A spatial and temporal transcriptomic atlas of mouse intestinal regeneration in the jejunum

The intestinal epithelium exhibits a remarkable capacity for regeneration following injury, yet the spatial and temporal dynamics of the damage-repair cycle remain incompletely understood. We present a spatial transcriptomics atlas of ionizing radiation-induced injury and repair in the mouse jejunum, capturing mRNA from 16,921 genes across approximately 26 million bins at 2-µm resolution in 23 biological samples spanning six days post-irradiation. Analysis reveals transcriptional patterns and niche signals undetectable by bulk or single-cell approaches, including spatially restricted interferon-target gene activation, an altered differentiation trajectory in the lower villus during early repair, two transcriptionally distinct crypt regenerative cell populations, and global transcriptional upregulation consistent with hypertranscription as a hallmark of intestinal regeneration, with evidence for hypertranscription extending to human Crohn's disease. In this work, we provide a spatiotemporal atlas of mouse intestinal regeneration at subcellular 2-µm resolution that will inform future therapeutic strategies for inflammatory bowel diseases and gastrointestinal pathologies arising from injury or cancer therapy.