Investigating recognition and sequence preference of Kaiso interactions with methylated DNA

Zinc finger (ZF) protein Kaiso is a methyl CpG binding protein that recognize the methylated CpG (mCpG) sites in DNA and mediates the transcription regulation. The C-terminal C2H2 ZF domains of Kaiso are involved in recognition of two mCpG sites in DNA. Study of the molecular mechanism of the Kaiso interactions with methylated DNA (meDNA) is crucial to understand the role of Kaiso in recognition of the mCpG sites and translation of methylation signal into downstream transcription outcomes. Structural investigation on sequence-specific interactions of Kaiso with meDNA sequences are still lacking. In this work, we performed molecular dynamics simulations to investigate recognition mechanism and binding of Kaiso to two distinct meDNA sequences, MeCG2 and MeECad. Our results reveal that Kaiso has sequence preference in its interactions to meDNA and interactions of the crucial residue E535 in Kaiso is different for the two distinct meDNA sequences. Kaiso showed an enhanced binding to MeECad sequence with 5’- flanking C/G base pair as compared to MeCG2 sequence with 5’- flanking T/A pair. Our results also show that, in addition to the core mCGmCG site, the flanking nucleotides are also important for the recognition of meDNA by Kaiso and formation of the stable Kaiso-MeDNA complex.