title: Oestrogen receptor β regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase.
abstract: BACKGROUND
  DNA methylation is one way to encode epigenetic information and plays a crucial role in regulating gene expression during embryonic development. DNA methylation marks are established by the DNA methyltransferases and, recently, a mechanism for active DNA demethylation has emerged involving the ten-eleven translocator proteins and thymine DNA glycosylase (TDG). However, so far it is not clear how these enzymes are recruited to, and regulate DNA methylation at, specific genomic loci. A number of studies imply that sequence-specific transcription factors are involved in targeting DNA methylation and demethylation processes. Oestrogen receptor beta (ERβ) is a ligand-inducible transcription factor regulating gene expression in response to the female sex hormone oestrogen. Previously, we found that ERβ deficiency results in changes in DNA methylation patterns at two gene promoters, implicating an involvement of ERβ in DNA methylation. In this study, we set out to explore this involvement on a genome-wide level, and to investigate the underlying mechanisms of this function.
  
  
  RESULTS
  Using reduced representation bisulfite sequencing, we compared genome-wide DNA methylation in mouse embryonic fibroblasts derived from wildtype and ERβ knock-out mice, and identified around 8000 differentially methylated positions (DMPs). Validation and further characterisation of selected DMPs showed that differences in methylation correlated with changes in expression of the nearest gene. Additionally, re-introduction of ERβ into the knock-out cells could reverse hypermethylation and reactivate expression of some of the genes. We also show that ERβ is recruited to regions around hypermethylated DMPs. Finally, we demonstrate here that ERβ interacts with TDG and that TDG binds ERβ-dependently to hypermethylated DMPs.
  
  
  CONCLUSIONS
  We provide evidence that ERβ plays a role in regulating DNA methylation at specific genomic loci, likely as the result of its interaction with TDG at these regions. Our findings imply a novel function of ERβ, beyond direct transcriptional control, in regulating DNA methylation at target genes. Further, they shed light on the question how DNA methylation is regulated at specific genomic loci by supporting a concept in which sequence-specific transcription factors can target factors that regulate DNA methylation patterns.
authors.affiliation: Department of Biochemistry and Molecular Biology, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Fudan University Shanghai Medical College, Shanghai, People's Republic of China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland.|Novartis Institutes for BioMedical Research, Novartis Pharma AG, Werk Klybeck, 4002 Basel, Switzerland.
authors.forename: William
authors.initials: W
authors.lastname: Duong
authors.affiliation: Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland.
authors.forename: Claudia
authors.initials: C
authors.lastname: Krawczyk
authors.affiliation: Genomatix Software GmbH, Bayerstr, 85a, 80335 Munich, Germany.
authors.forename: Nancy
authors.initials: N
authors.lastname: Bretschneider
authors.affiliation: Swedish Toxicology Science Research Center (Swetox), Forskargatan 20, 151 36 Södertälje, Sweden.
authors.forename: Gábor
authors.initials: G
authors.lastname: Borbély
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet at Novum, 141 83 Stockholm, Sweden.
authors.forename: Mukesh
authors.initials: M
authors.lastname: Varshney
authors.affiliation: Swedish Toxicology Science Research Center (Swetox), Forskargatan 20, 151 36 Södertälje, Sweden.
authors.forename: Christian
authors.initials: C
authors.lastname: Zinser
authors.affiliation: Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland.
authors.forename: Primo
authors.initials: P
authors.lastname: Schär
authors.affiliation: Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland.|Swedish Toxicology Science Research Center (Swetox), Forskargatan 20, 151 36 Södertälje, Sweden.|Department of Clinical Neurosciences, Karolinska Institutet, CMM L8:00, 171 76 Stockholm, Sweden.
authors.forename: Joëlle
authors.initials: J
authors.lastname: Rüegg
keywords: DNA methylation; Mouse embryonic fibroblasts; Mouse embryonic stem cells; Oestrogen receptor β; Reduced representation bisulfite sequencing; Thymine DNA glycosylase