The goal of this collaborative project is to identify transcriptional regulatory elements in the Drosophila melanogaster genome that are directly regulated by the Hox family of homeodomain proteins. To accomplish this goal, three experimental steps will be carried out. In the first, state-of-the art gene expression profiling methods will be used to analyze gene expression differences in embryos containing Hox gene mutations. The genotypes that will be used for gene profiling analysis incorporate redundant pain/vise comparisons to increase the probability that bona fide Hox-regulated genes will be identified. The second step will be to use one of two methods -- DamID or chromatin immunoprecipitation (ChIP) - to determine which genes in the Drosophila genome are directly bound by Hox proteins in vivo. Combined with the first step, these experiments will allow the identification of direct Hox target genes on a genome-wide scale. The third step in this analysis will be to use computational approaches to identify cis-regulatory elements that are shared between subsets of the directly regulated Hox target genes. Computationally-identified regulatory elements will be confirmed experimentally, both by in vitro protein-DNA binding experiments and by in vivo reporter gene analysis. Once these methods are worked out, they will be applicable to a wide variety of problems in biology. ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Resource-Related Research Projects (R24)
Project #
5R24GM074105-04
Application #
7391587
Study Section
Special Emphasis Panel (ZRG1-DEV-1 (01))
Program Officer
Carter, Anthony D
Project Start
2005-04-01
Project End
2010-03-31
Budget Start
2008-04-01
Budget End
2010-03-31
Support Year
4
Fiscal Year
2008
Total Cost
$417,031
Indirect Cost
Name
Columbia University (N.Y.)
Department
Biochemistry
Type
Schools of Medicine
DUNS #
621889815
City
New York
State
NY
Country
United States
Zip Code
10032
Ward, Lucas D; Bussemaker, Harmen J (2008) Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics 24:i165-71
Bussemaker, Harmen J; Ward, Lucas D; Boorsma, Andre (2007) Dissecting complex transcriptional responses using pathway-level scores based on prior information. BMC Bioinformatics 8 Suppl 6:S6
Joshi, Rohit; Passner, Jonathan M; Rohs, Remo et al. (2007) Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131:530-43
Sosinsky, Alona; Honig, Barry; Mann, Richard S et al. (2007) Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci U S A 104:6305-10
Bussemaker, Harmen J; Foat, Barrett C; Ward, Lucas D (2007) Predictive modeling of genome-wide mRNA expression: from modules to molecules. Annu Rev Biophys Biomol Struct 36:329-47
Moorman, Celine; Sun, Ling V; Wang, Junbai et al. (2006) Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A 103:12027-32