The early Drosophila embryo represents one of the premier systems for visualizing differential gene activity in animal development. During a one-hour interval, from 2 to 3 hours after fertilization, hundreds of genes are activated during the mid-blastula transition. These genes exhibit localized stripes and bands of expression that establish the different segments and tissues of larvae and adults. During this time the embryo is composed of a simple grid of synchronized nuclei located near the surface of the egg. It is therefore possible to visualize basic transcriptional processes, such as the regulation of enhancer-promoter interactions. We will use this system to investigate the physiological properties of transcriptional processes that are mainly studied in vitro or in cultured cells. Most of our proposed studies focus on mechanisms of transcriptional precision. For example, Snail, a key regulator of epithelial-mesenchyme transitions, is expressed in 800 mesoderm progenitor cells slated for invagination during gastrulation. Snail exhibits remarkably invariant expression in these cells (~180 mRNAs/cell), and the sharp lateral limits of its expression pattern delineate the boundary separating the future mesoderm and ectoderm. These features, homogenous expression and sharp lateral limits, are highly reproducible among the different embryos of a population. We have obtained evidence that this precision depends on paused RNA polymerase (paused Pol II), which appears to foster synchronous transcription in the different cells of a tissue. Preliminary studies suggest that replacing the paused Snail promoter with a nonpaused promoter results in stochastic activation of Snail expression and a curious bistable phenotype. Approximately 20% of the resulting embryos exhibit an essentially normal Snail pattern, including homogenous expression and sharp lateral limits, whereas 80% of sibling embryos lack Snail expression and display the same loss of mesoderm invagination seen in sna- mutants. These results suggest that transcriptional synchrony is important for the coordination of gene activity underlying the invagination of the mesoderm. We will attempt to determine the basis for this gastrulation bistability and explore the mechanisms responsible for transcriptional synchrony. In particular, we will test the idea that paused Pol II displaces inhibitory promoter-positioned nucleosomes (PPNs). We will also investigate the role of the promoter in developmental timing. Moreover, just as paused Pol II might serve to "prime" the core promoter for timely activation of gene expression, we will explore the role of histone modifications and general transcription factors for priming distal enhancers. And finally, we will use quantitative imaging methods to attempt to visualize long-range enhancer-promoter interactions in the Drosophila embryo.

Public Health Relevance

Switching genes on and off underlies many developmental and disease processes. We propose to use the unique advantages of the fruit fly embryo to study the mechanisms responsible for the reliable activation of gene expression in large populations of cells and tissues. Many of the proposed experiments focus on emerging evidence that genes are primed or prepared for activation in order to respond quickly and synchronously to developmental cues.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM046638-24
Application #
8578650
Study Section
Molecular Genetics A Study Section (MGA)
Program Officer
Hoodbhoy, Tanya
Project Start
1991-07-01
Project End
2017-06-30
Budget Start
2013-08-01
Budget End
2014-06-30
Support Year
24
Fiscal Year
2013
Total Cost
$361,245
Indirect Cost
$118,210
Name
University of California Berkeley
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
124726725
City
Berkeley
State
CA
Country
United States
Zip Code
94704
Levine, Michael (2014) The contraction of time and space in remote chromosomal interactions. Cell 158:243-4
Levine, Michael; Cattoglio, Claudia; Tjian, Robert (2014) Looping back to leap forward: transcription enters a new era. Cell 157:13-25
Boettiger, Alistair Nicol; Levine, Michael (2013) Rapid transcription fosters coordinate snail expression in the Drosophila embryo. Cell Rep 3:8-15
Lagha, Mounia; Bothma, Jacques P; Esposito, Emilia et al. (2013) Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo. Cell 153:976-87
Bothma, Jacques P; Magliocco, Joe; Levine, Michael (2011) The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo. Curr Biol 21:1571-7
Papatsenko, Dmitri; Levine, Michael (2011) The Drosophila gap gene network is composed of two parallel toggle switches. PLoS One 6:e21145
Papatsenko, Dmitri; Levine, Michael; Goltsev, Yury (2011) Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles. PLoS Biol 9:e1000584
Perry, Michael W; Boettiger, Alistair N; Bothma, Jacques P et al. (2010) Shadow enhancers foster robustness of Drosophila gastrulation. Curr Biol 20:1562-7
Perry, M W; Cande, J D; Boettiger, A N et al. (2009) Evolution of insect dorsoventral patterning mechanisms. Cold Spring Harb Symp Quant Biol 74:275-9
Papatsenko, Dmitri (2009) Stripe formation in the early fly embryo: principles, models, and networks. Bioessays 31:1172-80

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