Fission yeast cells belong to one of two specialized cell types, M or P. Specific environmental conditions trigger sexual differentiation, which leads to an internal program starting with pheromone signaling between M and P cells, followed by mating, meiosis, and sporulation. The initial steps of this process are controlled by Ste11p, a master transcriptional regulator that activates the expression of cell type-specific genes (only expressed in either M or P cells) as well as genes expressed in both M and P cells. Pheromone signaling is activated by Ste11p-dependent transcription and, in turn, enhances some of this transcription in a positive feedback. To obtain a genomewide view of Ste11p target genes, their cell-type specificity, and their dependence on pheromone, we used DNA microarrays along with different genetic and environmental manipulations of fission yeast cells. We identified 78 Ste11p-dependent genes, 12 and 4 of which are only expressed in M and P cells, respectively. These genes show differing grades of pheromone dependencies for Ste11p-activated transcription, ranging from complete independence to complete dependence on pheromone. We systematically deleted all novel cell type-specific genes and characterized their phenotype during sexual differentiation. A comparison with a similar data set from the distantly related budding yeast reveals striking conservation in both number and types of the proteins that define cell types. Given the divergent mechanisms regulating cell type-specific gene expression, our results highlight the plasticity of regulatory circuits, which evolve to allow adaptation to changing environments and lifestyles.expression profiling ͉ master transcriptional regulator ͉ mating type ͉ microarray ͉ Schizosaccharomyces pombe C ellular differentiation is driven to a large extent by specific programs of gene expression. Yeast has distinct cell types that are required for mating, meiosis, and sporulation; this sexual differentiation provides a useful model system to understand the differentiation into specialized cell types in multicellular organisms. How the regulation of gene expression leads to specialized cell types is relatively well understood at a genomewide level in the budding yeast Saccharomyces cerevisiae (1). In this yeast, two haploid cell types, a and ␣, mate with each other at the first opportunity to form diploid a͞␣ cells, which can undergo meiosis and sporulation under appropriate environmental conditions (reviewed in ref.2).Cells of the fission yeast Schizosaccharomyces pombe also come in two specialized cell types, called P (or hϩ) and M (or h-) mating types. Heterothallic strains have a fixed mating type (P or M), whereas homothallic strains (h90) can switch between both types. Unlike budding yeast, however, fission yeast cells will mate only under specific environmental conditions, most notably nitrogen starvation; the resulting diploid cells then immediately undergo meiosis and sporulation (reviewed in refs. 3 and 4). The two distantly related yeasts thus provid...