Abstract
A major question in metazoan development is how a limited set of DNA-binding transcription factors generate the much larger number of cell fates and states in the organism. In vivo , individual transcription factors are joined by varied sets of collaborating or competing proteins across cellular contexts. Brains provide particularly diverse transcriptional milieus across thousands of neuron types, where each cell is a phenotypic readout of intrinsic transcriptional regulation over developmental time. Today's methods allow interrogation of individual cells, transforming the diversity of neurons in the brain from an experimental hindrance to a benefit in interrogation of combinatorial transcription factor action. Here, we use the BTB domain transcription factor Fruitless as a model to determine how a single factor produces cell-type specific regulatory effects, in this case sexual dimorphisms. In Drosophila melanogaster , Fruitless is transcribed in a precise neuronal repertoire (irrespective of sex) but translated into protein only in male cells. By performing joint scRNA/ATACseq on fruitless neurons from both sexes (i.e. with and without Fru protein) we determine the transcriptional mechanisms by which Fruitless produces cell-type specific regulatory effects. We demonstrate that Fruitless's actions are constrained by the chromatin landscape produced by cell lineage. Within lineage-specific landscapes, type-specific transcriptional dimorphisms arise from varying "Fru power" across cell types, which emerges as a combination of Fruitless dose, DNA binding domain isoforms, and the motif repertoire of individual enhancers. Together, these mechanisms allow a single factor to produce multifaceted transcriptional effects that subtly alter individual neuron types and produce sex-specific circuit functions.