Homo- and heterodimerization of bHLH transcription factors balance stemness and bipotential differentiation in the Drosophila adult intestine

Multipotent adult stem cells must balance self-renewal with differentiation into various mature cell types. How this activity is molecularly regulated is poorly understood. By using genetic and molecular analyses in vivo, we show that a small network of basic Helix-Loop-Helix (bHLH) transcription factors controls both stemness and bi-potential differentiation in the Drosophila adult intestine. We find that homodimers of Daughterless (Da, homolog to mammalian E proteins) maintain the self-renewal of intestinal stem cells and antagonise the activity of heterodimers of Da and Scute (Sc, homolog to ASCL and known to promote intestinal secretory differentiation). Using RNAseq, we also find that Da and Sc induce complex transcriptional profiles in undifferentiated cells, which must be balanced by intestinal stem cells to perform their function. We find a novel role for the HLH factor Extramacrochaetae (Emc, homolog to Id proteins), titrating Da and Sc to promote absorptive differentiation. We further show that Emc prevents committed absorptive progenitors from de differentiating, underscoring the plasticity of these cells. Switching physical interaction partners in this way enables the active maintenance of stemness, but primes stem cells for differentiation along two alternative fates. Such regulatory logic could be recapitulated in other bipotent stem cell systems. The samples consist of adult intestinal midguts of the genotype esg-Gal4, tub-gal80[ts], UAS-GFP crossed to either a control strain or to strains with UAS- responder lines for either 'monomeric' daughterless, daughterless-specific RNAi, scute or the forced homodimer construct da:da. After activation of the transgene expression, the GFP+ cells were FAC-sorted, and their total RNA extracted, and sent for library preparation and sequencing to a commercial vendor. This was done in two batches, the first one comprising UAS-daughterless and UAS-daughterless-RNAi, the second with UAS-scute and UAS-da:da. Each batch had their control samples. Three replicates were prepared for each genotype (except for UAS-daughterless, which only had 2). Each replicate required pooling intestines from ~100 flies.