Preferential 5-Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein.
Tet (ten-eleven translocation) family proteins oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC), and are suggested to be involved in the active DNA demethylation pathway. In this study, we reconstituted positioned mononucleosomes using CpG-methylated 382 bp DNA containing the Widom 601 sequence and recombinant histone octamer, and subjected the nucleosome to treatment with Tet1 protein. The sites of oxidized methylcytosine were identified by bisulfite sequencing. We found that, for the oxidation reaction, Tet1 protein prefers mCs located in the linker region of the nucleosome compared with those located in the core region.
Department of Chemistry, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8502, Japan.
Seiichiro
S
Kizaki
Department of Chemistry, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8502, Japan.
Tingting
T
Zou
Department of Chemistry, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8502, Japan.
Yue
Y
Li
Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8501, Japan.
Yong-Woon
YW
Han
Department of Robotics, Graduate School of Engineering, Tohoku University, Aramaki aza Aoba 6-6-01M2-519, Aoba-ku, Sendai, 980-8579, Japan.
Yuki
Y
Suzuki
Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8501, Japan.
Yoshie
Y
Harada
Department of Chemistry, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8502, Japan. hs@kuchem.kyoto-u.ac.jp.|Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8501, Japan. hs@kuchem.kyoto-u.ac.jp.
Hiroshi
H
Sugiyama
D044503:5-Methylcytosine / Q000031:analogs & derivatives* / Q000737:chemistry*; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D004247:DNA / Q000378:metabolism*; D019175:DNA Methylation; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism; D010084:Oxidation-Reduction
C560973:5-formylcytosine; D009707:Nucleosomes; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; C000618843:5-carboxycytosine; D003596:Cytosine; D004247:DNA
AFM imaging; DNA; cytosine; nucleosomes; proteins