TIE-DYE: a combinatorial marking system to visualize and genetically manipulate clones during development in Drosophila melanogaster.

Two types of information are particularly valuable in understanding the development of a tissue or an organ from a small population of founder cells. First, it is useful to know the composition of the final structure in terms the contribution of individual founder cells. Second, it is important to understand cell-cell interactions. To facilitate the study of both of these aspects of organ development at a tissue-wide level, we have developed a method, TIE-DYE, that allows simultaneous lineage tracing of multiple cell populations as well as the genetic manipulation of a subset of these populations. Seven uniquely marked categories of cells are produced by site-directed recombination of three independent cassettes. We have used the TIE-DYE method to estimate the number of founder cells that give rise to the wing-imaginal disc during normal development and following compensatory growth caused by X-ray irradiation of the founder cells. We also show that four out of the seven types of marked clones can be genetically manipulated by gene overexpression or RNAi knockdown, allowing an assessment of the consequences of these manipulations on the entire wing disc. We demonstrate the utility of this system in studying the consequences of alterations in growth, patterning and cell-cell affinity.