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Literature DB >> 23352388

A common mode of recognition for methylated CpG.

Yiwei Liu¹, Xing Zhang, Robert M Blumenthal, Xiaodong Cheng.

Abstract

Much is known about vertebrate DNA methylation, however it is not known how methylated CpG within particular sequences is recognized. Two recent structures of C2H2 zinc finger (ZnF) proteins in complex with methylated DNA reveal a common recognition mode for 5-methylcytosine (5mC) that involves a 5mC-Arg-G triad. In the two ZnF proteins, an arginine that precedes the first Zn-binding histidine (RH motif) can interact with a 5mCpG or TpG dinucleotide. Among a family of >300 human Krüppel-associated box (KRAB) domain containing ZnF proteins examined, two-thirds contained at least one ZnF that included an RH motif. We propose that the RH-ZnF motifs provide specificity for 5mCpG, whereas the neighboring Zn fingers recognize the surrounding DNA sequence context.

Entities: Chemical Disease Gene Mutation Species

Mesh：

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Year: 2013 PMID： 23352388 PMCID： PMC3608759 DOI： 10.1016/j.tibs.2012.12.005

Source DB: PubMed Journal: Trends Biochem Sci ISSN： 0968-0004 Impact factor: 13.807

54 in total

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Journal: Genes Dev Date: 2001-07-01 Impact factor: 11.361

3. The p120(ctn)-binding partner Kaiso is a bi-modal DNA-binding protein that recognizes both a sequence-specific consensus and methylated CpG dinucleotides.

Authors: Juliet M Daniel; Christopher M Spring; Howard C Crawford; Albert B Reynolds; Akeel Baig
Journal: Nucleic Acids Res Date: 2002-07-01 Impact factor: 16.971

4. Recognition of 5'-YpG-3' sequences by coupled stacking/hydrogen bonding interactions with amino acid residues.

Authors: Jason S Lamoureux; Jason T Maynes; J N Mark Glover
Journal: J Mol Biol Date: 2004-01-09 Impact factor: 5.469

5. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases.

Authors: M Okano; S Xie; E Li
Journal: Nat Genet Date: 1998-07 Impact factor: 38.330

Review 6. SET domain proteins modulate chromatin domains in eu- and heterochromatin.

Authors: T Jenuwein; G Laible; R Dorn; G Reuter
Journal: Cell Mol Life Sci Date: 1998-01 Impact factor: 9.261

7. 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

8. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases.

Authors: T Bestor; A Laudano; R Mattaliano; V Ingram
Journal: J Mol Biol Date: 1988-10-20 Impact factor: 5.469

9. Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA.

Authors: I Ohki; N Shimotake; N Fujita; J Jee; T Ikegami; M Nakao; M Shirakawa
Journal: Cell Date: 2001-05-18 Impact factor: 41.582

10. Isolation and characterization of a novel zinc-finger protein with transcription repressor activity.

Authors: A J Williams; L M Khachigian; T Shows; T Collins
Journal: J Biol Chem Date: 1995-09-22 Impact factor: 5.157

51 in total

1. Common DNA methylation alterations in multiple brain regions in autism.

Authors: C Ladd-Acosta; K D Hansen; E Briem; M D Fallin; W E Kaufmann; A P Feinberg
Journal: Mol Psychiatry Date: 2013-09-03 Impact factor: 15.992

2. A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.

Authors: Evgenia N Nikolova; Robyn L Stanfield; H Jane Dyson; Peter E Wright
Journal: Biochemistry Date: 2020-05-12 Impact factor: 3.162

3. 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

A common mode of recognition for methylated CpG.

Review 1. DNA recognition by Cys2His2 zinc finger proteins.

2. The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor.

3. The p120(ctn)-binding partner Kaiso is a bi-modal DNA-binding protein that recognizes both a sequence-specific consensus and methylated CpG dinucleotides.

4. Recognition of 5'-YpG-3' sequences by coupled stacking/hydrogen bonding interactions with amino acid residues.

5. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases.

Review 6. SET domain proteins modulate chromatin domains in eu- and heterochromatin.

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

8. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases.

9. Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA.

10. Isolation and characterization of a novel zinc-finger protein with transcription repressor activity.

1. Common DNA methylation alterations in multiple brain regions in autism.

2. A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.

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

Review 4. Cross-talk between site-specific transcription factors and DNA methylation states.

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

Review 6. The Mechanisms of Generation, Recognition, and Erasure of DNA 5-Methylcytosine and Thymine Oxidations.

Review 7. Detecting and interpreting DNA methylation marks.

8. DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins.

9. CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso.

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