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Active DNA demethylation in human postmitotic cells correlates with activating histone modifications, but not transcription levels

Maja Klug1, Sven Heinz2, Claudia Gebhard1, Lucia Schwarzfischer1, Stefan W Krause3, Reinhard Andreesen1 and Michael Rehli1*

Author Affiliations

1 Department of Hematology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93042 Regensburg, Germany

2 Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA

3 Department of Internal Medicine 5, Hematology/Oncology, University of Erlangen-Nuernberg, Krankenhausstraße 12, 91054 Erlangen, Germany

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Genome Biology 2010, 11:R63  doi:10.1186/gb-2010-11-6-r63

Published: 18 June 2010

Abstract

Background

In mammals, the dynamics of DNA methylation, in particular the regulated, active removal of cytosine methylation, has remained a mystery, partly due to the lack of appropriate model systems to study DNA demethylation. Previous work has largely focused on proliferating cell types that are mitotically arrested using pharmacological inhibitors to distinguish between active and passive mechanisms of DNA demethylation.

Results

We explored this epigenetic phenomenon in a natural setting of post-mitotic cells: the differentiation of human peripheral blood monocytes into macrophages or dendritic cells, which proceeds without cell division. Using a global, comparative CpG methylation profiling approach, we identified many novel examples of active DNA demethylation and characterized accompanying transcriptional and epigenetic events at these sites during monocytic differentiation. We show that active DNA demethylation is not restricted to proximal promoters and that the time-course of demethylation varies for individual CpGs. Irrespective of their location, the removal of methylated cytosines always coincided with the appearance of activating histone marks.

Conclusions

Demethylation events are highly reproducible in monocyte-derived dendritic cells from different individuals. Our data suggest that active DNA demethylation is a precisely targeted event that parallels or follows the modification of histones, but is not necessarily coupled to alterations in transcriptional activity.