FOXO/DAF-16 modulates the transcription factor ROR/NHR-23 and inhibits the let-7 microRNA to maintain multipotency during dauer

Animals rapidly reprogram gene expression to adapt development to environmental stress. How gene regulatory programs that drive continuous development are repressed during stress-induced developmental arrest remains poorly understood. In Caenorhabditis elegans, starvation and overcrowding trigger entry into the stress-resistant, quiescent dauer stage. Here, we identify interactions among the conserved transcription factors DAF-16/FOXO and NHR-23/ROR, and the let-7 family of microRNAs as key regulators of the switch from continuous development to dauer. We show that loss of daf-16 during dauer causes elevated let-7 family microRNAs and premature expression of the adult collagen reporter col-19p::GFP. Reducing let-7 family activity suppresses this phenotype, whereas dauer-specific let-7 expression is sufficient to induce col-19p::GFP expression. Mechanistically, DAF-16 inhibits let-7 transcription in part by repressing nhr-23, which encodes a transcriptional activator of the let-7 family and molting-cycle genes. ChIP-seq analysis reveals DAF-16 binding upstream of nhr-23, and daf-16; daf-7 mutant dauers exhibit increased nhr-23 mRNA and NHR-23 protein, supporting a model in which DAF-16 directly represses nhr-23. Integrated ChIP-seq and transcriptomic analyses identify 1,183 genes activated and 681 genes repressed by DAF-16 during dauer. Repressed targets are enriched for pro-growth genes involved in mitotic DNA replication and translational elongation. DAF-16 targets include 59 transcription factors that may mediate broader transcriptional reprogramming during dauer to maintain multipotency and establish quiescence. Together, these findings reveal that DAF-16/FOXO establishes stress-induced developmental arrest by coupling activation of protective pathways with repression of conserved developmental timing, growth, and differentiation programs. Significance statementAnimals often pause development during environmental stress and then resume normal development when conditions improve. How developmental programs are temporarily halted without disrupting later cell fates remains poorly understood. We show that, during stress-induced dauer arrest in C. elegans, the conserved FOXO transcription factor DAF-16 represses the differentiation-promoting let-7 microRNA pathway. DAF-16 inhibits the ROR homolog NHR-23, which normally activates let-7 and molting-cycle genes. Genome-wide analyses further show that DAF-16 both activates stress-response genes and represses growth and developmental genes. These findings reveal how a conserved stress-responsive factor coordinates survival, developmental arrest, and maintenance of cellular multipotency.