title: Investigating stem cells in human colon by using methylation patterns.
abstract: The stem cells that maintain human colon crypts are poorly characterized. To better determine stem cell numbers and how they divide, epigenetic patterns were used as cell fate markers. Methylation exhibits somatic inheritance and random changes that potentially record lifelong stem cell division histories as binary strings or tags in adjacent CpG sites. Methylation tag contents of individual crypts were sampled with bisulfite sequencing at three presumably neutral loci. Methylation increased with aging but varied between crypts and was mosaic within single crypts. Some crypts appeared to be quasi-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 were present and replaced through periodic symmetric divisions. Methylation tags provide evidence that normal human crypts are long-lived, accumulate random methylation errors, and contain multiple stem cells that go through "bottlenecks" during life.
authors.affiliation: Department of Pathology, University of Southern California School of Medicine, Los Angeles, CA 90033, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Yatabe
authors.forename: S
authors.initials: S
authors.lastname: Tavaré
authors.forename: D
authors.initials: D
authors.lastname: Shibata
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000375:Aging / Q000235:genetics; D001483:Base Sequence; D058578:Biglycan; D003106:Colon / Q000166:cytology*; D018899:CpG Islands; D019175:DNA Methylation; D016326:Extracellular Matrix Proteins; D005260:Female; D000072576:Homeobox Protein Nkx-2.5; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D007223:Infant; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D009030:Mosaicism; D017570:MyoD Protein / Q000235:genetics*; D011509:Proteoglycans / Q000235:genetics*; D013234:Stem Cells / Q000166:cytology*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: C546884:BGN protein, human; D058578:Biglycan; D016326:Extracellular Matrix Proteins; D000072576:Homeobox Protein Nkx-2.5; D018398:Homeodomain Proteins; D017570:MyoD Protein; C057363:MyoD1 myogenic differentiation protein; C095552:NKX2-5 protein, human; D011509:Proteoglycans; D014157:Transcription Factors