Mechanism of life-long maintenance of neuron identity despite molecular fluctuations

Abstract

Cell fate is maintained over long timescales, yet molecular fluctuations can lead to spontaneous loss of this differentiated state. We uncovered a mechanism that explains lifelong maintenance of ASE neuron fate in C. elegans by the terminal selector transcription factor CHE-1. Fluctuations in CHE-1 level are buffered by the reservoir of CHE-1 bound at its target promoters, which ensure continued che-1 expression by preferentially binding the che-1 promoter. We validated this mechanism by showing that che-1 expression was resilient to induced transient CHE-1 depletion, while both expression of CHE-1 targets and ASE function were lost. We identified a 130 bp che-1 promoter fragment responsible for this resilience, with deletion of a homeodomain binding site in this fragment causing stochastic loss of ASE identity long after its determination. Because network architectures that support this mechanism are highly conserved in cell differentiation, it may explain stable cell fate maintenance in many systems. KeywordsNeuronal cell fate, bistability, gene regulatory network, stochastic gene expression, molecular fluctuations, homeodomain proteins, chemotaxis, C. elegans, terminal selector CHE-1, a transcription factor whose expression is transiently induced by the nuclear hormone receptor NHR-67 at the time of determination (Sarin et al. 2009). CHE-1 induces the expression of 500-1000 ASE-specific target genes, such as chemosensory receptors, ion-channels, and neuropeptides, by binding ASE motifs within their promoters (Etchberger et al. 2007). Its continued presence is required for expression of target genes after subtype determination (Etchberger et al. 2009). CHE-1 also upregulates its own expression. This positive feedback loop is necessary for sustaining che-1 expression and ASE cell fate directly after cell determination (Etchberger et al. 2007; Leyva-Diaz and Hobert 2019). Yet, it is unknown whether this positive feedback loop is sufficient for long-term maintenance of ASE fate. The impact of molecular noise, such as variability in CHE-1 protein copy number, on ASE fate maintenance has not been studied. Overall, it is an open question whether a reversible, bistable switch based on positive CHE-1 autoregulation would be sufficiently stable to maintain ASE fate for the animal's lifetime, or if additional mechanisms are necessary to ensure that, once ASE fate is determined, che-1 expression becomes independent of CHE-1 itself and can no longer spontaneously switch off.We show that sufficiently long, transiently induced depletion of CHE-1 caused permanent loss of ASE fate, indicating that it is controlled by a switch that remains reversible long after specification. This raises the question how the switch is protected against molecular noise, which could cause it to spontaneously lose ASE fate. Combining experimental measurements of the key parameters that control the magnitude of noise, i.e. the copy numbers and lifetimes of che-1 mRNA and protein, with stochastic models of the che-1 genetic network, revealed a novel...

Activation of a neural stem cell transcriptional program in parenchymal astrocytes

“…Another (and compatible) interpretation is that Rbpj protein may remain bound at its target promoters long after the Rbpj gene has been deleted, and that the neurogenic program is initiated only when the protein level has fallen below a certain threshold. Such stable transcription factor-DNA interaction is a mechanism by which some transcription factors buffer against fluctuating transcription levels ( Traets et al, 2020 ).…”