We describe the genome-wide distributions and temporal dynamics of nucleosomes and post-translational histone modifications throughout the maternal-to-zygotic transition in embryos of Drosophila melanogaster. At mitotic cycle 8, when few zygotic genes are being transcribed, embryonic chromatin is in a relatively simple state: there are few nucleosome free regions, undetectable levels of the histone methylation marks characteristic of mature chromatin, and low levels of histone acetylation at a relatively small number of loci. Histone acetylation increases by cycle 12, but it is not until cycle 14 that nucleosome free regions and domains of histone methylation become widespread. Early histone acetylation is strongly associated with regions that we have previously shown to be bound in early embryos by the maternally deposited transcription factor Zelda, suggesting that Zelda triggers a cascade of events, including the accumulation of specific histone modifications, that plays a role in the subsequent activation of these sequences.
For a fertilized egg to develop into an embryo, many genes must be switched on and off at specific times. A fertilized egg (or zygote) contains genetic material from both parents; and the life of the fruit fly Drosophila melanogaster begins with the nuclei that contain this genetic material repeatedly dividing for the first 2 hr. These nuclear divisions are initially controlled by molecules that the mother deposits into the egg cell. However, as these molecules degrade, the zygote's genome is activated and its own genes take control of embryonic development, in a process referred to as the ‘maternal-to-zygotic transition’.
In the fruit fly zygote, this burst of regulated gene activation is likely to be accompanied by changes to the way that the DNA is packed inside the nuclei. Most DNA in a cell is packaged into a structure called chromatin, which can be marked at specific sites by chemical modifications. For example, chromatin can be acetylated or methylated, which alters its physical structure, helping the underlying genes to be either activated or repressed.
In the fruit fly, the first genes to be switched on (as well as many early developmental genes) have a DNA motif that is recognized, and is bound by, a protein called Zelda. The Zelda protein plays a major role in activating the genome of the early fruit fly embryo, by marking thousands of genes and regulatory regions for activation. This is somewhat similar to the activity of so-called ‘pioneer’ factors that alter chromatin structure to allow particular genes to be switched on or off, and to trigger the formation and development of specific tissues.
Here, Li et al. have investigated whether the Zelda protein—like known pioneer factors—also affects chromatin during the maternal-to-zygotic transition. Different chromatin modifications across the whole fruit fly genome were characterized at specific time-points during the maternal-to-zygotic transition, and the information gathered was then analyzed along with previous data on gene activity.
In the early stages of the maternal-to-zygotic transition, Li et al. found very few of the chromatin features that characterize more mature cells. This indicates that the chromatin is in a so-called ‘naïve’ state. As the transition progresses, Li et al. observed that the chromatin becomes acetylated before it is methylated, and that marks associated with activation appear before those associated with repression. Chromatin acetylation was strongly associated with the early binding of the Zelda protein to its target genes.
Li et al.'s findings show when, and in what order, the different features of mature chromatin appear in Drosophila zygotes. A future challenge will be to identify whether Zelda directly recruits the proteins that cause chromatin acetylation, or whether it blocks the changes to chromatin that repress gene expression.