Synchronous and Stochastic Patterns of Gene Activation in the Drosophila Embryo

Stalled Development? Most developmental control genes that pattern the Drosophila embryo appear to have stalled RNA polymerase II (Pol II) bound to them prior to their activation. Classical studies on the Drosophila heat shock genes have shown that stalled Pol II renders these genes “poised” for rapid induction by stress. Boettiger and Levine (p. 471) now provide evidence for another potential function of stalled Pol II: Stalled genes exhibit synchronous patterns of gene activation in the early Drosophila embryo so that most or all cells in an embryonic tissue display nascent transcripts at the onset of expression. This synchrony might promote transcriptional precision during development. Synchronous activation of genes with stalled RNA polymerase improves transcriptional coordination. Drosophila embryogenesis is characterized by rapid transitions in gene activity, whereby crudely distributed gradients of regulatory proteins give way to precise on/off patterns of gene expression. To explore the underlying mechanisms, a partially automated, quantitative in situ hybridization method was used to visualize expression profiles of 14 developmental control genes in hundreds of embryos. These studies revealed two distinct patterns of gene activation: synchronous and stochastic. Synchronous genes display essentially uniform expression of nascent transcripts in all cells of an embryonic tissue, whereas stochastic genes display erratic patterns of de novo activation. RNA polymerase II is “pre-loaded” (stalled) in the promoter regions of synchronous genes, but not stochastic genes. Transcriptional synchrony might ensure the orderly deployment of the complex gene regulatory networks that control embryogenesis.