Modeling Biological Networks

• IV.6.vi Subproject 6 – Transcription Factor Responses and Regulatory Networks in Drosophila Development
  • IV.6.vi.a Introduction
  • IV.6.vi.b Advantages of the Drosophila Model
  • IV.6.vi.c Datasources
  • IV.6.vi.d Microarray Methodology
  • IV.6.vi.e Specific Aims
  • IV.6.vi.f Research Plan
    • IV.6.vi.f.1 Aim 1
    • IV.6.vi.f.2 Aim 2
    • IV.6.vi.f.3 Aim 3
  • IV.6.vi.g Significance
• [ Other Subprojects ]

< Previous | Page 29 of 35 | Next >

The completed Drosophila genome sequence, ongoing EST projects, and the increasing application of high-throughput genomics techniques by fly workers point to the potential for a comprehensive functional genomics of Drosophila. Global gene expression studies in yeast (Saccharomyces) have already proven exceptionally valuable (as used in Subprojects 1 and 2) because they complement a wealth of pre-existing genetic and regulatory information. The molecular genetics of Drosophila will benefit from the same complementary information and the ability to routinely harvest global gene expression results from wild-type and mutant cells will greatly reinforce Drosophila's utility for explaining development and regulation in multicellular eukaryotes.

The Drosophila research community of >= 1,500 laboratories has an enviable tradition of open and shared resources. The Drosophila Stock Center at Indiana University Bloomington maintains and distributes a large public collection of mutants, including deletion sets, new P-element insertions, and GAL4 drivers. Flybase (operated jointly by Berkeley, Cambridge, Harvard, and Indiana University and housed in the CGB) has been an especially successful and influential model organism database; its work is supplemented by other major databases of molecular, genomic, and scholarly information including those of the Berkeley Drosophila Genome Project and the European Drosophila Genome Project, and Interactive Fly. The Berkeley Drosophila Genome Project has also taken the lead in making available ESTs: a set of 5,000 cDNA clones representing non-redundant ESTs has been distributed (under community leadership) to a set of primary recipients, including Indiana University, for further distribution. Some other important genomics-related tools for Drosophila are available or under development: a set of ca. 5,000 adult testis cDNA clones is archived at the U.K. Human Genome Mapping Project Resource Center. On-going projects in several laboratories are isolating new P-element insertion mutations throughout the genome and new deletions covering all or selected parts of the genome.

Traditionally molecular geneticists have concentrated their efforts on understanding a few genes. What roles do they play in the cell or in development? How are they regulated? Traditionally the particular genes studied have been selected because (a) their absence results in a detectable phenotype, or (b) they have proven accessible in molecular screens. One promising consequence of the genome programs has been to spawn new technologies that foster a global outlook on changing patterns of gene expression and new data analysis techniques like those in Subprojects 1-3.

While we can examine global gene expression patterns in a number of ways, the most prevalent use is DNA microarrays. In microarrays, individual DNAs -- cDNAs or gene sequences -- are deposited as a two-dimensional array of microscopic dots, typically on a glass slide. For a sequenced organism, one slide can contain the complete set of genes. Using such slides as substrates, hybridizing with probes representing individual RNA populations (usually as fluorescently-labeled cDNAs) allows assessment of the steady-state expression of all the cell's genes with considerable specificity and sensitivity. Judicious comparisons between experiments using different probes can determine changing patterns of gene expression. Developing software to facilitate the harvesting and reduction of the large-scale data produced, creating repositories to collect and facilitate public access to the databases of results, and devising efficient and effective algorithms to organize, analyze, and understand the results are all areas which this proposal directly addresses.