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Literature DB >> 30031306

Detecting and interpreting DNA methylation marks.

Ren Ren¹, John R Horton¹, Xing Zhang¹, Robert M Blumenthal², Xiaodong Cheng³.

Abstract

The generation, alteration, recognition, and erasure of epigenetic modifications of DNA are fundamental to controlling gene expression in mammals. These covalent DNA modifications include cytosine methylation by AdoMet-dependent methyltransferases and 5-methylcytosine oxidation by Fe(II)-dependent and α-ketoglutarate-dependent dioxygenases. Sequence-specific transcription factors are responsible for 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 5-methyluracil (thymine).

Entities: CellLine Chemical Disease Gene Mutation Species

Mesh：

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Year: 2018 PMID： 30031306 PMCID： PMC6322410 DOI： 10.1016/j.sbi.2018.06.004

Source DB: PubMed Journal: Curr Opin Struct Biol ISSN： 0959-440X Impact factor: 6.809

130 in total

1. The YTH domain is a novel RNA binding domain.

Authors: Zhaiyi Zhang; Dominik Theler; Katarzyna H Kaminska; Michael Hiller; Pierre de la Grange; Rainer Pudimat; Ilona Rafalska; Bettina Heinrich; Janusz M Bujnicki; Frédéric H-T Allain; Stefan Stamm
Journal: J Biol Chem Date: 2010-02-18 Impact factor: 5.157

2. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes.

Authors: Judith F Kribelbauer; Oleg Laptenko; Siying Chen; Gabriella D Martini; William A Freed-Pastor; Carol Prives; Richard S Mann; Harmen J Bussemaker
Journal: Cell Rep Date: 2017-06-13 Impact factor: 9.423

3. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution.

Authors: Ho Sung Rhee; B Franklin Pugh
Journal: Cell Date: 2011-12-09 Impact factor: 41.582

4. C/EBPβ (CEBPB) protein binding to the C/EBP|CRE DNA 8-mer TTGC|GTCA is inhibited by 5hmC and enhanced by 5mC, 5fC, and 5caC in the CG dinucleotide.

Authors: Syed Khund Sayeed; Jianfei Zhao; Bangalore K Sathyanarayana; Jaya Prakash Golla; Charles Vinson
Journal: Biochim Biophys Acta Date: 2015-03-13

5. WT1 recruits TET2 to regulate its target gene expression and suppress leukemia cell proliferation.

Authors: Yiping Wang; Mengtao Xiao; Xiufei Chen; Leilei Chen; Yanping Xu; Lei Lv; Pu Wang; Hui Yang; Shenghong Ma; Huaipeng Lin; Bo Jiao; Ruibao Ren; Dan Ye; Kun-Liang Guan; Yue Xiong
Journal: Mol Cell Date: 2015-01-15 Impact factor: 17.970

6. An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity.

Authors: Tom J Petty; Soheila Emamzadah; Lorenzo Costantino; Irina Petkova; Elena S Stavridi; Jeffery G Saven; Eric Vauthey; Thanos D Halazonetis
Journal: EMBO J Date: 2011-04-26 Impact factor: 11.598

7. Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.

Authors: Kyohei Arita; Mariko Ariyoshi; Hidehito Tochio; Yusuke Nakamura; Masahiro Shirakawa
Journal: Nature Date: 2008-09-03 Impact factor: 49.962

8. Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome.

Authors: Hebing Chen; Yao Tian; Wenjie Shu; Xiaochen Bo; Shengqi Wang
Journal: PLoS One Date: 2012-07-19 Impact factor: 3.240

9. Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA.

Authors: Dominik Theler; Cyril Dominguez; Markus Blatter; Julien Boudet; Frédéric H-T Allain
Journal: Nucleic Acids Res Date: 2014-11-11 Impact factor: 16.971

10. Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance.

Authors: Robert M Vaughan; Bradley M Dickson; Evan M Cornett; Joseph S Harrison; Brian Kuhlman; Scott B Rothbart
Journal: Nucleic Acids Res Date: 2018-05-18 Impact factor: 16.971

16 in total

1. Cytosine methylation of mitochondrial DNA at CpG sequences impacts transcription factor A DNA binding and transcription.

Authors: Vishantie Dostal; Mair E A Churchill
Journal: Biochim Biophys Acta Gene Regul Mech Date: 2019-02-23 Impact factor: 4.490

2. Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38.

Authors: Nicholas O Hudson; Frank G Whitby; Bethany A Buck-Koehntop
Journal: J Biol Chem Date: 2018-10-24 Impact factor: 5.157

Review 3. The Methyl-CpG-Binding Domain 2 and 3 Proteins and Formation of the Nucleosome Remodeling and Deacetylase Complex.

Authors: Gage Leighton; David C Williams
Journal: J Mol Biol Date: 2019-10-15 Impact factor: 5.469

Detecting and interpreting DNA methylation marks.

1. The YTH domain is a novel RNA binding domain.

2. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes.

3. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution.

4. C/EBPβ (CEBPB) protein binding to the C/EBP|CRE DNA 8-mer TTGC|GTCA is inhibited by 5hmC and enhanced by 5mC, 5fC, and 5caC in the CG dinucleotide.

5. WT1 recruits TET2 to regulate its target gene expression and suppress leukemia cell proliferation.

6. An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity.

7. Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.

8. Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome.

9. Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA.

10. Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance.

1. Cytosine methylation of mitochondrial DNA at CpG sequences impacts transcription factor A DNA binding and transcription.

2. Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38.

Review 3. The Methyl-CpG-Binding Domain 2 and 3 Proteins and Formation of the Nucleosome Remodeling and Deacetylase Complex.

Review 4. Detection of DNA Modifications by Sequence-Specific Transcription Factors.

5. Molecular mechanism of methyl-dependent and spatial-specific DNA recognition of c-Jun homodimer.

Review 6. The language of chromatin modification in human cancers.

Review 7. TET-dioxygenase deficiency in oncogenesis and its targeting for tumor-selective therapeutics.

Review 8. Molecular basis of transcriptional pausing, stalling, and transcription-coupled repair initiation.

9. DNA Methylation and Chromatin: Role(s) of Methyl-CpG-Binding Protein ZBTB38.

Review 10. Zinc Finger Readers of Methylated DNA.