title: Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions.
abstract: Distal regulatory elements, including enhancers, play a critical role in regulating gene activity. Transcription factor binding to these elements correlates with Low Methylated Regions (LMRs) in a process that is poorly understood. Here we ask whether and how actual occupancy of DNA-binding factors is linked to DNA methylation at the level of individual molecules. Using CTCF as an example, we observe that frequency of binding correlates with the likelihood of a demethylated state and sites of low occupancy display heterogeneous DNA methylation within the CTCF motif. In line with a dynamic model of binding and DNA methylation turnover, we find that 5-hydroxymethylcytosine (5hmC), formed as an intermediate state of active demethylation, is enriched at LMRs in stem and somatic cells. Moreover, a significant fraction of changes in 5hmC during differentiation occurs at these regions, suggesting that transcription factor activity could be a key driver for active demethylation. Since deletion of CTCF is lethal for embryonic stem cells, we used genetic deletion of REST as another DNA-binding factor implicated in LMR formation to test this hypothesis. The absence of REST leads to a decrease of hydroxymethylation and a concomitant increase of DNA methylation at its binding sites. These data support a model where DNA-binding factors can mediate turnover of DNA methylation as an integral part of maintenance and reprogramming of regulatory regions.
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
authors.forename: Angelika
authors.initials: A
authors.lastname: Feldmann
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ; Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Robert
authors.initials: R
authors.lastname: Ivanek
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
authors.forename: Rabih
authors.initials: R
authors.lastname: Murr
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ; Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Dimos
authors.initials: D
authors.lastname: Gaidatzis
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ; Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Lukas
authors.initials: L
authors.lastname: Burger
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ; Faculty of Science, University of Basel, Basel, Switzerland.
authors.forename: Dirk
authors.initials: D
authors.lastname: Schübeler
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D000818:Animals; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002454:Cell Differentiation; D018899:CpG Islands / Q000235:genetics; D003596:Cytosine / Q000031:analogs & derivatives / Q000494:pharmacology; D019175:DNA Methylation / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics*; D053595:Embryonic Stem Cells; D005786:Gene Expression Regulation / Q000187:drug effects; D016678:Genome; D051379:Mice; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic; D000099229:RE1-Silencing Transcription Factor
chemical_list: D044503:5-Methylcytosine; D000076246:CCCTC-Binding Factor; D003596:Cytosine; D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D014157:Transcription Factors; D000099229:RE1-Silencing Transcription Factor; C000619698:Ctcf protein, mouse; C011865:5-hydroxymethylcytosine