Biology subjects

Kim, J. K.

Publications and source records attributed to Kim, J. K..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Robust Ultrasensitive Transcriptional Switch in Noisy Cellular Environments

Ultrasensitive transcriptional switches enable sharp transitions between on and off states of transcription and are essential for cells to respond to environmental cues precisely. However, conventional switches, relying on direct repressor-DNA binding, are extremely sensitive to noise. Here, we discovered an alternative design combining three indirect transcriptional repression mechanisms, sequestration, blocking, and displacement, to generate a noise-resilient ultrasensitive switch. Although sequestration alone can generate an ultrasensitive switch, it remains sensitive to noise because the unintended transcriptional state induced by noise can persist for long periods. However, by jointly utilizing blocking and displacement, these noise-induced transitions can be rapidly restored to the original transcriptional state. Because this transcriptional switch is effective in noisy cellular contexts, it goes beyond previous synthetic transcriptional switches utilizing direct repression mechanisms, making it particularly valuable for robust synthetic system design. Our findings also provide insights into the evolution of robust ultrasensitive switches in real cells. Specifically, the concurrent use of seemingly redundant indirect repression mechanisms in diverse biological systems appears to be a strategy to achieve noise-resilience of ultrasensitive switches. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/553401v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@e6f1e6org.highwire.dtl.DTLVardef@1369deorg.highwire.dtl.DTLVardef@8b9f19org.highwire.dtl.DTLVardef@7a2fec_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2023

Central and peripheral clocks synergistically enhance circadian robustness, flexibility and performance of cardiac pacemaking

The strong circadian ([~]24h) rhythms in heart rate (HR) are critical for flexible regulation of cardiac pacemaking function throughout the day. While this circadian flexibility in HR is robustly sustained in diverse conditions, it declines as the heart ages, accompanied by reduced maximal HR performance. The intricate regulation of circadian HR patterns involves the orchestration of sympathetic and parasympathetic nervous activities (SNA and PNA) alongside local circadian rhythmicity (LCR) within the heart. However, their intricate interactions that sustain the resilience and adaptability of circadian rhythms, as well as the mechanisms that underpin their deterioration during the aging process, remain enigmatic. To address these questions, we developed a mathematical model describing autonomic control and LCR in sinoatrial nodal cells (SANC) that accurately captures distinct circadian patterns in adult and aged mice. Our model underscores the indispensable synergy among SNA, PNA, and LCR in preserving circadian flexibility, robustness, and performance in SANC. SNA predominantly enhances SANC robustness and performance, while PNA primarily drives SANC flexibility, complemented by LCR and SNA. LCR acts as a booster, further enhancing SANC flexibility and performance. However, the delicate balance of this synergy is disrupted with age, resulting in diminished SANC performance and flexibility. Specifically, age-related impairment of PNA selectively dampens SANC flexibility while ion channel remodeling disrupts all SANC functions. Our work shed light on their critical synergistic interactions in regulating time-of-day cardiac pacemaking function and dysfunction, which may help to identify potential therapeutic targets within the circadian clock for the prevention and treatment of cardiac arrhythmias. Author SummaryThe mammalian heart relies on the sinoatrial node, known as the cardiac pacemaker, to orchestrate heartbeats. These heartbeats slow down during sleep and accelerate upon waking, in anticipation of daily environmental changes. The hearts ability to rhythmically adapt to these 24-hour changes, known as circadian rhythms, is crucial for flexible cardiac performance throughout the day, accommodating various physiological states. However, with aging, the hearts circadian flexibility gradually weakens, accompanied by a decline in maximal heart rate. Previous studies have implicated the involvement of a master circadian clock and a local circadian clock within the heart, but their time-of-day interactions and altered dynamics during aging remain unclear. In this study, we developed a mathematical model to simulate the regulation of sinoatrial nodal cell pacemaking function by the master and local circadian clocks in adult and aged mice. Our results revealed distinct roles played by these clocks in determining circadian patterns of sinoatrial nodal cells and shed light on their critical synergistic interactions in regulating time-of-day cardiac pacemaking function and dysfunction.

physiology↗

bioRxiv2023

Density Physics-Informed Neural Network reveals sources of cell heterogeneity in signal transduction

The transduction time between signal initiation and final response provides valuable information on the underlying signaling pathway, including its speed and precision. Furthermore, multimodality in transduction-time distribution informs that the response is regulated by multiple pathways with different transduction speeds. Here, we developed Density physics-informed neural network (Density-PINN) to infer the transduction-time distribution, challenging to measure, from measurable final stress response time traces. We applied Density-PINN to single-cell gene expression data from 16 promoters regulated by unknown pathways in response to antibiotic stresses. We found that promoters with slower signaling initiation and transduction exhibit larger cell-to-cell heterogeneity in response intensity. However, this heterogeneity was greatly reduced when the response was regulated by slow and fast pathways together. This suggests a strategy for identifying effective signaling pathways for consistent cellular responses to disease treatments. Density-PINN can also be applied to understand various time delay systems, including infectious diseases.

systems biology↗

bioRxiv2023

Dual targeting of hepatocyte DGAT2 and stellate cell FASN alleviates nonalcoholic steatohepatitis in mice.

Nonalcoholic steatohepatitis (NASH) is a malady of multiple cell types associated with hepatocyte triglyceride (TG) accumulation, macrophage inflammation, and stellate cell-induced fibrosis, with no approved therapeutics yet available. Here, we report that stellate cell fatty acid synthase (FASN) in de novo lipogenesis drives the autophagic flux that is required for stellate cell activation and fibrotic collagen production. Further, we employ a dual targeting approach to NASH that selectively depletes collagen through selective stellate cell knockout of FASN (using AAV9-LRAT Cre in FASNfl/fl mice), while lowering hepatocyte triglyceride by depleting DGAT2 with a GalNac-conjugated, fully chemically modified siRNA. DGAT2 silencing in hepatocytes alone or in combination with stellate cell FASNKO reduced liver TG accumulation in a choline-deficient NASH mouse model, while FASNKO in hepatocytes alone (using AAV8-TBG Cre in FASNfl/fl mice) did not. Neither hepatocyte DGAT2 silencing alone nor FASNKO in stellate cells alone decreased fibrosis (total collagen), while loss of both DGAT2 plus FASN caused a highly significant attenuation of NASH. These data establish proof of concept that dual targeting of DGAT2 plus FASN alleviates NASH progression in mice far greater than targeting either gene product alone.

molecular biology↗

bioRxiv2023

Noisy delay denoises biochemical oscillators

Genetic oscillations are generated by delayed transcriptional negative feedback loops, wherein repressor proteins inhibit their own synthesis after a temporal production delay. This delay is distributed because it arises from a sequence of noisy processes, including transcription, translation, folding, and translocation. Because the delay determines repression timing and therefore oscillation period, it has been commonly believed that delay noise weakens oscillatory dynamics. Here, we demonstrate that noisy delay can surprisingly denoise genetic oscillators. Moderate delay noise unexpectedly sharpens oscillation peaks and improves temporal peak reliability without impacting period. We show that this denoising phenomenon occurs in a variety of well-studied genetic oscillators and we use queueing theory to uncover the universal mechanisms that produce it.

systems biology↗

bioRxiv2023

Partial in vivo reprogramming enables injury-free intestinal regeneration via autonomous Ptgs1 induction

Tissue regeneration after injury involves the dedifferentiation of somatic cells, a natural adaptive reprogramming process that leads to the emergence of injury-responsive cells with fetal-like characteristics in the intestinal epithelium. However, there is no direct evidence that adaptive reprogramming involves a shared molecular mechanism with direct cellular reprogramming. Here, we induced dedifferentiation of intestinal epithelial cells through forced partial reprogramming in vivo using "Yamanaka factors" (Oct4, Sox2, Klf4, and c-Myc: OSKM). The OSKM-induced dedifferentiation showed similar molecular features of intestinal regeneration, including a rapid transition from homeostatic cell types to injury-responsive-like cell types. These injury-responsive-like cells, sharing a gene signature of revival stem cells and atrophy-induced villus epithelial cells, actively assisted tissue regeneration following ionizing radiation-induced acute tissue damage. In contrast to normal intestinal regeneration, which involves epi-mesenchymal crosstalk through induction of Ptgs2 (encoding Cox2) upon injury, the OSKM expression promotes the autonomous production of prostaglandin E2 via epithelial Ptgs1 (encoding Cox1) expression. These results indicate that prostaglandin synthesis is a common mechanism for intestine epithelial regeneration but involves a different enzyme (Ptgs1 for Cox1) when partial reprogramming is directly applied to the intestinal epithelium.

cell biology↗

bioRxiv2023

Red2Flpe-SCON: A Versatile, Multicolor Strategy for Generating Mosaic Conditional Knockout Mice

Image-based lineage tracing enables tissue turnover kinetics and lineage potentials of different adult cell populations to be investigated. Previously, we reported a genetic mouse model system, Red2Onco, which ectopically expressed mutated oncogenes together with red fluorescent proteins (RFP). This system enabled the expansion kinetics and neighboring effects of oncogenic clones to be dissected. We now report Red2Flpe-SCON: a new mosaic knockout system that uses multicolor reporters to label both mutant and wild-type cells. We have developed the Red2Flpe mouse line for red clone-specific Flpe expression, as well as the FRT-based SCON (Short Conditional IntrON) method to facilitate tunable conditional mosaic knockouts in mice. We used the Red2Flpe-SCON method to study Sox2 mutant clonal analysis in the esophageal epithelium of adult mice which revealed that the stem cell gene, Sox2, is not essential for adult stem cell maintenance itself, but rather for stem cell proliferation and differentiation.

genetics↗

bioRxiv2022

A framework for deriving analytic long-term behavior of biochemical reaction networks

The long-term behaviors of biochemical systems are described by their steady states. Deriving these states directly for complex networks arising from real-world applications, however, is often challenging. Recent work has consequently focused on network-based approaches. Specifically, biochemical reaction networks are transformed into weakly reversible and deficiency zero networks, which allows the derivation of their analytic steady states. Identifying this transformation, however, can be challenging for large and complex networks. In this paper, we address this difficulty by breaking the complex network into smaller independent subnetworks and then transforming the subnetworks to derive the analytic steady states of each subnetwork. We show that stitching these solutions together leads to the the analytic steady states of the original network. To facilitate this process, we develop a user-friendly and publicly available package, COMPILES (COMPutIng anaLytic stEady States). With COMPILES, we can easily test the presence of bistability of a CRISPRi toggle switch model, which was previously investigated via tremendous number of numerical simulations and within a limited range of parameters. Furthermore, COMPILES can be used to identify absolute concentration robustness (ACR), the property of a system that maintains the concentration of particular species at a steady state regardless of any initial concentrations. Specifically, our approach completely identifies all the species with and without ACR in a complex insulin model. Our method provides an effective approach to analyzing and understanding complex biochemical systems. Author summarySteady states describe the long-term behaviors of biochemical systems, which are typically based on ordinary differential equations. To derive a steady state analytically, significant attention has been given in recent years to network-based approaches. While this approach allows a steady state to be derived as long as a network has a special structure, complex and large networks rarely have this structural property. We address this difficulty by breaking the network into smaller and more manageable independent subnetworks, and then use the network-based approach to derive the analytic steady state of each subnetwork. Stitching these solutions together allows us to derive the analytic steady state of the original network. To facilitate this process, we develop a user-friendly and publicly available package, COMPILES. COMPILES identifies critical biochemical properties such as the presence of bistability in a genetic toggle switch model and absolute concentration robustness in a complex insulin signaling pathway model.

systems biology↗

bioRxiv2022

A general model-based causal inference overcomes the curse of synchrony and indirect effect

To identify causation, model-free inference methods, such as Granger Causality, have been widely used due to their flexibility. However, they have difficulty distinguishing synchrony and indirect effects from direct causation, leading to false predictions. To overcome this, model-based inference methods that test the reproducibility of data with a specific mechanistic model to infer causality were developed. However, they can only be applied to systems described by a specific model, greatly limiting their applicability. Here, we address this limitation by deriving an easily testable condition for a general monotonic ODE model to reproduce time-series data. We built a user-friendly computational package, GOBI (General ODE-Based Inference), which is applicable to nearly any monotonic system with positive and negative regulations described by ODE. GOBI successfully inferred positive and negative regulations in various networks at both the molecular and population levels, unlike existing model-free methods. Thus, this accurate and broadly applicable inference method is a powerful tool for understanding complex dynamical systems.

systems biology↗

bioRxiv2022

Inferring delays in partially observed gene regulatory networks

MotivationCell function is regulated by gene regulatory networks (GRNs) defined by protein-mediated interaction between constituent genes. Despite advances in experimental techniques, we can still measure only a fraction of the processes that govern GRN dynamics. To infer the properties of GRNs using partial observation, unobserved sequential processes can be replaced with distributed time delays, yielding non-Markovian models. Inference methods based on the resulting model suffer from the curse of dimensionality. ResultsWe develop a simulation-based Bayesian MCMC method for the efficient and accurate inference of GRN parameters when only some of their products are observed. We illustrate our approach using a two-step activation model: An activation signal leads to the accumulation of an unobserved regulatory protein, which triggers the expression of observed fluorescent proteins. With prior information about observed fluorescent protein synthesis, our method successfully infers the dynamics of the unobserved regulatory protein. We can estimate the delay and kinetic parameters characterizing target regulation including transcription, translation, and target searching of an unobserved protein from experimental measurements of the products of its target gene. Our method is scalable and can be used to analyze non-Markovian models with hidden components. AvailabilityAccompanying code in R is available at https://github.com/Mathbiomed/SimMCMC. Contactjaekkim@kaist.ac.kr or kresimir.josic@gmail.com or cbskust@korea.ac.kr Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2022

Spatially coordinated collective phosphorylation filters spatiotemporal noises for precise circadian timekeeping

The circadian ([~]24h) clock is based on a negative feedback loop centered around the PERIOD protein (PER), translated in the cytoplasm and then enters the nucleus to repress its own transcription at the right time of day. Such precise nucleus entry is mysterious because thousands of PER molecules transit through crowded cytoplasm and arrive at the perinucleus across several hours. To understand this, we developed a mathematical model describing the complex spatiotemporal dynamics of PER as a single random time delay. We find that the spatially coordinated bistable phosphoswitch of PER, which triggers the phosphorylation of accumulated PER at the perinucleus, leads to the synchronous and precise nuclear entry of PER. This leads to robust circadian rhythms even when PER arrival times are heterogenous and perturbed due to changes in cell crowdedness, cell size, and transcriptional activator levels. This shows how the circadian clock compensates for spatiotemporal noise. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/513792v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@36522eorg.highwire.dtl.DTLVardef@4d64c9org.highwire.dtl.DTLVardef@113f670org.highwire.dtl.DTLVardef@1983acb_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe time window when PER protein arrives at the perinucleus is wide and keeps changing. C_LIO_LIA bistable phosphoswitch enables precise nuclear entry of PER protein. C_LIO_LIThis leads to robust circadian rhythms when cell congestion level and size change. C_LIO_LIThis describes how the circadian clock compensates for spatiotemporal noise. C_LI

systems biology↗

bioRxiv2022

Drosophila Males Use 5'-to-3' Phased Biogenesis to Make Stellate-silencing piRNAs that Lack Homology to Maternally Deposited piRNA Guides

PIWI-interacting RNAs (piRNAs) direct PIWI proteins to silence complementary targets such as transposons. In animals with a maternally specified germline, e.g. Drosophila melanogaster, maternally deposited piRNAs initiate piRNA biogenesis in the progeny. Normal fertility in D. melanogaster males requires repression of tandemly repeated Stellate genes by piRNAs from Suppressor of Stellate [Su(Ste)]. Because the Su(Ste) loci are on the Y chromosome, Su(Ste) piRNAs are not deposited in oocytes. How the male germline produces Su(Ste) piRNAs in the absence of maternally deposited Su(Ste) piRNAs is unknown. Here, we show that Su(Ste) piRNAs are made in the early male germline via 5'-to-3' phased piRNA biogenesis triggered by maternally deposited 1360/Hoppel transposon piRNAs. Strikingly, deposition of Su(Ste) piRNAs from XXY mothers obviates the need for phased piRNA biogenesis in sons. Together, our study uncovers the developmentally programmed mechanism that allows fly mothers to protect their sons using a Y-linked piRNA locus.

developmental biology↗

bioRxiv2022

ztf-16 is a novel heterochronic modulator that opposes adult cell fate in dauer and continuous life histories in Caenorhabditis elegans

Animal development is a complex yet robust process that can withstand lengthy and variable interruptions. In Caenorhabditis elegans, adverse conditions can trigger entry into dauer diapause, a stress-resistant, developmentally arrested stage that occurs midway through larval development. Favorable conditions promote recovery from dauer and the completion of development. During larval development, hypodermal seam cells are multipotent and divide at each stage. At adulthood, seam cells differentiate and express the adult-specific COL-19 collagen. The larval-to-adult transition is controlled by a network of genes called the heterochronic pathway, including the LIN-29 transcription factor that directly activates col-19 expression, and the let-7 microRNA that indirectly promotes lin-29 expression. Notably, most heterochronic genes that oppose adult cell fate are dispensable after dauer. We performed a genetic screen for heterochronic genes that act after dauer and identified ztf-16, encoding a zinc finger transcription factor in the hunchback/Ikaros-like family. We found that ztf-16 opposes precocious expression of the adult cell fate marker col-19p::gfp equally during both life histories, making ztf-16(-) the first precocious heterochronic mutant to be unaffected by dauer. Our data indicate that ztf-16 regulates col-19p::gfp via a novel, lin-29-independent mechanism. Endogenous ztf-16b::gfp expression is regulated by let-7 and ztf-16 acts genetically downstream of let-7, but lin-29 is not required for col-19p::gfp expression in ztf-16 mutant larvae or adults. Taken together, this work illuminates a novel aspect of the heterochronic pathway relevant to both dauer and non-dauer development.

genetics↗

bioRxiv2022

Paradoxical activation of SREBP1c and de novo lipogenesis by hepatocyte-selective ACLY depletion in obese mice.

Hepatic steatosis associated with high fat diets, obesity and type 2 diabetes is thought to be the major driver of severe liver inflammation, fibrosis, and cirrhosis. Cytosolic acetyl-coenzyme A (AcCoA), a central metabolite and substrate for de novo lipogenesis (DNL), is produced from citrate by ATP-citrate lyase (ACLY) and from acetate through AcCoA synthase short chain family member 2 (ACSS2). However, the relative contributions of these two enzymes to hepatic AcCoA pools and DNL rates in response to high fat feeding is unknown. We report here that hepatocyte-selective depletion of either ACSS2 or ACLY caused similar 50% decreases in liver AcCoA levels in obese mice, showing that both pathways contribute to generation of this DNL substrate. Unexpectedly however, the hepatocyte ACLY depletion in obese mice paradoxically increased total DNL flux measured by D2O incorporation into palmitate, while in contrast ACSS2 depletion had no effect. The increase in liver DNL upon ACLY depletion was associated with increased expression of nuclear sterol regulatory element-binding protein 1c (SREBP1c) and of its target DNL enzymes. This upregulated DNL enzyme expression explains the increased rate of palmitate synthesis in ACLY depleted livers. Furthermore, this increased flux through DNL may also contribute to the observed depletion of AcCoA levels due to its increased conversion to Malonyl CoA (MalCoA) and palmitate. Together, these data indicate that in HFD fed obese mice, hepatic DNL is not limited by its immediate substrates AcCoA or MalCoA, but rather by activities of DNL enzymes.

molecular biology↗

bioRxiv2022

A new immunocompetent rectal cancer model to study radiation therapy

We describe a new mouse model of rectal cancer (RC) involving rapid tumor organoid engraftment via orthotopic transplantation; the resulting RC tumors invaded inward from the mucosal surface and metastasized to distant organs. Histologically the tumors closely resemble human RC and mirror remodeling of the tumor microenvirnoment (TME) in response to radiation. This murine RC model thus recapitulates the pathogenesis of human RC, thereby fulfilling the need for a physiologically accurate model for preclinical efficacy studies.

cancer biology↗

bioRxiv2022

Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations

Transcriptional repression can occur via various mechanisms, such as blocking, sequestration, and displacement. For instance, the repressors can hold the activators to prevent binding with DNA or can bind to the DNA-bound activators to block their transcriptional activity. Although the transcription can be completely suppressed with a single mechanism, multiple repression mechanisms are utilized together to inhibit transcriptional activators in many systems, such as circadian clocks and NF-{kappa}B oscillators. This raises the question of what advantages arise if seemingly redundant repression mechanisms are combined. Here, by deriving equations describing the multiple repression mechanisms, we find that their combination can synergistically generate a sharply ultrasensitive transcription response and thus strong oscillations. This rationalizes why the multiple repression mechanisms are used together in various biological oscillators. The critical role of such combined transcriptional repression for strong oscillations is further supported by our analysis of formerly identified mutations disrupting the transcriptional repression of the mammalian circadian clock. The hitherto unrecognized source of the ultrasensitivity, the combined transcriptional repressions, can lead to robust synthetic oscillators with a previously unachievable simple design.

systems biology↗

bioRxiv2021

Hierarchical Bayesian models of transcriptional and translational regulation processes with delays

MotivationSimultaneous recordings of gene network dynamics across large populations have revealed that cell characteristics vary considerably even in clonal lines. Inferring the variability of parameters that determine gene dynamics is key to understanding cellular behavior. However, this is complicated by the fact that the outcomes and effects of many reactions are not observable directly. Unobserved reactions can be replaced with time delays to reduce model dimensionality and simplify inference. However, the resulting models are non-Markovian, and require the development of new inference techniques. ResultsWe propose a non-Markovian, hierarchical Bayesian inference framework for quantifying the variability of cellular processes within and across cells in a population. We illustrate our approach using a delayed birth-death process. In general, a distributed delay model, rather than a popular fixed delay model, is needed for inference, even if only mean reaction delays are of interest. Using in silico and experimental data we show that the proposed hierarchical framework is robust and leads to improved estimates compared to its non-hierarchical counterpart. We apply our method to data obtained using time-lapse microscopy and infer the parameters that describe the dynamics of protein production at the single cell and population level. The mean delays in protein production are larger than previously reported, have a coefficient of variation of around 0.2 across the population, and are not strongly correlated with protein production or growth rates. AvailabilityAccompanying code in Python is available at https://github.com/mvcortez/Bayesian-Inference. Contactkresimir.josic@gmail.comkresimir.josic@gmail.com, jaekkim@kaist.ac.kr jaekkim@kaist.ac.kr, cbskust@korea.ac.kr cbskust@korea.ac.kr

systems 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↗