Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance

Area of Science:

• Molecular Biology
• Epigenetics
• Structural Biology

Background:

• Epigenetic mechanisms are crucial for long-term heritable changes in gene expression.
• Cryptococcus neoformans exhibits epigenetic evolution over millions of years.
• DNMT5 is a novel maintenance cytosine methyltransferase in fungi, unique in its ATP dependence and hemimethyl-DNA specificity.

Purpose of the Study:

• To elucidate the novel properties and mechanism of DNMT5.
• To understand how DNMT5 achieves high fidelity in DNA methylation.
• To investigate the role of the SNF2 ATPase domain in DNMT5 function.

Main Methods:

• Cryo-electron microscopy (cryo-EM) structure determination of CnDNMT5 in three functional states.
• Biochemical assays to analyze enzyme activity and DNA binding specificity.

Main Results:

• Cryo-EM structures revealed an allosteric cascade initiated by hemimethylated DNA binding.
• The SNF2 ATPase domain undergoes significant conformational changes, activating the enzyme.
• ATP binding triggers catalytic pocket reconfiguration for methylation and ejects unmethylated DNA, ensuring fidelity.

Conclusions:

• DNMT5 utilizes an unprecedented chaperone-like mechanism involving SNF2 ATPase domain remodeling.
• Energy-dependent structural changes enable precise DNA methylation and epigenetic memory maintenance.
• This study provides insights into the molecular basis of epigenetic inheritance in fungi.