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

Published: 28 May 2013

Additional files

Additional file 1:

A more detailed description of material and methods accompanying the manuscript. Table S2. List of primer sequences used in this study. Table S3. List of the 4C primer sequences used in this study. Legends to Figures S1-S8

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Additional file 2:

Figure S1: Expression of marker genes in the purified cell populations. Expression of a set of marker genes, derived from Affimetrix micro-array experiments, in the three sorted cell populations. Figure S2: Mapping statistics. Statistics on the high-throughput sequencing described in this manuscript. Figure S3: TSS methylation and gene expression in the SI. Figure showing genome browser view of different genes. Figure S4: No changes in HMR distribution or expression of transposons. Figure showing the lack of HMR distribution at transposons. Figure S5: Two examples of confirmation of DMRs called between the methylomes. Manual BS-Seq conformation of two DMRs called in the methylomes. Figure S6: Additional ChIP-qPCR and ChIP-Seq analysis. Chip-qPCR and Chip-seq analysis of the DMRs called between SI stem cells and villus. Figure S7: 4C domainograms of three intergenic DMRs. Additional 4C experiments performed on DMRs called between SI stem cells and villus. Figure S8: A role for TCF4 in DMR formation. Additional data implication TCF4 in DMR formation in the SI.

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Additional file 3:

Table S1. List of genes differentially expressed between the SI and hair bulge stem cell compartment.

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