|
|
Cherbas Lab |
|
|
Research:
|
Drosophila Transcripts A Collaborative Project funded by the Indiana Metabolomics and Cytomics Initiative. Gene Expression Profiles and Cellular Identity in Drosophila melanogaster Collaborating Faculty: Justen Andrews, Peter Cherbas, Thom Kaufman, Justin Kumar A cell is defined – to a first approximation – by the genes that it expresses. Similarly, the succession of cell states in development can be described – to a first approximation – as a series of linked gene expression patterns. The patterns are linked because the genes expressed at time t reflect the expression of regulatory (transcription factor) genes at time t – Δ. Much of modern developmental biology has been devoted to documenting examples of just these kinds of relationships, concentrating on the small ensembles of important genes accessible to traditional analytical tools. We believe that major goals for the next few years will be (a) to identify the global gene expression pattern that characterizes each developmental intermediate and each mature cell type; (b) to identify the subset of those genes that are transcription factors; (c) to associate those transcription factors with their target genes -- by analysis of regulatory elements in genomic DNA; and (d) to observe the resulting stepwise changes in gene expression. This is, of course, an oversimplified picture. Step (c) in particular presents enormous challenges, because we are far from being able to pinpoint effective, cell-specific regulatory elements by “reading” DNA sequences. Still major efforts to meet this goal are underway, including an NIH-sponsored program (ENCODE). A more sophisticated (and longer-winded) summary would describe how our ability to read DNA will be refined by successive approximation -- observing the differences between predicted results (step c) and observed results (step d). In furtherance of this research program, the we plan an effort to catalog gene expression on a tissue-by-tissue basis throughout the post-embryonic development of Drosophila. Drosophila is one of the preeminent model organisms for biomedical research: Powerful genetic, genomic, and developmental tools and resources make it experimentally accessible and the extraordinary conservation of disease genes and signaling pathways between humans and insects makes the effort cost effective for both medical and agricultural research. To be plausible our large-scale consortium proposal will need to supply persuasive answers to a number of questions: (a) How fine-grained (spatially and temporally) must such an analysis be? (b) How can biological foresight (choice of genetic background and temporal and spatial markers help meet these standards? (c) Can material be microdissected (or otherwise isolated) with sufficient precision? (d) Can RNA samples be amplified with sufficient accuracy? (e) Will our experimental design and the quality of the microarrays support conclusions of sufficient quality? (f) Do we have robust plans for statistical analysis of individual experiments and for the statistical accumulation of data from multiple experiments? (g) Have we developed robust and useful tools for storing the results and making them accessible? Many of the goals of this project have been subsumed in a pending grant proposal to the NIH (joint with Berkeley, Washington University St. Louis, University Connecticut, Harvard, and the Affymetrix Corp.
|
|