Body tissues comprise many different cells that originate from specific precursors. Understanding this complex organization of cells requires methods to label small cellular populations from their birth and throughout differentiation as well as to precisely manipulate them. The most effective and versatile method among these is the use of engineered transgenes whose expression can be turned on or off in a controlled manner.

Binary expression systems are one of such strategies that allow fine control of transgene expression in model organisms. In Drosophila melanogaster, the archetypal binary expression system is GAL4-UAS, in which the yeast transcription factor gene GAL4 is under the control of a promoter of interest. GAL4 in turn activates a second exogenously inserted transgene bearing an upstream activating sequence (UAS). This binary system can be additionally regulated by GAL80, a GAL4 repressor.

Liqun Luo's group at Stanford University was in search of additional repressible binary expression systems that could be used as alternatives or in combination with the GAL4 system. They found a good candidate in the bread mold Neurospora crassa and named it the Q system. The Q system consists of a transcriptional activator, QF, which binds to a specific sequence, Q-UAS, as well as its repressor, QS. In flies, QS activity can be blocked by quinic acid added to the fly's food, providing another level of control over transgene expression. Whereas other binary expression systems have been modified to achieve similar levels of control, “this one has all the bells and whistles built into it,” explains Luo.

Scheme for coupled MARCM, one of the applications of the Q system. FLP recombinase−mediated mitotic recombination followed by specific chromosome segregation produces two distinct daughter cells lacking QS or GAL80 and thus capable of expressing different transgenes. Credit: Kim Caesar

One common application of the GAL4 system is to create mosaic animals via mosaic analysis with a repressible cell marker (MARCM). In MARCM, cell division is essentially coupled with the loss of a transcriptional repressor in one of the two daughter cells, thus allowing marker expression solely in this cell and all of its progeny. MARCM has been widely used for lineage analysis, neural circuit tracing and high-resolution mosaic analysis of gene function. Luo's group, the developers of MARCM, now shows that Q system–based MARCM can be used with GAL4-MARCM to independently mark and manipulate two populations of cells and study their cell-cell interactions.

Using this 'coupled MARCM' approach, they traced lineages and studied cell division patterns of neuroblasts in the fly olfactory system and of cellular populations of the wing imaginal disc. They show that combining these two binary systems into logic gates creates a whole battery of new expression patterns that can help gain genetic access to specific cells.

Without a doubt, one of the major powers of the GAL4 system is its ability to manipulate many cell types through thousands of GAL4 lines generated by the fly community over the years. Similarly, the broader community should now be encouraged to generate large numbers of QF lines with different expression patterns. A current limitation of the Q system is the inability to generate ubiquitously expressing QF transgenic flies, a hurdle that Luo hopes will soon be overcome.

Albeit with some differences, the Q system also works in mammalian cells. Future work is needed to make this tool conducive for mouse transgenesis, and it will be equally interesting to know if it can be applied to worms or zebrafish. Luo is optimistic that researchers will not be discouraged by the high number of transgenes required for some of the Q system applications—eight for coupled MARCM. “If it can do things uniquely, people will overcome their high energy barrier and delve into it,” he adds with confidence.