Proliferation and differentiation of intestinal stem cells depends on the zinc finger transcription factor BCL11/Chronophage

The molecular programs that drive proliferation and differentiation of intestinal stem cells (ISCs) are essential for organismal fitness. Notch signalling regulates the binary fate decision of ISCs, favouring enterocyte commitment when Notch activity is high and enteroendocrine cell (EE) fate when activity is low. However, the gene regulatory mechanisms that underlie this process on an organ scale remain poorly understood. Here, we find that the expression of the C2H2-type zinc-finger transcription factor Chronophage (Cph), homologous to mammalian BCL11, increases specifically along the ISC-to-EE lineage when Notch is inactivated. We show that the expression of Cph is regulated by the Achaete-Scute Complex (AS-C) gene, scute, which directly binds to multiple sites within the Cph locus to promote its expression. Our genetic and single-cell RNA sequencing experiments demonstrate that Cph maintains the ISC and EE populations and is necessary to remodel the transcriptome of progenitor cells with low Notch activity. By identifying and functionally validating Cph target genes, we uncover a novel role for sugar free frosting (sff) in directing proliferative and lineage commitment steps of ISCs. Our findings provide mechanistic insight into how Cph maintains intestinal epithelial homeostasis, and together with our evolutionary analysis of Cph/BCL11, suggests that it may represent a general mechanism used by adult somatic stem cells in other tissues to balance proliferation and differentiation. Overall design: To gain insights into the function of Chronophage we performed single-cell RNA sequencing of the Drosophila melanogaster intestine under different conditions: knockout of Notch (NotchKO), knockdown of Notch (NotchRNAi) and knockdown of Notch and Chronophage (NotchRNAiCphRNAi). For both the knockout and the knockdown experiments a control exists. All experiments were preformed in duplicates.