One of the most interesting features of all immune cells is their rapid, precise and highly organised response to infection or other assaults on the body. They are therefore set up to dramatically change their gene and protein expression profile rapidly following a signal, which come in many and varied forms - from infections and allergens to signals from within the body that lead to an aberrant autoimmune response.

During this process a plethora of genes that are normally silent are switched on and an equal number that are normally active are turned off. The types of genes that respond are either generic - no matter what the signal is these genes will change their expression - or they are exquisitely specific to the assault; for example, bacterial pathogens will induce one suite of genes and viral attack will produce a different array. There is a very controlled and organised response at the gene level.

Professor Frances Shannon's group at the John Curtin School of Medical Research at ANU is trying to unravel the molecular mechanisms by which these genes in the nucleus see the immune signal and respond appropriately. They are addressing this aim at two levels: by looking at single genes and on a genome-wide scale.

The work has led to important findings in defining the role of architectural proteins and the packaging of DNA in the cell nucleus in controlling immune-related gene expression. Shannon sees this as some of her group's most important findings.

The single genes Shannon's team study encode cytokines, which are secreted by cells to mediate the immune response. One reason to look at this family of genes is that they usually undergo very large changes in transcription upon stimulation.

Shannon originally became interested in inducible gene expression as a postdoc with Dr Julian Wells at Adelaide University, investigating the role of histones in chromatin structure and gene expression. That was long before this area became so popular - chromatin was regarded as somewhat of a "backwater" in the gene transcription world back then, Shannon says.

Shannon then went on to establish her own lab using cells of the immune system and the recently cloned cytokine genes as good models of inducible gene expression. The two cytokine genes that she studies in particular are interleukin-2 (IL-2) and granulocyte-macrophage colony-stimulating factor (GM-CSF). IL-2 is a T-cell cytokine important in T cell activation and immune regulation. GM-CSF is also produced by T cells but is more involved in regulating the myeloid response.

For some time, Shannon has researched the transcription factors controlling these genes, and mapping their critical promoter/enhancer regions. "We then became interested in how the packaging of these genes into chromatin changes in response to an immune stimulus," she says. "Also, we asked how the interplay between transcription factors and this packaging works to control gene expression."

Gene promoters

One of the interesting and landmark findings underlying the work Shannon will present at Lorne was published by the group in 2005. Gene promoters are normally covered by nucleosomes, the fundamental packaging unit of chromatin that comprises DNA wrapped around a core of histone proteins.

It was thought until a few years ago that nucleosomes were very stable and that they were rarely removed from the DNA. If so, how then did the transcription machinery assemble on the genes? Shannon says the previous idea of chromatin remodelling at gene promoter was rather vague: "somehow, in a very hand-waving manner, the nucleosomes became more loosely associated with the DNA to allow the transcription complex to assemble," she says.

"Sliding was also invoked as a model and probably applies to some genes. What we found in T cells during immune activation was that the nucleosomes actually fall off the IL-2 gene control region (the promoter) completely, but not off the rest of the gene, and that it happens in a very precise and organised manner.

"Then, the transcriptional machinery assembles in its place - the transcriptional factors, the polymerase enzymes, and all of the other goodies needed to generate a transcriptional complex ... and all of this happens only at the promoter of the gene."

This process is highly dynamic - if the signal is removed, the nucleosome assembles again very rapidly, and it is possible to shuttle between the two states by removing and replacing the signal. Further work also showed that the nucleosome loss was exquisitely dependent on the integrity of the transcriptional complex and if just one transcriptional factor is deleted or the relevant signalling pathway blocked by inhibitors, then the disassembly of the nucleosomes at the promoter will not occur.

"We were very surprised with this result that just removing one transcription factor had such a dramatic effect," she says.

These findings went against prevailing dogma, but actually served to explain some of the group's past results on histone acetylation. At the same time, researchers working on inducible genes in yeast published exactly the same findings, showing that the mechanism Shannon's group observed in immune cells was applicable to other organisms.

"These findings had major implications for how the field views chromatin remodelling events at gene control regions. It also reminded us: never dismiss a crazy result!"