Epigenetics involves modifications to DNA that alter gene activity without changing the DNA sequence. One of the most studied of these is DNA methylation, a process where a methyl group is added to a DNA molecule, influencing how genes are expressed. Among the different types of DNA methylation, CHH methylation is a particularly dynamic form. It is especially prominent within the plant kingdom, where it helps maintain the stability of the genome.
Understanding the DNA Methylation Contexts
The addition of a methyl group to a cytosine (C) base occurs within specific DNA sequence contexts. In plants, there are three primary contexts: CG, CHG, and CHH. In these sequences, G stands for guanine, and H represents any nucleotide base except guanine (adenine, cytosine, or thymine).
The sequence contexts structurally affect how methylation is maintained. The CG and CHG contexts are symmetrical, meaning the complementary DNA strand has a matching sequence that can serve as a template. This symmetry allows established methylation patterns to be easily copied to the new DNA strand during DNA replication.
The CHH context, however, is asymmetrical. There is no corresponding cytosine on the opposite strand to guide methylation after replication. This means CHH methylation cannot be passively maintained. Instead, it must be actively established after each round of cell division through a process known as de novo methylation.
The Mechanism of CHH Methylation
The primary mechanism for establishing CHH methylation in plants is the RNA-directed DNA methylation (RdDM) pathway. The pathway identifies and silences specific DNA sequences, particularly repetitive or foreign ones. The process begins when the cell transcribes unwanted DNA sequences, such as those from invasive genetic elements, into RNA molecules.
An enzyme named Dicer-like 3 (DCL3) processes these RNA transcripts, cutting them into small fragments called small interfering RNAs (siRNAs). These siRNAs act as guide molecules that specify which part of the genome to target. Each siRNA is loaded onto an Argonaute (AGO) protein, most commonly AGO4, to form a silencing complex.
The siRNA-AGO complex scans the cell’s nucleus, searching for matching RNA transcripts being produced from the target DNA location. These transcripts are made by an enzyme called RNA Polymerase V (Pol V). By binding to these transcripts, the complex is anchored to the precise DNA location that matches the siRNA.
Once anchored, the AGO protein recruits the final enzyme in the pathway: Domains Rearranged Methyltransferase 2 (DRM2). DRM2 adds a methyl group to cytosine bases within the CHH context at the targeted DNA sequence. This de novo methylation marks the sequence for silencing, which prevents the gene or element from being expressed.
Biological Functions of CHH Methylation
A primary function of CHH methylation in plants is silencing transposable elements (TEs). TEs are segments of DNA, or “jumping genes,” that can change their position within the genome. If unregulated, their movement can disrupt gene function, cause chromosomal rearrangements, and lead to genomic instability. The RdDM pathway uses CHH methylation to suppress TE activity, keeping them locked in place.
Beyond controlling TEs, CHH methylation plays a role in gene regulation. Methylating regions adjacent to genes can influence their expression, often leading to silencing. This function is not static and changes throughout a plant’s life. For example, dynamic CHH methylation patterns are observed during developmental stages like seed and fruit development, helping to time gene expression.
CHH methylation is also involved in a plant’s environmental response. Changes in its patterns have been observed in plants under stress, helping them adapt gene expression to challenging conditions. In some cases, these epigenetic changes can be passed down through generations, providing a form of heritable adaptation.
CHH Methylation in Animals
CHH methylation is not exclusive to plants and also occurs in animals, including mammals, though its distribution is different. In mammalian genomes, most methylation occurs in the CG context. CHH methylation is present at much lower levels but is concentrated in specific cell types and at particular developmental stages.
High levels of CHH methylation are found in cells with significant genomic reorganization or activity, such as neurons and early embryonic cells. In the brain, CHH methylation accumulates as neurons mature and may play a part in learning and memory by helping to fine-tune gene expression. During early development, it appears in pluripotent stem cells and is regulated as they differentiate into various tissues.
The mechanisms establishing CHH methylation in animals are distinct from the plant-based RdDM pathway. Although some components may be shared, the machinery and regulation have evolved separately. The precise functions of CHH methylation in animals are still an active area of scientific investigation, as researchers work to understand its contribution to development and cellular identity.