Detecting Rhythmic Gene Expression in Single Cell Transcriptomics

An autonomous, environmentally-synchronizable circadian rhythm is a ubiquitous feature of life on Earth. In multicellular organisms, this rhythm is generated by a transcription--translation feedback loop present in nearly every cell that drives daily expression of thousands of genes in a tissue--dependent manner. Identifying the genes that are under circadian control can elucidate the mechanisms by which physiological processes are coordinated in multicellular organisms. Today, transcriptomic profiling at the single-cell level provides an unprecedented opportunity to understand the function of cell-level clocks. However, while many cycling detection algorithms have been developed to identify genes under circadian control in bulk transcriptomic data, it is not known how best to adapt these algorithms to single-cell RNAseq data. Here, we benchmark commonly used circadian detection methods on their reliability and efficiency when applied to single cell RNAseq data. Our results provide guidance on adapting existing cycling detection methods to the single-cell domain, and elucidate opportunities for more robust and efficient rhythm detection in single-cell data. We also propose a subsampling procedure combined with harmonic regression as an efficient, reliable strategy to detect circadian genes in the single--cell setting.