DNA Methylation: Structure, Maintenance, and Biological Function

DNA methylation is a primary epigenetic mechanism that involves the chemical modification of the DNA molecule.
The modification consists of adding a methyl group–defined as one carbon atom bonded to three hydrogen atoms ( $CH_3$ )–to the DNA sequence.
Methyl groups are ubiquitous in cellular biology and are used in various contexts:
- Marking and modifying DNA.
- Modifying RNA molecules.
- Marking proteins for various regulatory functions.
In the context of this study, the focus is specifically on the addition of these groups to DNA to regulate genomic activity.

Target Site: Epigenetic DNA methylation specifically occurs on CpG dinucleotides.
Terminology: A "dinucleotide" refers to a sequence of two nucleotides. In this case, a Cytosine ( $C$ ) followed immediately by a Guanine ( $G$ ).
The Role of the "p": In the term "CpG," the "p" represents the phosphate backbone that chemically connects the Cytosine and Guanine nucleotides within the same DNA strand.
Symmetry of Methylation:
- DNA methylation is typically present on both strands of the DNA double helix.
- Because DNA strands are antiparallel and complementary, a $5'-CpG-3'$ sequence on the top strand will correspond to a $5'-CpG-3'$ sequence on the bottom strand when read in the standard orientation.
- Thus, if the Cytosine on the top strand is methylated, the corresponding Cytosine on the bottom strand is usually methylated as well. This is referred to as being "fully methylated."

The transfer of methyl groups to DNA is catalyzed by a family of enzymes known as DNA Methyltransferases ( $DNMT$ s).
De Novo Methyltransferases ( $DNMT3a$ and $DNMT3b$ ):
- The term "de novo" means "of new."
- These enzymes are responsible for establishing and laying down new patterns of DNA methylation where none previously existed.
Maintenance Methyltransferase ( $DNMT1$ ):
- $DNMT1$ is responsible for maintaining and copying existing methylation patterns during cell division (mitosis).
- It ensures that the epigenetic information is passed faithfully from the parent cell to the daughter cells.

The Replication Problem: When a cell undergoes DNA replication, DNA polymerase synthesize new strands based on the template. However, DNA polymerase only recognizes standard nucleotide base pairing ( $A$ , $T$ , $C$ , $G$ ) and is incapable of "seeing" or copying the methyl groups from the parent strand to the new strand.
Hemimethylated DNA: After replication, the resulting DNA is "hemimethylated" ( $\text{hemi} = \text{half}$ ). This means the parent template strand retains its methyl groups, but the newly synthesized daughter strand is unmethylated.
The Role of $DNMT1$ :
1. $DNMT1$ has a high affinity for binding to hemimethylated DNA.
2. When $DNMT1$ binds to these sites, it tracks along the DNA and undergoes a conformational change that activates its methyltransferase ability.
3. It then methylates the Cytosine on the second (new) strand.
The Metaphor of the "Unhappiest Enzyme": $DNMT1$ is described as "unhappy" because it seeks out hemimethylated sites, but the very act of binding to them and performing its function converts the site into a fully methylated one. Once the site is fully methylated, $DNMT1$ loses its affinity for it and moves off (or "flies away"), making it a self-displacing enzyme that constantly changes its environment to a state it no longer prefers.

Gene Silencing: DNA methylation generally occurs at the gene promoter, which is the sequence at the start of a gene that regulates its activity.
Effect on Transcription:
- Active/Open Promoters: When unmethylated, promoters allow transcription factors to bind and initiate the expression of RNA.
- Methylated Promoters: The presence of methyl groups prevents transcription factors from binding to the DNA. Consequently, the gene is switched off and not expressed.
Crucial Biological Processes:
- Tissue Differentiation: As an embryo develops, cells must differentiate into specific tissues. Methylation facilitates this by switching off genes that are not required for a specific cell type's function.
- X Chromosome Inactivation: In females, one of the two X chromosomes is largely silenced via DNA methylation.
  - Caveat: Certain regions, such as the pseudoautosomal regions and specific "escapee" genes, remain unmethylated and active.
- Developmental Phases: Methylation patterns are reset and laid down during gametogenesis (the formation of egg and sperm) and early embryonic development.
- Pathology and Aging: Methylation patterns are dynamic and can change during the aging process. Significant abnormalities in methylation patterns are a hallmark of certain diseases, most notably cancer.

Conceptual Question: Why is it vital for daughter cells to maintain the exact same epigenetic patterns (DNA methylation) as their parent cell after mitosis?
Further Study: This question, regarding the importance of epigenetic consistency in daughter cells, will be the focus of the upcoming drop-in session discussion.