An Adversarial DNA N⁶-Methyladenine-Sensor Network Preserves Polycomb Silencing

Area of Science:

• Epigenetics
• Molecular Biology
• Genomics

Background:

• DNA methylation, specifically N6-methyladenine (6mA), is prevalent in bacteria and phage and present in mammalian genomes.
• The functional role of 6mA in mammals remains largely uncharacterized.

Purpose of the Study:

• To investigate the enzymes responsible for 6mA deposition and removal in mammals.
• To elucidate the functional consequences of 6mA accumulation and depletion in mammalian systems.
• To identify proteins that interact with 6mA and their role in epigenetic regulation.

Main Methods:

• Enzymatic assays to identify Mettl4 as the methyltransferase and Alkbh4 as the dioxygenase for 6mA.
• Analysis of gene expression and developmental phenotypes in Mettl4-deficient mice.
• Identification and characterization of 6mA sensor domains in MPND and ASXL1.
• Investigation of the interaction between 6mA and histone modification H2A-K119Ub via the Polycomb repressive deubiquitinase (PR-DUB) complex.

Main Results:

• Mettl4 deposits 6mA, while Alkbh4 removes it, correlating 6mA accumulation with transcriptional silencing.
• Mice lacking Mettl4 exhibit depleted 6mA, sublethality, and craniofacial abnormalities.
• MPND and ASXL1 contain 6mA sensor domains that remove H2A-K119Ub.
• Mettl4-mediated 6mA deposition leads to the degradation of MPND and ASXL1, maintaining H2A-K119Ub levels.

Conclusions:

• A native mammalian 6mA network exists, involving Mettl4 and Alkbh4, that regulates gene silencing.
• This network utilizes sensor proteins (MPND, ASXL1) to link 6mA to histone modification (H2A-K119Ub) and Polycomb-mediated repression.
• The findings reveal an adversarial architecture preserving Polycomb silencing through dynamic regulation of 6mA and H2A-K119Ub.