Systematic identification of oscillatory gene expression in single cell types

ABSTRACT Many biological cycles are driven by oscillatory gene expression coordinated across cell types. For example, larval development in Caenorhabditis elegans involves coordinated cyclic changes in cell division, behavior, and growth, the latter requiring production of a structured extracellular matrix called the cuticle. Here, we combine single-cell RNA sequencing and novel computational approaches to identify oscillatory gene expression in individual cell types. We find that many cell types exhibit looping structures in PCA and UMAP space that correspond to transcriptional oscillations at each larval stage. Oscillatory gene expression is found in all cuticle-producing cell types, including glia, but not detected in neurons or muscle. We develop rigorous statistical approaches for de novo identification of oscillatory genes and cell types, yielding >5,000 genes. While many oscillatory genes relate to cuticle production, each cell type expresses largely distinct genes, suggesting that cuticle production is a patchwork of cell-type-specific programs. Finally, we derive a potential set of regulatory transcription factors that can explain coordinated oscillatory gene expression and find that shared upstream factors likely control gene timing across cell types. Together, our results suggest that shared regulators control cell-type-specific oscillatory gene expression, including in previously overlooked cell types such as glia.