Characterization of a developmental oscillator in C. elegans

Gene expression oscillations can act as fundamental time-keeping mechanisms to instruct developmental events temporally and spatially. The present work investigates such a developmental oscillator in C. elegans that encompasses thousands of oscillating transcripts. The regulation of these transcript oscillations and their functional relevance for development remained elusive. In this thesis, I present insights into the general oscillator characteristics, the regulation of oscillating genes and the contribution of oscillatory gene expression to physiological outcomes.
Using a temporally highly resolved RNA sequencing time course covering all C. elegans larval stages (L1-L4) and early adulthood in combination with single worm microscopy studies, we characterize oscillatory gene expression in detail and provide evidence that oscillations peak once per larval stage and are synchronized with the molting cycle. Consequently, we propose oscillatory gene expression and larval development to be coupled. Furthermore, oscillations are arrested (i.e. absent) temporarily in freshly hatched L1 larvae and worms released from dauer arrest, and permanently in adults. The particular oscillator phase at which we observe the arrested oscillator corresponds to the oscillator phase detected around the molt exit. Given that developmental checkpoints have been reported around the time of molt exit we propose the C. elegans oscillator to constitute a developmental clock supporting a checkpoint function.
Investigations on the mechanisms leading to rhythmic transcript abundance by RNA polymerase II ChIP-sequencing and transcriptional reporter studies revealed that transcription is mainly responsible for oscillating transcript levels. Together with the fact that oscillatory gene expression is coupled to development, transcription factors were of particular interest in this thesis. We characterize BLMP-1, an oscillating transcription factor that was shown to alter developmental timing. We provide evidence that BLMP-1 acts to regulate the duration of molts, is required for cuticle integrity and acts as a coupling factor to synchronize a group of oscillating genes with the remaining oscillating genes and development. Furthermore, we could show epistatic behavior of blmp-1 with dre-1, an oscillating E3 ubiquitin ligase that degrades BLMP-1 protein. These observations shed light on the regulatory network underlying the C. elegans developmental oscillator and are important to understand its architecture and physiological impact.