expression lost (blue, mean IQW: 27.5), gained (yellow, mean IQW: 23.0) over time, or no temporal expression dynamics (grey, mean IQW: 22.8), visualized as a histogram. IQW was taken from the developmental stage where consensus cluster expression was highest. (E) Gene ontology analysis of genes with expression lost / gained over time. (F) Table showing chi-square intersection analysis between gene sets with temporal dynamics over the segmentation period of zebrafish development and cell cycle dynamics during the 14 somite stage. Data format: expected intersection size (chi-square statistic).