Biological Chemistry and Molecular Pharmacology
The bithorax complex in the fruit fly is a cluster of “homeotic” genes which confer distinct identities on the different segments of the fly. The genes are strikingly aligned on the DNA in the order of the segments they affect. The genes, and their alignment, are conserved from nematodes to humans. Many of the interactions of bithorax mutations are difficult to explain with the known forms of transcriptional regulation. The paradoxes hopefully reflect novel molecular mechanisms.
The segments of a fly are “numbered” by genes which appear in stripes in the early embryo; these stripes turn on the homeotic genes in the proper positions. After a few hours, the striped gene products disappear, but cells must remember their segmental address. Memory is conferred by a gene called Polycomb . In Polycomb mutants, the homeotic genes turn on everywhere when the stripes fade. Polycomb keeps the homeotic genes appropriately repressed, most likely by altering the chromosome structure.
There are over 20 genes known which work together with Polycomb; some of these encode products which assemble with Polycomb protein in a high molecular weight complex. We have mapped sites at which Polycomb acts, and we have used gene conversion to delete these sites; the resulting flies have novel segmental transformations. We have also shown that Polycomb repression changes chromosome structure; repressed regions are less accessible in-vivo to various DNA binding proteins.
The bithorax complex spans over 300 kb, but it encodes only 3 transcription factors. Most of the rest of the DNA is transcribed into a variety of non-coding RNAs. One very large non-coding transcript (>130 kb) includes a microRNA precursor. We have used gene conversion to delete this miRNA. Mutant males can't mate, and females don't lay their eggs. Mutant animals show a derepression of one homeotic gene in the most posterior part of the nervous system, which may affect reproductive behaviors. All the other non-coding RNAs have no known function, although several labs have suggested they may establish zones of activation and repression in the early embryo. We are mapping the transcription units for these RNAs, and defining the body segments in which they are expressed. We are mutating the RNAs and looking for phenotypes, and we will isolate these RNAs in biochemical complexes, to see if their binding partners suggest a function.
The focus of our lab is the bithorax complex in the fruit fly, Drosophila melanogaster, which is the prototypic target of Polycomb repression.
Fitzgerald, D. P., and W. Bender, Polycomb Group Repression Reduces DNA Accessibility. Mol. Cell. Biol. (2001) 21: 6585-6597.
Bender, W., and D. P.Fitzgerald, Transcription activates repressed domains in the Drosophila bithorax complex. Development (2002) 129: 4923-4930.
Ali, J. Y., and W. Bender. Cross-Regulation among the Polycomb Group Genes in Drosophila melanogaster . Mol. Cell. Biol. (2004) 24: 7737-7747.
Mihaly, J., Barges, S., Sipos, L., Maeda, R., Cléard, F., Hogga, I., Bender, W., Gyurkovics, H., and F. Karch. Dissecting the regulatory landscape of the Abd-B gene of the bithorax complex. Development (2006) 133: 2983-2993.
Sipos, L., Kozma, G., Molnár, E, and W. Bender. In situ Dissection of a Polycomb Response Element in Drosophila melanogaster. Proc. Nat. Acac. Sci. USA (2007) 104: 12,416-12,421.