Little is known about human crypt stem cells. Although strategies which create and follow visible crypt markers are impractical for humans, it may be possible to analyze endogenous sequences which inherently record crypt histories. To better distinguish between otherwise identical crypts without experimental intervention, epigenetic patterns were used as cell fate markers. Methylation exhibits somatic inheritance and random site independent changes which potentially create binary information strings or tags in adjacent CpG sites that drift with time. Instead of visual examinations, methylation tag contents of individual crypts are sampled and read with bisulfite sequencing. Tags at three presumably neutral loci were different between crypts and between cells within crypts. Methylation increased with aging but was mosaic between crypts, and between alleles and loci within single crypts. Some crypts were quasi‑clonal because they contained more unique tags than expected from a single stem cell. The complex epigenetic patterns analyzed with coalescence theory were more consistent with crypt niches in which multiple stem cells are replaced through periodic symmetric divisions. Methylation tags suggest normal human crypts are long lived, contain multiple stem cells, undergo continuous purification, and accumulate random methylation errors at some loci. Proposed studies will further verify methylation tags as cell fate markers and better characterize stem cell dynamics in normal human colon.
