Cherbas Lab
Research:
Drosophila development is coordinated by a hormone -- ecdysone -- that triggers molting and metamorphosis. Ecdysone is a steroid, but that hardly matters. What does matter is that it works through an apparatus -- the nuclear receptor complex -- that apparently became established in the earliest animal cells. Other hormones that work through nuclear receptors may be more familiar: thyroid hormone, retinoic acids, vitamin D, glucocorticoids, estrogens, androgens, etc.
The nuclear receptors are used as switches to trigger large-scale changes in gene expression patterns.
Insect metamorphosis is a dramatic example of these kinds of changes. In Drosophila at metamorphosis most cells that did interesting things in the maggot (muscles, epidermis, gut, etc.) commit suicide. The adult develops from a few clusters of set-aside cells (the imaginal discs and histoblasts). [As usual, the nervous system is a little more complicated, though similar.] A maggot and the fly it develops into are like identical twins: they share a genome.
It is no surprise that these wholesale morphological changes are accompanied by widespread changes in gene expression: the best estimate is that more than 30% of the known fly genes are activated or repressed during metamorphosis. Changes on this scale must be coordinated -- the death of larval cells before the appearance of their adult substitutes would be catastrophic -- and, like a conductor's baton, releases of ecdysone do the coordinating.
These observations suggest at least several large questions:
- How does ecdysone turn on or turn off a gene?
- How does it manage to regulate different genes in different kinds of cells?
- How are cells' responses integrated into meaningful patterns? i.e. does the hormone regulate modules of genes devoted to particular tasks?
The ecdysone receptor is a Type I nuclear receptor. It is a heterodimer of two proteins (EcR and USP). The dimer binds to target DNA sequences, EcREs (palindromes of 5'-AGGTCA-3"), whether or not ecdysone is present.
In the absence of ecdysone the dimer "seeds" formation of a complex with corepressors. This complex represses expression of nearby genes.
When ecdysone binds to EcR the dimer
changes shape, sheds its corpressors, and seeds formation of a
coactivator complex that activates nearby genes.
Understanding how ecdysone turns a gene on or off means (in part) identifying the corepressors and coactivators and learning how the complexes form and work.
The genome encodes more corepressors and coactivators than can work in any one cell. So one way that different cells have different responses is that they probably contain different complements of corepressors/coactivators. In addition, we know that the binding of nearby transcription factors can enhance (or block) the formation of nuclear receptor complexes. So the complement of these transcription factors also contributes to the differentiation of responses. Finally, chromatin structures differ in different cells as a consequence of differential TF binding (and of transcription itself).
Understanding the cell-to-cell differentiation of the response requires identifying the critical differences in all of these factors.
Until recently most studies of gene regulation in eukaryotes, including ours, have concentrated on one (or a few) "model genes." Newer techniques have afforded us the opportunity to look at global changes in gene expression -- and to wonder how the hundreds of changes we observe are related.
Understanding the logic of the response means identifying patterns of change and relating them to TF complements and to the pattern of regulatory sequences in DNA.