Open Access Research article

Lack of increases in methylation at three CpG-rich genomic loci in non-mitotic adult tissues during aging

Michelle W Chu1, Kimberly D Siegmund2, Carrie L Eckstam1, Jung Yeon Kim16, Allen S Yang3, Gary C Kanel1, Simon Tavaré45 and Darryl Shibata1*

Author Affiliations

1 Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA

2 Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA

3 Department of Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA

4 Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA

5 Department of Oncology, University of Cambridge, Cambridge, UK

6 Department of Pathology, Inje University Sanggye-Paik Hospital, Sanggye 7 dong 761-7, Nowon-gu, Seoul, Korea

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BMC Medical Genetics 2007, 8:50  doi:10.1186/1471-2350-8-50

Published: 31 July 2007



Cell division occurs during normal human development and aging. Despite the likely importance of cell division to human pathology, it has been difficult to infer somatic cell mitotic ages (total numbers of divisions since the zygote) because direct counting of lifetime numbers of divisions is currently impractical. Here we attempt to infer relative mitotic ages with a molecular clock hypothesis. Somatic genomes may record their mitotic ages because greater numbers of replication errors should accumulate after greater numbers of divisions. Mitotic ages will vary between cell types if they divide at different times and rates.


Age-related increases in DNA methylation at specific CpG sites (termed "epigenetic molecular clocks") have been previously observed in mitotic human epithelium like the intestines and endometrium. These CpG rich sequences or "tags" start unmethylated and potentially changes in methylation during development and aging represent replication errors. To help distinguish between mitotic versus time-associated changes, DNA methylation tag patterns at 8–20 CpGs within three different genes, two on autosomes and one on the X-chromosome were measured by bisulfite sequencing from heart, brain, kidney and liver of autopsies from 21 individuals of different ages.


Levels of DNA methylation were significantly greater in adult compared to fetal or newborn tissues for two of the three examined tags. Consistent with the relative absence of cell division in these adult tissues, there were no significant increases in tag methylation after infancy.


Many somatic methylation changes at certain CpG rich regions or tags appear to represent replication errors because this methylation increases with chronological age in mitotic epithelium but not in non-mitotic organs. Tag methylation accumulates differently in different tissues, consistent with their expected genealogies and mitotic ages. Although further studies are necessary, these results suggest numbers of divisions and ancestry are at least partially recorded by epigenetic replication errors within somatic cell genomes.