Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1

Carina Frauer; Andrea Rottach; Daniela Meilinger; Sebastian Bultmann; Karin Fellinger; Stefan Hasenöder; Mengxi Wang; Weihua Qin; Johannes Söding; Fabio Spada; Heinrich Leonhardt

doi:10.1371/journal.pone.0016627

Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1

PLoS One. 2011 Feb 2;6(2):e16627. doi: 10.1371/journal.pone.0016627.

Authors

Carina Frauer¹, Andrea Rottach, Daniela Meilinger, Sebastian Bultmann, Karin Fellinger, Stefan Hasenöder, Mengxi Wang, Weihua Qin, Johannes Söding, Fabio Spada, Heinrich Leonhardt

Affiliation

¹ Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians University Munich, Planegg, Germany.

Abstract

Several mammalian proteins involved in chromatin and DNA modification contain CXXC zinc finger domains. We compared the structure and function of the CXXC domains in the DNA methyltransferase Dnmt1 and the methylcytosine dioxygenase Tet1. Sequence alignment showed that both CXXC domains have a very similar framework but differ in the central tip region. Based on the known structure of a similar MLL1 domain we developed homology models and designed expression constructs for the isolated CXXC domains of Dnmt1 and Tet1 accordingly. We show that the CXXC domain of Tet1 has no DNA binding activity and is dispensable for catalytic activity in vivo. In contrast, the CXXC domain of Dnmt1 selectively binds DNA substrates containing unmethylated CpG sites. Surprisingly, a Dnmt1 mutant construct lacking the CXXC domain formed covalent complexes with cytosine bases both in vitro and in vivo and rescued DNA methylation patterns in dnmt1⁻/⁻ embryonic stem cells (ESCs) just as efficiently as wild type Dnmt1. Interestingly, neither wild type nor ΔCXXC Dnmt1 re-methylated imprinted CpG sites of the H19a promoter in dnmt1⁻/⁻ ESCs, arguing against a role of the CXXC domain in restraining Dnmt1 methyltransferase activity on unmethylated CpG sites.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence / physiology
Animals
Cells, Cultured
CpG Islands / genetics
DNA (Cytosine-5-)-Methyltransferase 1
DNA (Cytosine-5-)-Methyltransferases / chemistry*
DNA (Cytosine-5-)-Methyltransferases / genetics
DNA (Cytosine-5-)-Methyltransferases / metabolism
DNA (Cytosine-5-)-Methyltransferases / physiology
DNA Methylation / physiology
DNA-Binding Proteins / chemistry*
DNA-Binding Proteins / genetics
DNA-Binding Proteins / metabolism
DNA-Binding Proteins / physiology
Enzyme Activation / genetics
Enzyme Activation / physiology
Humans
Mice
Mixed Function Oxygenases
Models, Molecular
Molecular Sequence Data
Mutagenesis, Site-Directed
Protein Binding / genetics
Protein Binding / physiology
Protein Structure, Tertiary / genetics
Protein Structure, Tertiary / physiology
Proto-Oncogene Proteins / chemistry*
Proto-Oncogene Proteins / genetics
Proto-Oncogene Proteins / metabolism
Proto-Oncogene Proteins / physiology
Sequence Deletion / physiology
Sequence Homology, Amino Acid
Zinc Fingers / genetics
Zinc Fingers / physiology*

Substances

DNA-Binding Proteins
Proto-Oncogene Proteins
Mixed Function Oxygenases
TET1 protein, human
DNA (Cytosine-5-)-Methyltransferase 1
DNA (Cytosine-5-)-Methyltransferases
DNMT1 protein, human
Dnmt1 protein, mouse