DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

Sabrina Adam,Nicole E Radde,Maximilian Hornisch,Pavel Bashtrykov,Hiwot Anteneh,Jiuwei Lu,Albert Jeltsch,Jikui Song,Vincent Wagner

doi:10.1038/s41467-020-17531-8

Sabrina Adam, Nicole E Radde + Show 7 more

Open Access

https://doi.org/10.1038/s41467-020-17531-8

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Abstract

DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. Here, we systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. Moreover, flanking sequences influence the conformational dynamics of the active site and cofactor binding pocket. Importantly, we show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. Overall, our findings uncover the intricate interplay between CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylation.

Highlights

DNA methylation maintenance by DNA methyltransferase 1 (DNMT1) is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive
It has even been demonstrated that alteration of the flanking sequence preferences of DNMT3A provides a key mechanistic basis for cancer promoting effects of the somatic DNMT3A R882H mutation, which is frequently observed in acute myeloid leukemia (AML)[23,24]
Kinetic studies have revealed that DNMT1 has a processive reaction mechanism, in which it methylates many hemimethylated CpG sites without dissociating from the DNA16,26,27

Summary

Introduction

DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. We systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. We show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. The activity of DNMT1 in maintenance DNA methylation is supported by its substrate preference for hemimethylated CpG sites, as well as a high level of enzymatic processivity[14,15,16,17,18]. We show that the flanking sequence profiles of DNMT1 are highly correlated with genomic methylation patterns in human and mouse cells, suggesting that flanking sequence preferences of DNMT1 shape genomewide DNA methylation patterns

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