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Literature DB >> 26152719

The Mechanisms of Generation, Recognition, and Erasure of DNA 5-Methylcytosine and Thymine Oxidations.

Hideharu Hashimoto¹, Xing Zhang¹, Paula M Vertino², Xiaodong Cheng³.

Abstract

One of the most fundamental questions in the control of gene expression in mammals is how the patterns of epigenetic modifications of DNA are generated, recognized, and erased. This includes covalent cytosine methylation of DNA and its associated oxidation states. An array of AdoMet-dependent methyltransferases, Fe(II)- and α-ketoglutarate-dependent dioxygenases, base excision glycosylases, and sequence-specific transcription factors is responsible for changing, maintaining, and interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases 5-methylcytosine and thymine (5-methyluracil).

Entities: Chemical

Keywords: DNA 5mC oxidation; DNA demethylation; DNA enzyme; DNA methylation; DNA methyltransferase; DNA-binding protein; DNA-protein interaction; Tet dioxygenases; base excision DNA glycosylases; modification-dependent and sequence-specific transcription factors; transcription factor

Mesh：

Substances：

Year: 2015 PMID： 26152719 PMCID： PMC4543634 DOI： 10.1074/jbc.R115.656884

Source DB: PubMed Journal: J Biol Chem ISSN： 0021-9258 Impact factor: 5.157

99 in total

Review 1. The discovery of histone demethylases.

Authors: Yujiang Geno Shi; Yuichi Tsukada
Journal: Cold Spring Harb Perspect Biol Date: 2013-09-01 Impact factor: 10.005

2. N6-methyladenine DNA modification in Drosophila.

Authors: Guoqiang Zhang; Hua Huang; Di Liu; Ying Cheng; Xiaoling Liu; Wenxin Zhang; Ruichuan Yin; Dapeng Zhang; Peng Zhang; Jianzhao Liu; Chaoyi Li; Baodong Liu; Yuewan Luo; Yuanxiang Zhu; Ning Zhang; Shunmin He; Chuan He; Hailin Wang; Dahua Chen
Journal: Cell Date: 2015-04-30 Impact factor: 41.582

3. An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence.

Authors: Yiwei Liu; Hidehiro Toh; Hiroyuki Sasaki; Xing Zhang; Xiaodong Cheng
Journal: Genes Dev Date: 2012-10-11 Impact factor: 11.361

4. Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation.

Authors: Lulu Hu; Ze Li; Jingdong Cheng; Qinhui Rao; Wei Gong; Mengjie Liu; Yujiang Geno Shi; Jiayu Zhu; Ping Wang; Yanhui Xu
Journal: Cell Date: 2013-12-05 Impact factor: 41.582

5. UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.

Authors: Hideharu Hashimoto; John R Horton; Xing Zhang; Xiaodong Cheng
Journal: Epigenetics Date: 2009-01-10 Impact factor: 4.528

6. Kinetic and catalytic mechanism of HhaI methyltransferase.

Authors: J C Wu; D V Santi
Journal: J Biol Chem Date: 1987-04-05 Impact factor: 5.157

Review 7. A common mode of recognition for methylated CpG.

Authors: Yiwei Liu; Xing Zhang; Robert M Blumenthal; Xiaodong Cheng
Journal: Trends Biochem Sci Date: 2013-01-23 Impact factor: 13.807

8. 5-Hydroxymethylcytosine plays a critical role in glioblastomagenesis by recruiting the CHTOP-methylosome complex.

Authors: Hiroki Takai; Koji Masuda; Tomohiro Sato; Yuriko Sakaguchi; Takeo Suzuki; Tsutomu Suzuki; Ryo Koyama-Nasu; Yukiko Nasu-Nishimura; Yuki Katou; Haruo Ogawa; Yasuyuki Morishita; Hiroko Kozuka-Hata; Masaaki Oyama; Tomoki Todo; Yasushi Ino; Akitake Mukasa; Nobuhito Saito; Chikashi Toyoshima; Katsuhiko Shirahige; Tetsu Akiyama
Journal: Cell Rep Date: 2014-10-02 Impact factor: 9.423

9. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase.

Authors: Zhizhong Gong; Teresa Morales-Ruiz; Rafael R Ariza; Teresa Roldán-Arjona; Lisa David; Jian Kang Zhu
Journal: Cell Date: 2002-12-13 Impact factor: 41.582

10. An AP endonuclease functions in active DNA demethylation and gene imprinting in Arabidopsis [corrected].

Authors: Yan Li; Dolores Córdoba-Cañero; Weiqiang Qian; Xiaohong Zhu; Kai Tang; Huiming Zhang; Rafael R Ariza; Teresa Roldán-Arjona; Jian-Kang Zhu
Journal: PLoS Genet Date: 2015-01-08 Impact factor: 5.917

21 in total

Review 1. Introduction: Metals in Biology: α-Ketoglutarate/Iron-Dependent Dioxygenases.

Authors: F Peter Guengerich
Journal: J Biol Chem Date: 2015-07-07 Impact factor: 5.157

2. 5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4.

Authors: Syed Khund-Sayeed; Ximiao He; Timothy Holzberg; Jun Wang; Divya Rajagopal; Shriyash Upadhyay; Stewart R Durell; Sanjit Mukherjee; Matthew T Weirauch; Robert Rose; Charles Vinson
Journal: Integr Biol (Camb) Date: 2016-08-03 Impact factor: 2.192

The Mechanisms of Generation, Recognition, and Erasure of DNA 5-Methylcytosine and Thymine Oxidations.

Review 1. The discovery of histone demethylases.

2. N6-methyladenine DNA modification in Drosophila.

3. An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence.

4. Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation.

5. UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.

6. Kinetic and catalytic mechanism of HhaI methyltransferase.

Review 7. A common mode of recognition for methylated CpG.

8. 5-Hydroxymethylcytosine plays a critical role in glioblastomagenesis by recruiting the CHTOP-methylosome complex.

9. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase.

10. An AP endonuclease functions in active DNA demethylation and gene imprinting in Arabidopsis [corrected].

Review 1. Introduction: Metals in Biology: α-Ketoglutarate/Iron-Dependent Dioxygenases.

2. 5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4.

Review 3. DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications.

Review 4. Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors.

5. Characterization of How DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins.

Review 6. Epithelial-mesenchymal transition: Insights into nickel-induced lung diseases.

Review 7. Naturally occurring modified ribonucleosides.

8. Distinctive Klf4 mutants determine preference for DNA methylation status.

9. Absence of MeCP2 binding to non-methylated GT-rich sequences in vivo.

Review 10. From Genetics to Epigenetics: New Perspectives in Tourette Syndrome Research.