scRNA-seq time series in the regenerating colon

The circadian clock is a molecular timer present throughout the body including the gastrointestinal tract, where it regulates daily rhythms in physiology through the timing of rhythmic gene expression. Dysfunctional rhythms, caused by loss of clock timing and/or environmental disruption is implicated with gastrointestinal pathology. The large intestine (colon) is composed of many different types of cells with distinct gene expression programs and functions. How daily rhythms in transcript abundance are coordinated in the intestine at a cell-specific level is not known. Using single cell transcriptomics, we analyzed 24-hour gene expression in 21 different cell types of the proximal and distal regions of the colon. We find that daily gene expression is not uniform; rhythmic genes, including circadian clock components, differ in their timing and rhythmic transcriptional programs that are cell-type specific. During regeneration, epithelium, stroma, and immune system cells display strong rhythms in metabolic, protein processing, and stress response genes. We further show that regeneration reprograms clock gene timing in epithelial cells to shift by a 12-hours offset compared to the surrounding tissue. These data reveal an unexpected complexity to daily transcriptional timing in a tissue undergoing regeneration, and provide a resource for future studies by identifying the cellular source of 24-hour transcript rhythms.