Understanding DNA, CPG Sites, and Methylation

Dec 7, 2024

DNA and CPG Sites Lecture

DNA Bases and Pairing

  • DNA consists of four bases:
    • Cytosine (C)
    • Guanine (G)
    • Thymine (T)
    • Adenine (A)
  • Base pairing:
    • Cytosine pairs with Guanine
    • Thymine pairs with Adenine

CPG Sites

  • Definition: Regions where a cytosine is followed by a guanine in the 5' to 3' direction.
  • Connection: Cytosine connected to guanine by a phosphodiester bond (not base paired).
  • Expected Frequency: 6.25%
  • Observed Frequency in Humans: About 1%

Single Nucleotide Mutations

  • Spontaneous Deamination:
    • Unmethylated cytosine can turn into uracil.
    • Uracil is not a DNA base and is removed by uracil DNA glycosylase.
  • Methylation and Mutations:
    • Methylation at the 5 position forms 5-methylcytosine.
    • Deamination of 5-methylcytosine turns it into thymine (inefficient to repair).
    • Thymine DNA glycosylase (TDG) attempts to correct TG mismatches.
    • Leads to CG suppression due to mutation to TG over time in vertebrates.

CG Suppression

  • Vertebrates: Low observed frequency of CPGs due to methylation.
  • Invertebrates (e.g., Drosophila, C. elegans): Expected frequency due to little/no methylation.

CPG Islands

  • Definition: Regions of at least 200 base pairs with GC percentage > 50% and observed/expected CPG ratio > 60%.
  • Characteristics: Tend to be unmethylated and linked to active genes.

Methylation and Gene Expression

  • Inactive Genes: Methylation leads to CG suppression over time.
  • Active Genes: CPG islands are protected, acting as promoters initiating gene transcription.
  • Promoter Regions: 70% of human promoters are CPG-rich.

Development and Methylation

  • During early development, CPG island promoters must be active during de novo methylation waves.
  • X Chromosome Inactivation: In female eutherian mammals, methylation of CPG islands results in gene silencing.

Implications for Cancer

  • Cancer Tissues: Exhibit different methylation patterns.
  • Hypermethylation in CPG island promoters can lead to loss of gene expression, including DNA repair genes, promoting cancer.

CPG Islands as Promoters

  • Characteristics: Often lack long-range sequence conservation, sometimes missing core elements like the TATA box.
  • Chromatin Structure: High levels of acetylation in H3 and H4 histones, depleted H1, indicating transcriptional activity.

Note: This summary is based on a detailed lecture explaining DNA structure, mutations, and the significance of CPG sites and methylation in gene expression and suppression, particularly in relation to vertebrate DNA and cancer development.

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