Functional dissection of a gene expression oscillator in C. elegans

Gene expression oscillations control diverse biological processes. One such example of gene expression oscillations, are those found for thousands of genes during C. elegans larval development. However, it remains unclear whether and how gene expression oscillations regulate development processes in C. elegans. In this work, I aimed to study the molecular architecture and the system properties of the C. elegans oscillator to provide insight into potential developmental functions and reveal features that are unique, as well as those that are shared among oscillators.
Here, performing temporally highly resolved mRNA-sequencing across all larval stages (L1-L4) of C. elegans development, we identified 3,739 genes, whose transcripts revealed high-amplitude oscillations (>2-fold from peak to trough), peaking once every larval stage with stable amplitudes, but variable periods. Oscillations appeared tightly coupled to the molts, but were absent from freshly hatched larvae, developmentally arrested dauer larvae and adults. Quantitative characterization of transitions between oscillatory and stable states of the oscillator showed that the stable states are similar to a particular phase of the oscillator, which coincided with molt exit. Given that these transitions are sensitive to food, we
postulate that feeding might impact the state of the oscillator. These features appear rather unique, and hence a better understanding may help to reveal general principles of gene expression oscillators.
Our RNAPII ChIP-seq revealed rhythmic occupancy of RNAPII at the promoters of oscillating genes, suggesting that mRNA transcript oscillations arise from rhythmic transcription. Given that oscillations are coupled to the repetitive molts and that the molecular mechanisms that regulate molting are unknown, we aimed to find transcription factors important for molting and oscillations. Hence, we screened 92 transcription factors that oscillate on the mRNA level for their role in molting and identified grh-1, myrf1, blmp-1, bed-3, nhr-23, nhr-25 and ztf-6. We showed that oscillatory activity of GRH-1 is required for timely completion of the molt, to prevent cuticle rupturing, and for oscillatory expression of structural components of the cuticle and ‘ECM regulators’, among others, including grh-1 itself. Hence, we propose GRH-1 as a putative component of the (sub-)oscillator that regulates molting. We showed that loss of BLMP-1 increased the duration of molts, affected cuticle integrity, and changed the oscillatory dynamics of a subset of genes in diverse ways. We postulate that BLMP-1 acts as factor that couples gene expression oscillations, and potentially sub-oscillators or repetitive developmental processes.
In conclusion, this work provides insight into the function of the oscillator, and its system properties. Moreover, we identified relevant factors, which we propose as a starting point to unravel the molecular wiring of the C. elegans oscillator and its functional relevance.