Title |
The Stem Cell Population of the Human Colon Crypt: Analysis via Methylation Patterns
|
---|---|
Published in |
PLoS Computational Biology, March 2007
|
DOI | 10.1371/journal.pcbi.0030028 |
Pubmed ID | |
Authors |
Pierre Nicolas, Kyoung-Mee Kim, Darryl Shibata, Simon Tavaré |
Abstract |
The analysis of methylation patterns is a promising approach to investigate the genealogy of cell populations in an organism. In a stem cell-niche scenario, sampled methylation patterns are the stochastic outcome of a complex interplay between niche structural features such as the number of stem cells within a niche and the niche succession time, the methylation/demethylation process, and the randomness due to sampling. As a consequence, methylation pattern studies can reveal niche characteristics but also require appropriate statistical methods. The analysis of methylation patterns sampled from colon crypts is a prototype of such a study. Previous analyses were based on forward simulation of the cell content of the whole crypt and subsequent comparisons between simulated and experimental data using a few statistics as a proxy to summarize the data. In this paper we develop a more powerful method to analyze these data based on coalescent modelling and Bayesian inference. Results support a scenario where the colon crypt is maintained by a high number of stem cells; the posterior indicates a number greater than eight and the posterior mode is between 15 and 20. The results also provide further evidence for synergistic effects in the methylation/demethylation process that could for the first time be quantitatively assessed through their long-term consequences such as the coexistence of hypermethylated and hypomethylated patterns in the same colon crypt. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 7 | 8% |
United Kingdom | 3 | 3% |
France | 1 | 1% |
Ukraine | 1 | 1% |
Switzerland | 1 | 1% |
Unknown | 75 | 85% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 31 | 35% |
Researcher | 23 | 26% |
Professor > Associate Professor | 7 | 8% |
Student > Master | 6 | 7% |
Student > Bachelor | 5 | 6% |
Other | 11 | 13% |
Unknown | 5 | 6% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 38 | 43% |
Biochemistry, Genetics and Molecular Biology | 11 | 13% |
Mathematics | 7 | 8% |
Medicine and Dentistry | 7 | 8% |
Engineering | 6 | 7% |
Other | 11 | 13% |
Unknown | 8 | 9% |