Transcriptomics informed discovery of developmentally essential transcription factors

Transcription factors (TFs) regulate cell differentiation in multicellular organisms and were mostly identified by forward genetics in model organisms. However, genomes contain several-fold more TFs without known roles. To classify these orphans, we investigated conservation, cell-type specificity and temporal expression of the ∼290 TFs of Dictyostelia amoebas, which aggregate when starved to form migrating slugs and fruiting bodies consisting of spores and three somatic cell types. Here we deleted seven somatically expressed TF genes and found that four knock-outs were developmentally defective. ariA- lost slug migration and robust fruiting body formation. gtaJ- skipped slug migration and directly developed aggregates into robust fruiting bodies. mybAA- formed multi-tipped aggregates, defective slugs and fruiting bodies with few spores. Hierarchical clustering of the expression profiles of mybAA and 45 other multi-tip suppressing genes grouped mybAA with seven autophagy genes, with similar developmental defects as mybAA-, suggesting that mybAA induces autophagy gene expression. mybM- slugs poorly migrated and fruiting bodies had kinked, rough stalks, but normally expressed cell-type marker genes, indicating defective morphogenesis. Overall, transcriptomics informed TF selection proved useful for gene function discovery.