Over the years, the focus of this grant has been on the regulation of segmentation genes and homeotic genes, including even-skipped (eve) and Abdominal-B (Abd-B). However, the early Drosophila embryo offers a number of outstanding opportunities for "systems" level studies in developmental biology, such as quantitative modeling and whole-genome assays. During the past few years we have attempted to use ChIP-chip and ChIP-seq assays along with quantitative methods to achieve a more global view of gene regulation in the Drosophila embryo. These studies led to a few surprising findings, including the occurrence of stalled or paused Pol II in the promoter regions of many or most developmental control genes, and the identification of "shadow" enhancers--remote copies of an enhancer that were missed by conventional gene fusion assays. During the upcoming funding period we will attempt to determine the significance of these new findings. We will use quantitative in situ hybridization methods to examine the induction of stalled and non-stalled genes in the early embryo to determine whether they display distinctive activities. We will also compare the responses of genes that contain or lack shadow enhancers to genetic perturbation. In particular, are genes with shadow enhancers better buffered to changes in gene dose than comparable genes lacking shadows? Finally, we are keen to apply ChIP-seq and chromosome conformation capture (3C) assays to understand the basis for short-range transcriptional repression. For example, do such repressors block enhancer-promoter interactions by precluding the recruitment of chromosomal coactivators such as p300/ CBP? The research plan is composed of three specific aims: 1) quantitative confocal image analysis of stalled and nonstalled developmental patterning genes;2) the use of 3C (chromosome conformation capture) and ChIP-seq assays to determine whether short- range transcriptional repressors inhibit enhancer-promoter interactions;and 3) determine the role of noncoding RNAs, such as bxd, in the regulation of Ubx and other Hox genes.

Public Health Relevance

Switching genes on and off is at the heart of a variety of developmental and physiological processes. The advent of powerful new technologies, particularly advances in imaging methods and genome sequencing technologies, provides unprecedented opportunities to understand gene regulation on a global scale. We will apply these emerging technologies to a well-defined model system, the early fruit fly (Drosophila) embryo.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM034431-29
Application #
8383486
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Hoodbhoy, Tanya
Project Start
1984-12-01
Project End
2013-11-30
Budget Start
2012-12-01
Budget End
2013-11-30
Support Year
29
Fiscal Year
2013
Total Cost
$266,088
Indirect Cost
$79,795
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
Oktaba, Katarzyna; Zhang, Wei; Lotz, Thea Sabrina et al. (2015) ELAV links paused Pol II to alternative polyadenylation in the Drosophila nervous system. Mol Cell 57:341-8
Bothma, Jacques P; Garcia, Hernan G; Esposito, Emilia et al. (2014) Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. Proc Natl Acad Sci U S A 111:10598-603
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
Chopra, Vivek S; Hendrix, David A; Core, Leighton J et al. (2011) The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo. Mol Cell 42:837-44
Hilgers, Valerie; Perry, Michael W; Hendrix, David et al. (2011) Neural-specific elongation of 3' UTRs during Drosophila development. Proc Natl Acad Sci U S A 108:15864-9
Levine, Michael (2011) Paused RNA polymerase II as a developmental checkpoint. Cell 145:502-11
Perry, Michael W; Boettiger, Alistair N; Levine, Michael (2011) Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proc Natl Acad Sci U S A 108:13570-5
Papatsenko, Dmitri; Levine, Michael; Goltsev, Yury (2011) Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles. PLoS Biol 9:e1000584
Papatsenko, Ilya; Levine, Mike; Papatsenko, Dmitri (2010) Temporal waves of coherent gene expression during Drosophila embryogenesis. Bioinformatics 26:2731-6

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