Epigenetics

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Epigenetics

• Epigenetics, inheritance from cell to cell or
  organism to organism by changes in chromatin /or
  DNA but not in the DNA sequence
• There are two forms of epigenetics
• In vertebrates and higher plants methylation of
  C residues of DNA
• In eukaryotes inherited changes in chromatin
  structure
• includes modification of chromatin proteins
• alterations in histone content
• changes involving which proteins are stably
  incorp. into chromatin

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Human DNA Methylation
NH2
NH2
CH3
N
N
N
N
O
O
cytosine C 95.5 - 96.5
5-methylcytosine m5C 3.5 - 4.5
CG dinucleotide ? m5CG dinucleotide CpG
m5CpG
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DNA Methylation in Mammals

• 4 genes encode mammalian DNA methyltransferases
• DNMT1 (main enzyme for maintaining methylation)
• DNMT2 (low enzymatic activity but stimulates
  other enzymes)
• DNMT3A (especially important for de novo
  methylation)
• DNMT3B (especially important for de novo
  methylation)
• De novo vs. maintenance methylation (see handout)
• Loss of most DNA methylation is lethal in mice
• When mostly unmethylated, active promoter regions
  become methylated, downregulation of
  transcription usually results
• Some of tissue-specific differences in DNA
  methylation help maintain or initiate
  transcription differences
• m5C residues are hotspots for mutation (see
  handout)

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Patterns of Mammalian DNA Methylation

• CpG-rich DNA sequences are often unmethylated
  
• Called CpG islands
• CpG islands often overlap promoters
• CpG islands usually unmethylated
• Promoter methylation usually represses gene
  expression
• In cancers, some promoters are turned off by
  methylation

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DNA Methylation Silencing Normal Development

• Some Genes With Strong Evidence from Studies of
  Tissues
• X-linked ? efficiency of maintaining silencing
  XIST Xin genes
• see handout
• Imprinted e.g. methylation regulating
  imprinting center
• see handout
• Testis-specific e.g. testes histone genes
• Other tissue-specific e.g., IFN?

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Normal
1qh
1qh
Frequent Anomalies in Chromosomes 1 16 in
Untreated ICF Lymphoid Metaphases
Chr1
1qh
16qh
16qh
Normal
Chr16
b, c, d 1qh decondensation h i 16qh
decondensation Pericentromeric
Rearrangements (PRs) e, f, j pericentromeric
breaks m - t multiradial chromosomes
1qh
1qh
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DNA Methylation and Carcinogenesis
DNA methylation
no change
abnormal increases
abnormal decreases
Many normally highly methylated sequences (often
DNA repeats) become hypomethylated
increase spontaneous mutations due to m5C-to-T
hotspots
Some CpG island promoters become hypermethylated
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How DNA Hypermethylation Can Contribute to
Carcinogenesis
Often cancer-associated DNA hypermethylation of
the CpG island promoter of a tumor suppressor
gene occurs according to one of these 2 pathways
inactivation of 1 of the alleles by
hypermethylation and inactivation of the other by
deletion or mutation
inactivation of both alleles of the gene by
hypermethylation
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Cancer-Specific DNA Hypermethylation An Example

• Cell cycle regulatory gene p16 in lung cancer
• Repression of p16 by hypermethylation in its CpG
  island promoter helps yield unregulated cell
  growth
• Hypermethylation of the p16 CpG island is
  correlated with cigarette smoking
• This hypermethylation helps predict post-surgery
  survival
• Clinical trials with 5-azadeoxycytidine
  (Decitabine),
• a DNA methylation inhibitor, are in progress
• But DNA hypomethylation is also associated with
  cancer!

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Applications of DNA Methylation Studies to
Cancer Diagnosis and Prognosis
DNA methylation
diagnosis
prognosis

methylation of tumor suppressor genes or
hypomethylation of DNA sequences
tumor samples possibly, blood sputum samples
even for solid tumors
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Applications of DNA Methylation Studies to
Cancer Treatment
DNA methylation
patient-specific therapy from mutation and DNA
methylation analysis of tumor
therapy directed to DNA hypermethylation
drugs to inhibit DNA methylation or chromatin
condensation Decitibine or, better, more
specific drugs gene therapy to restore lost
function of tumor suppressor genes
testing DNA to use best drugs for that
patient, e.g., not alkylating agent if a mismatch
repair gene (MLH1) is methylated