Massive zygotic transcription begins in many organisms during the midblastula transition when the cell cycle of the dividing egg slows down. A few genes are transcribed before this stage but how this differential activation is accomplished is still an open question. We have performed ChIP-seq experiments on tightly staged Drosophila embryos and show that massive recruitment of RNA polymerase II (Pol II) with widespread pausing occurs de novo during the midblastula transition. However, ∼100 genes are strongly occupied by Pol II before this timepoint and most of them do not show Pol II pausing, consistent with a requirement for rapid transcription during the fast nuclear cycles. This global change in Pol II pausing correlates with distinct core promoter elements and associates a TATA-enriched promoter with the rapid early transcription. This suggests that promoters are differentially used during the zygotic genome activation, presumably because they have distinct dynamic properties.
Fertilized eggs—zygotes—develop into embryos via several distinct stages. In many animals, the zygote initially undergoes rapid rounds of genome replication; however, this hectic activity is not controlled by the zygote itself. Instead, the mother deposits RNA molecules in the egg as it forms inside her, and after the egg has been fertilized, these RNA molecules are translated into proteins that guide the development of the early embryo. Only at a stage called midblastula transition does the zygote take over control by transcribing its own RNA molecules.
Fruit flies start to transcribe their own genes en masse after completing thirteen rounds of DNA replication. However, some genes are already transcribed during the rapid cycles of DNA replication earlier in development. How these early genes are transcribed, and how the embryo shifts to more widespread transcription during the midblastula transition, are not well understood. In particular, it is not known if the molecular machinery needed to transcribe the genes is recruited a long time before transcription starts, or if it is recruited ‘just in time’. Here, Chen et al. explore how genes are switched on in the fruit fly zygote.
Genes are transcribed by a protein complex called RNA polymerase, which binds to DNA sequences, called promoters, within the genes. Chen et al. used a technique called ChIP-Seq to determine how much RNA polymerase was bound to the DNA before, during and after the midblastula transition. Before the transition—from about eight rounds of DNA replication onward—RNA polymerase was bound to only about 100 genes, and was active in most of these cases. In contrast, after the transition, RNA polymerase had been recruited to the promoters of around 4000 genes (fruit flies have a total of about 14,000 genes). However, it was often found in a paused, rather than active, form, at these genes, which is thought to help ensure that their transcription can occur on a precise schedule.
Chen et al. then used computer analyses to test the theory that differences in the DNA sequences of the gene promoters might determine which genes the RNA polymerase bound to, and whether or not the polymerase underwent pausing or became active immediately. Strikingly, there were clear differences in the sequence motifs that recruited RNA polymerase to the promoters of genes that were transcribed immediately and those that showed pausing of the polymerase. Moreover, genes that were transcribed before the midblastula transition were shorter, on average, than those transcribed after. This suggests that transcription during the rapid genome replication cycles has to occur quickly and therefore lacks pausing. Together, these findings present a biological rationale for differences in how genes are first transcribed during fruit fly development.