title: Altering TET dioxygenase levels within physiological range affects DNA methylation dynamics of HEK293 cells.
abstract: The TET family of dioxygenases (TET1/2/3) can convert 5-methylcytosine (5 mC) into 5-hydroxymethylcytosine (5 hmC) and has been shown to be involved in active and passive DNA demethylation. Here, we demonstrate that altering TET dioxygenase levels within physiological range can affect DNA methylation dynamics of HEK293 cells. Overexpression of TET1 increased global 5 hmC levels and was accompanied by mild DNA demethylation of promoters, gene bodies and CpG islands. Conversely, the simultaneous knockdown of TET1, TET2, and TET3 led to decreased global 5 hmC levels and mild DNA hypermethylation of above-mentioned regions. The methylation changes observed in the overexpression and knockdown studies were mostly non-reciprocal and occurred with different preference depending on endogenous methylation and gene expression levels. Single-nucleotide 5 hmC profiling performed on a genome-wide scale revealed that TET1 overexpression induced 5 mC oxidation without a distribution bias among genetic elements and structures. Detailed analysis showed that this oxidation was related to endogenous 5 hmC levels. In addition, our results support the notion that the effects of TET1 overexpression on gene expression are generally unrelated to its catalytic activity.
authors.affiliation: a Institute of Human Genetics; University Hospital Essen; University Duisburg-Essen ; Essen , Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Grosser
authors.forename: Nicholas
authors.initials: N
authors.lastname: Wagner
authors.forename: Katrin
authors.initials: K
authors.lastname: Grothaus
authors.forename: Bernhard
authors.initials: B
authors.lastname: Horsthemke
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D018899:CpG Islands; D003596:Cytosine / Q000031:analogs & derivatives / Q000032:analysis; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D049308:Dioxygenases / Q000235:genetics* / Q000378:metabolism*; D055785:Gene Knockdown Techniques; D057809:HEK293 Cells; D006801:Humans; D006899:Mixed Function Oxygenases; D011401:Promoter Regions, Genetic; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism; D015854:Up-Regulation
chemical_list: D004268:DNA-Binding Proteins; D011518:Proto-Oncogene Proteins; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D006899:Mixed Function Oxygenases; C462539:TET1 protein, human; C578792:TET3 protein, human; D049308:Dioxygenases; C541081:TET2 protein, human
keywords: 450K; RRHP; TET1; TET2; TET3; demethylation; epigenetics; hydroxymethylcytosine; methylcytosine