Chrono-atlas of cell-type specific daily gene expression rhythms 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 dysfunction and 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 all major cell types of the proximal and distal regions of the colon following injury. We find that daily gene expression is not uniform: rhythmic genes, including circadian clock components, clock targets, and systemic programs, differ in their timing and are cell-type specific. Cells of the epithelium, stroma, and immune system to display strong rhythms in metabolic, protein processing, and stress response genes during regeneration. While stromal and muscle cells exhibit robust circadian clock gene rhythms irrespective of injury, epithelial cells show weaker clock oscillations that become 12-hours antiphasic during regeneration. These data, completed with smFISH validation, reveal an unexpected complexity to daily transcript levels in the colon, and provide a resource for future studies by identifying the cellular source of 24-hour transcript rhythms.