Question 3: Contrasting Molecular Writers Plants utilize distinct methyltransferases to maintain DNA methylation in different sequence contexts (CG, CHG, and CHH). • Task: Contrast the recruitment mechanism of MET1 with that of CMT3. Specifically, explain why CMT3 requires a "self-reinforcing loop" with H3K9me2 while MET1 does not. • Logic Challenge: If a hypothetical experiment replaced the plant’s CMT3 enzyme with a mammalian Dnmt1 (which primarily targets hemimethylated CG sites), what would be the likely effect on the silencing of transposable elements (TEs) that are typically rich in CHG methylation?

What is MET1 in plants?

The plant homolog of mammalian Dnmt1, responsible for maintaining CG methylation.

How is MET1 recruited to its targets?

It recognizes hemimethylated CG sites (where only the parental strand is methylated after replication) with the assistance of VIM1. It uses the existing methylation as a direct template.

Does MET1 require external epigenetic signals like histone marks to find its targets?

No, MET1 does not require histone marks because it uses the hemimethylated DNA template itself.

What is CMT3?

A plant-specific chromomethylase that maintains CHG methylation.

How is CMT3 recruited to its targets?

It possesses a chromodomain that binds to H3K9me2 (dimethylation of lysine 9 on histone H3).

Why does CMT3 require a "self-reinforcing loop" with H3K9me2?

Because CHG maintenance does not rely on simple recognition of hemimethylated DNA. The loop creates a feedback cycle: CMT3 binds H3K9me2 to write CHG methylation, while H3K9 methyltransferases bind methylated CHG sites to write more H3K9me2.

What is the function of the self-reinforcing loop between CMT3 and H3K9me2?

It ensures that heterochromatic regions (like transposable elements) remain stably silenced through both DNA and histone modifications.

What would happen if a plant's CMT3 enzyme were replaced with mammalian Dnmt1?

Significant loss of silencing and reactivation of transposable elements.

Why would mammalian Dnmt1 fail to maintain CHG methylation in plants?

Because Dnmt1 lacks the specialized chromodomain required to bind plant H3K9me2 marks, so it cannot participate in the self-reinforcing loop.

What type of methylation are transposable elements in plants typically rich in?

CHG methylation.

What happens to CHG methylation at TEs if CMT3 is absent or non-functional?

Progressive loss of CHG methylation during successive rounds of cell division.

What broader consequence does loss of CHG methylation have on heterochromatin?

It likely breaks the feedback loop with H3K9me2, causing heterochromatin at TE loci to decondense and become transcriptionally active.

What happens when transposable elements become transcriptionally active?

They can jump to new chromosomal locations, inducing physical DNA mutations in developmentally important genes and compromising genomic integrity over generations.

What phenotype is observed in ddm1 or cmt3 mutants regarding TEs?

The "unleashing" of TEs allows them to transpose, potentially causing mutatio