Little is known about the way higher-order chromatin structure influences gene expression and chromosome topology in general. Genetic analysis in Drosophila has led to the discovery of two classes of genes, the regulators of homeotic genes and the modifiers of position-effect variegation, which seem to be good candidates for encoding some of the factors regulating chromatin functions. The Trithorax-like gene we described here is required for the normal expression of the homeotic genes and is a modifier of position-effect variegation. We found that Trithorax-like encodes the GAGA factor which is involved in the formation of an accessible chromatin structure at promoter sequences. Our genetic analysis suggests that the chromatin modelling function of the GAGA factor is not restricted to promoter regions.

The bithorax complex specifies the identity of parasegments 5‐14 of Drosophila. Although nine parasegment‐specific functions, abx/bx, bxd/pbx and iab‐2 to iab‐8,9 have been identified, the whole bithorax complex appears to encode only three classes of proteins, Ubx, abd‐A and Abd‐B. Many observations suggest that the parasegment‐specific functions act as positive cis‐regulatory elements of Ubx, abd‐A and Abd‐B. We report the molecular genetics of a new gain‐of‐function mutation, Fab‐7, which transforms parasegment 11 into parasegment 12. Induction of Abd‐B mutations in cis (one of which removes the Abd‐B homeobox) causes reversion of the dominant phenotype, demonstrating that Fab‐7 misregulates Abd‐B. A 4 kb deletion, 30 kb downstream from the Abd‐B transcription unit, is solely responsible for the Fab‐7 phenotype. We consider that the parasegment‐specific functions lie in DNA domains that are sequentially and independently ‘opened’ along the chromosome. Once a domain is opened, the cis‐regulatory sequences within it can carry out their function. We propose that the Fab‐7 deletion removes a boundary separating the iab‐6 and iab‐7 cis‐regulatory regions (the functions specific for parasegments 11 and 12) allowing the open configuration of iab‐6 to invade iab‐7 in parasegment 11. This is strongly supported by our finding that Fab‐7 can be caused to revert by lesions not only in iab‐7 but also in iab‐6.

A very large cis-regulatory region of approximately 300 kb is responsible for the complex patterns of expression of the three homeotic genes of the bithorax complex Ubx, abd-A and Abd-B. This region can be subdivided in nine parasegment-specific regulatory subunits. Recent genetic and molecular analysis has revealed the existence of two novel cis-regulatory elements Mcp and Fab-7. Mcp is located between iab-4 and iab-5, the parasegment-specific regulatory subunits which direct Abd-B in parasegments 9 and 10. Similarly, Fab-7 is located between iab-6 and iab-7, the parasegment 11 and 12-specific regulatory units. Mcp and Fab-7 appear to function as domain boundaries that separate adjacent cis-regulatory units. We report the analysis of two new Mcp mutant deletions (McpH27 and McpB116) that allow us to localize sequences essential for boundary function to a approximately 0.4 kb DNA segment. These essential sequences closely coincide to a approximately 0.3 kb nuclease hypersensitive region in chromatin. We also show that sequences contributing to the Fab-7 boundary appear to be spread over a larger stretch of DNA, but like Mcp have an unusual chromatin structure.

Position-effect variegation is the inactivation in some cells of a gene translocated next to heterochromatin, the region of the chromosome that is permanently condensed. The number of copies of the Drosophila gene Suvar(3)7 is a dose-limiting factor in this phenomenon, and seems from its sequence that it encodes a protein with five widely spaced zinc-fingers. This novel arrangement of zinc-fingers could help in packaging the chromatin fibre into heterochromatin, and also reflect a novel method of controlling the expression from DNA domains.