Investigating stem cells in human colon by using methylation patterns

The stem cells that maintain human colon crypts are poorly characterized. T o better determine stem cell numbers and how they divide, epigenetic patter ns were used as cell fate markers. Methylation exhibits somatic inheritance and random changes that potentially record lifelong stem cell division his tories as binary strings or tags in adjacent CpG sites. Methylation tag con tents of individual crypts were sampled with bisulfite sequencing at three presumably neutral loci. Methylation increased with aging but varied betwee n crypts and was mosaic within single crypts. Some crypts appeared to be qu arsi-clonal as they contained more unique tags than expected if crypts were maintained by single immortal stem cells. The complex epigenetic patterns were more consistent with a crypt niche model wherein multiple stem cells w ere present and replaced through periodic symmetric divisions. Methylation tags provide evidence that normal human crypts are long-lived, accumulate r andom methylation errors, and contain multiple stem cells that go through " bottlenecks" during life.