Developmental Decision Making
The embryos of species with very large eggs face a very large challenge. They need to immediately divide their cytoplasm into a more manageable volume. In order to do this, embryos undertake several rapid rounds of cleavage divisions before beginning to grow and differentiate. Interestingly, in many species these extremely rapid divisions are almost entirely driven by maternally loaded proteins and RNAs as the embryo is globally transcriptionally repressed until the cell cycles lengthen. Similarly, the early cleavage cycles lack cell cycle checkpoints and the cells remain non-motile. The transition from the rapid cleavage phase, to the beginning of differentiation is known as the mid-blastula transition, or MBT. In the fruit fly Drosophila, this transition is accompanied by cellularization since the early cleavage divisions are syncytial.
Coordination between the number of cell divisions and the events of the MBT is critical for proper development. We are interested in understanding the general biological principals that underly the sensing of cell size, regulation of developmental progression, and control of transcription during this dynamic time period in development. Our research broadly falls into thee categories outlined below:
1. Cell size and the Cell Cycle
Pioneering work in the frog Xenopus, demonstrated that the MBT is timed by measuring the ratio of DNA to cytoplasm, which increases exponentially with each S-phase as a result of cell division without growth. In this light the timing of the MBT can be seen as a cell size control problem. Our work identified histones as one important factor whose titration onto chromatin can be used to measure the amount of DNA that the embryo has generated, and thus cell size. Ongoing projects in the lab seek to understand how the core histones are measured against the DNA and how the oocyte ensures the correct deposition of histones into the embryo during oogenesis. We are also interested in other mechanisms by which cells may measure their size during the MBT and in other developmental contexts.
The chromatin environment of the early embryo is highly dynamic. Initially the DNA is constantly either in a state of replication or mitotic condensation. The chromatin in these cells is largely undifferentiated (analogous to the state of embryonic stem cells in mammals), with very little transcription, no heterochromatin, and no topologically associated domains (TADs). This all changes in the cycles leading up to the MBT in which transcription initiates, heterochromatin is specified, and TADs form for the first time. Recently, we have found that the replication-coupled H3 is titrated against the increasing number of genomes and replaced by replication-independent H3.3. Moreover we can alter the number of divisions before zygotic genome activation by altering the maternal loading of replication-dependent histones. Ongoing projects in the lab seek to understand how chromatin composition changes during development, differentiation, and aging and to elucidate the functional consequences of these changes.
3. Zygotic Genome Activation
Transcription initiation is not an instantaneous event. Rather, it occurs over a period of several cell cycles and is spatially regulated for many genes. Moreover, different genes become activated at different times and with different kinetics. We are interested in understanding how different genes know when and where to be activated and what genomic features underly different activation behaviors. Ongoing projects in the lab seek to understand how different perturbations affect the initial activation of the whole genome using sequencing technologies and individual genes at very high temporal resolution through imaging.