A 5′-Flanking C/G Pair at the Core Region Enhances the Recognition and Binding of Kaiso to Methylated DNA

Methyl CpG binding proteins (MBPs) are transcription
factors that
recognize the methylated CpG sites in DNA and mediate the DNA methylation
signal into various downstream cellular processes. The C2H2 zinc finger
(ZF) protein, Kaiso, also an MBP, preferentially binds to two symmetrically
methylated CpG sites in DNA sequences via C-terminal C2H2 ZF domains
and mediates the transcription regulation process. Investigation of
the molecular mechanism of the recognition of methylated DNA (meDNA)
by Kaiso is important to understand how this protein reads and translates
this methylation signal into downstream transcription outcomes. Despite
previous studies in Kaiso-meDNA interactions, detailed structural
investigations on the sequence-specific interaction of Kaiso with
the meDNA sequence are still lacking. In this work, we used molecular
modeling and molecular dynamics (MD) simulation-based computational
approaches to investigate the recognition of various methylated DNA
sequences by Kaiso. Our MD simulation results show that the Kaiso-meDNA
interaction is sequence specific. The recognition of meDNA by Kaiso
is enhanced in the MeECad sequence compared to the MeCG2 sequence.
Compared to the 5′-flanking T/A pair in MeCG2, both MeCG2_mutCG
and MeECad sequences show that a C/G base pair allows GLU535 of Kaiso
to preferably recognize and bind the core mCpG site. The core mCGmCG
site is crucial for the recognition process and formation of a stable
complex. Our results reveal that the 5′-flanking nucleotides
are also important for the enhanced binding and recognition of methylated
sites.