Biology subjects

Wirick, M. J.

Publications and source records attributed to Wirick, M. J..

3 recordsLinked to original sources

bioRxiv2026

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.

molecular biology↗

bioRxiv2025

daf-16/FOXO promotes the activity of ligand-bound DAF-12/NHR to coordinate dauer recovery and post-dauer seam cell fate

Animal development occurs in the context of varying environmental conditions. Many animal species can withstand adverse conditions by entering a stress-resistant and developmentally arrested diapause stage. If conditions improve, animals can recover and complete development. In Caenorhabditis elegans larvae that encounter adverse environments, dauer diapause can interrupt developmental progression after the second larval molt. During continuous (non-dauer) development, a heterochronic molecular timer comprised primarily of microRNAs and their targets controls the progression of stage-specific cell fates in lateral hypodermal seam cells. In unfavorable conditions, the DAF-16/FOXO transcription factor promotes dauer formation in part through opposing production of the ligand for the DAF-12 nuclear hormone receptor. Ligand-free DAF-12 promotes dauer formation and represses expression of heterochronic microRNAs in the let-7 family. Here, we show that daf-16 acts before dauer formation in anticipation of growth after dauer by promoting both dauer exit and developmental progression. We found that daf-16(0) post-dauer adults showed delayed dauer exit, reiterative heterochronic defects, and reduced expression of let-7-family microRNAs. These phenotypes were suppressed by addition of the DAF-12 ligand, dafachronic acid. Dafachronic acid is synthesized from cholesterol, and dauer larvae sequester cholesterol in the intestinal lumen until dauer exit. We found that a fluorescent cholesterol analog was not retained in daf-16 mutant larvae during dauer recovery. Timed auxin-mediated depletion of DAF-16 indicated that daf-16 is required before dauer formation to prevent reiterative seam cell fates in post-dauer animals. We propose a model whereby daf-16 acts prior to dauer formation to enable dafachronic acid synthesis by retaining cholesterol during dauer recovery. Ligand-bound DAF-12 then promotes dauer exit and expression of let-7-family microRNAs, thereby promoting developmental progression. Thus, daf-16 coordinates dauer entry with anticipation of recovery and post-dauer development.

developmental biology↗

bioRxiv2021

daf-16/FOXO blocks adult cell fate in Caenorhabditis elegans dauer larvae via lin-41/TRIM71

Many tissue-specific stem cells maintain the ability to produce multiple cell types during long periods of non-division, or quiescence. FOXO transcription factors promote quiescence and stem cell maintenance, but the mechanisms by which FOXO proteins promote multipotency during quiescence are still emerging. The single FOXO ortholog in C. elegans, daf-16, promotes entry into a quiescent and stress-resistant larval stage called dauer in response to adverse environmental cues. During dauer, stem and progenitor cells maintain or re-establish multipotency to allow normal development to resume after dauer. We find that during dauer, daf-16/FOXO prevents epidermal stem cells (seam cells) from prematurely adopting differentiated, adult characteristics. In particular, dauer larvae that lack daf-16 misexpress collagens that are normally adult-enriched. Using col-19p::gfp as an adult cell fate marker, we find that all major daf-16 isoforms contribute to opposing col-19p::gfp expression during dauer. By contrast, daf-16(0) larvae that undergo non-dauer development do not misexpress col-19p::gfp. Adult cell fate and the timing of col-19p::gfp expression are regulated by the heterochronic gene network, including lin-41 and lin-29. lin-41 encodes an RNA-binding protein orthologous to LIN41/TRIM71 in mammals, and lin-29 encodes a conserved zinc finger transcription factor. In non-dauer development lin-41 opposes adult cell fate by inhibiting the translation of lin-29, which directly activates col-19 transcription and promotes adult cell fate. We find that during dauer, lin-41 blocks col-19p::gfp expression, but surprisingly, lin-29 is not required in this context. Additionally, daf-16 promotes the expression of lin-41 in dauer larvae. The col-19p::gfp misexpression phenotype observed in dauer larvae with reduced daf-16 requires the downregulation of lin-41, but does not require lin-29. Taken together, this work demonstrates a novel role for daf-16/FOXO as a heterochronic gene that promotes expression of lin-41/TRIM71 to contribute to multipotent cell fate in a quiescent stem cell model.

genetics↗