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Sequence-specific recognition of methylated DNA by human zinc-finger proteins.

Sasai N, Nakao M, Defossez PA - Nucleic Acids Res. (2010)

Bottom Line: The last three proteins can bind either methylated DNA or unmethylated consensus sequences; how this is achieved is largely unclear.Here, we report that the human zinc-finger proteins Kaiso, ZBTB4 and ZBTB38 can bind methylated DNA in a sequence-specific manner, and that they may use a mode of binding common to other zinc-finger proteins.This suggests that many other sequence-specific methyl binding proteins may exist.

View Article: PubMed Central - PubMed

Affiliation: CNRS UMR7216, Université Paris-Diderot, Paris, France.

ABSTRACT
DNA methylation is an essential epigenetic mark. Three classes of mammalian proteins recognize methylated DNA: MBD proteins, SRA proteins and the zinc-finger proteins Kaiso, ZBTB4 and ZBTB38. The last three proteins can bind either methylated DNA or unmethylated consensus sequences; how this is achieved is largely unclear. Here, we report that the human zinc-finger proteins Kaiso, ZBTB4 and ZBTB38 can bind methylated DNA in a sequence-specific manner, and that they may use a mode of binding common to other zinc-finger proteins. This suggests that many other sequence-specific methyl binding proteins may exist.

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Summary of the binding data and interpretation. (A) Two components contribute to the binding of ZBTB4 to an optimal site: the E350 residue is necessary for recognition of the methylated cytosine (black lollipop), while other positions in the zinc fingers recognize the flanking sequences of methylated DNA. (B) Because its affinity for methylated cytosine is high, ZBTB4 can bind methylated DNA even if the flanking sequence is suboptimal. (C) ZBTB4 can also recognize thymine instead of methylated cytosine, but with lower affinity. The E350A mutant of ZBTB4 has lost affinity for methylated cytosine, but maintains the recognition of flanking sequences (D). It cannot bind to methylated DNA lacking the optimal flanking sequence (E), but still binds the consensus unmethylated target (F).
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Figure 5: Summary of the binding data and interpretation. (A) Two components contribute to the binding of ZBTB4 to an optimal site: the E350 residue is necessary for recognition of the methylated cytosine (black lollipop), while other positions in the zinc fingers recognize the flanking sequences of methylated DNA. (B) Because its affinity for methylated cytosine is high, ZBTB4 can bind methylated DNA even if the flanking sequence is suboptimal. (C) ZBTB4 can also recognize thymine instead of methylated cytosine, but with lower affinity. The E350A mutant of ZBTB4 has lost affinity for methylated cytosine, but maintains the recognition of flanking sequences (D). It cannot bind to methylated DNA lacking the optimal flanking sequence (E), but still binds the consensus unmethylated target (F).

Mentions: Mutant E350A of ZBTB4 retained a weak capacity to bind the meZ4BS (Figure 4C), but we found that mutating the nucleotides flanking the methylated CpG completely abolished binding (Figure 4D). Collectively, these data argue that residue E350 of ZBTB4 is critical for recognizing methylated cytosine when bound to its high affinity binding site, and that ZBTB4 simultaneously recognizes flanking sequences via several residues in zinc fingers (Figure 5).Figure 5.


Sequence-specific recognition of methylated DNA by human zinc-finger proteins.

Sasai N, Nakao M, Defossez PA - Nucleic Acids Res. (2010)

Summary of the binding data and interpretation. (A) Two components contribute to the binding of ZBTB4 to an optimal site: the E350 residue is necessary for recognition of the methylated cytosine (black lollipop), while other positions in the zinc fingers recognize the flanking sequences of methylated DNA. (B) Because its affinity for methylated cytosine is high, ZBTB4 can bind methylated DNA even if the flanking sequence is suboptimal. (C) ZBTB4 can also recognize thymine instead of methylated cytosine, but with lower affinity. The E350A mutant of ZBTB4 has lost affinity for methylated cytosine, but maintains the recognition of flanking sequences (D). It cannot bind to methylated DNA lacking the optimal flanking sequence (E), but still binds the consensus unmethylated target (F).
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Related In: Results  -  Collection

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Figure 5: Summary of the binding data and interpretation. (A) Two components contribute to the binding of ZBTB4 to an optimal site: the E350 residue is necessary for recognition of the methylated cytosine (black lollipop), while other positions in the zinc fingers recognize the flanking sequences of methylated DNA. (B) Because its affinity for methylated cytosine is high, ZBTB4 can bind methylated DNA even if the flanking sequence is suboptimal. (C) ZBTB4 can also recognize thymine instead of methylated cytosine, but with lower affinity. The E350A mutant of ZBTB4 has lost affinity for methylated cytosine, but maintains the recognition of flanking sequences (D). It cannot bind to methylated DNA lacking the optimal flanking sequence (E), but still binds the consensus unmethylated target (F).
Mentions: Mutant E350A of ZBTB4 retained a weak capacity to bind the meZ4BS (Figure 4C), but we found that mutating the nucleotides flanking the methylated CpG completely abolished binding (Figure 4D). Collectively, these data argue that residue E350 of ZBTB4 is critical for recognizing methylated cytosine when bound to its high affinity binding site, and that ZBTB4 simultaneously recognizes flanking sequences via several residues in zinc fingers (Figure 5).Figure 5.

Bottom Line: The last three proteins can bind either methylated DNA or unmethylated consensus sequences; how this is achieved is largely unclear.Here, we report that the human zinc-finger proteins Kaiso, ZBTB4 and ZBTB38 can bind methylated DNA in a sequence-specific manner, and that they may use a mode of binding common to other zinc-finger proteins.This suggests that many other sequence-specific methyl binding proteins may exist.

View Article: PubMed Central - PubMed

Affiliation: CNRS UMR7216, Université Paris-Diderot, Paris, France.

ABSTRACT
DNA methylation is an essential epigenetic mark. Three classes of mammalian proteins recognize methylated DNA: MBD proteins, SRA proteins and the zinc-finger proteins Kaiso, ZBTB4 and ZBTB38. The last three proteins can bind either methylated DNA or unmethylated consensus sequences; how this is achieved is largely unclear. Here, we report that the human zinc-finger proteins Kaiso, ZBTB4 and ZBTB38 can bind methylated DNA in a sequence-specific manner, and that they may use a mode of binding common to other zinc-finger proteins. This suggests that many other sequence-specific methyl binding proteins may exist.

Show MeSH