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Mechanisms of Transcriptional Precision in the Drosophila Embryo


Contemplating how a single cell can turn into the trillions of specialized cells that make a human being staggers the imagination. We still do not fully understand how the information in a genome is interpreted by a cell to orchestrate this incredible process. One thing that we do know is that much of the complexity we see in the natural world comes down to how essentially the same set of proteins are differentially deployed. One of the key places where this is controlled is at the level of transcription which is the first step in protein production. In this thesis we attempt to shed light on this process by looking at how transcription is regulated in the early Drosophila embryo with a focus on mechanisms of transcriptional precision. We developed imaging and segmentation techniques that allowed for the quantitative visualization of the transcriptional state of thousands of nuclei in the embryo. Using this approach we discovered the phenomenon of repression lag, whereby genes containing large introns are not only slow to be switched on (intron delay), but are also slow to be repressed. Many sequence-specific repressors have been implicated in early development, but the mechanisms by which they silence gene expression have remained elusive. We found that elongating Pol II complexes complete transcription after the onset of repression. As a result, moderately sized genes are fully silenced only after tens of minutes of repression. We propose that this "repression lag" imposes a severe constraint on the regulatory dynamics of embryonic patterning.

Having laid the foundations for using quantitative imaging in the early Drosophila embryo we next sought to understand the mechanisms underlying developmental timing, the temporal control of gene expression. Previous studies have provided considerable information about the spatial regulation of gene expression, but there is very little information regarding the temporal coordination of expression. Paused RNA Polymerase (pausd Pol II) is a pervasive feature of Drosophila embryos and mammalian stem cells, but its role in development is uncertain. We demonstrate that there is a spectrum of paused Pol II, which determines the "time to synchrony" the time required to achieve coordinate gene expression across the different cells of a tissue. To determine whether synchronous patterns of gene activation are significant in development, we manipulated the timing of snail expression, which controls the coordinated invagination of 1000 mesoderm cells during gastrulation. Replacement of the strongly paused snail promoter with moderately paused or nonpaused promoters resulted in stochastic activation of snail expression and the progressive loss of mesoderm invagination. Computational modeling of the dorsal-ventral patterning network recapitulated these variable and bistable gastrulation profiles, and emphasized the importance of timing of gene activation in development. We concluded that paused Pol II and transcriptional synchrony are essential for coordinating cell behavior during morphogenesis.

These studies and others have helped launch a new approach to the well-established problem of differential gene expression in animal development. The quantitative imaging methods developed here have permitted the assessment of temporal dynamics of gene expression and the underlying mechanisms for coordinating gene expression across the different cells of a tissue. The next frontier will be to apply these methods to live embryos, thereby permitting an even deeper analysis of gene dynamics in development.

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