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DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus

Lucas TJ Kaaij1, Marc van de Wetering1, Fang Fang3, Benjamin Decato3, Antoine Molaro2, Harmen JG van de Werken1, Johan H van Es1, Jurian Schuijers1, Elzo de Wit1, Wouter de Laat1, Gregory J Hannon2, Hans C Clevers1, Andrew D Smith3 and René F Ketting14*

Author affiliations

1 Hubrecht Institute-KNAW & University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands

2 Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA

3 Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA

4 Institute for Molecular Biology, Ackermannweg 4, D-55128 Mainz, Germany

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Citation and License

Genome Biology 2013, 14:R50  doi:10.1186/gb-2013-14-5-r50

Published: 28 May 2013



DNA methylation is of pivotal importance during development. Previous genome-wide studies identified numerous differentially methylated regions upon differentiation of stem cells, many of them associated with transcriptional start sites.


We present the first genome-wide, single-base-resolution view into DNA methylation dynamics during differentiation of a mammalian epithelial stem cell: the mouse small intestinal Lgr5+ stem cell. Very little change was observed at transcriptional start sites and our data suggest that differentiation-related genes are already primed for expression in the stem cell. Genome-wide, only 50 differentially methylated regions were identified. Almost all of these loci represent enhancers driving gene expression in the differentiated part of the small intestine. Finally, we show that binding of the transcription factor Tcf4 correlates with hypo-methylation and demonstrate that Tcf4 is one of the factors contributing to formation of differentially methylated regions.


Our results reveal limited DNA methylation dynamics during small intestine stem cell differentiation and an impact of transcription factor binding on shaping the DNA methylation landscape during differentiation of stem cells in vivo.

Adult stem cells; Differentiation; DNA Methylation; Methylome; Enhancer; Tcf4