Epigenetics

Question 1

Epigenetics

Answer 1

• A change in phenotype/gene expression
• Caused by events that do not change the underlying DNA sequence
  
  • heritable through mitosis or meiosis

Question 2

Can Epigenetic mechanisms influence Homeostasis?

Answer 2

Yes

• Changing environmental conditions can alter epigenetic marks
  
  • –>changes in gene expression in a cell nucleus
• Changes are heritable
• Epigenetic alterations can dramatically change homeostasis
  
  • short time interval with lasting consequences

Question 3

Variations in Chromatin Structure modulate the use of the genome via…?

Answer 3

1. Histone modifications
2. DNA methylation
3. Noncoding RNAs
4. Histone variants
5. Chromatin modifying machines

Question 4

What is the importance of DNA Methylation?

Answer 4

• DNA Methylation does not interfere with DNA base pairing
• DNMT = DNA Methyltransferase (H –> CH3)
  
  • results in gene silencing via proteins
    
    • ​DNMT 1 = methylates NEW DNA strand
  • MBD = methylated binding domain (MBD)
    
    • Readers
    • Mutations = Rett Syndrome & Autism
• TET = Ten Eleven Translocate (CH3 –>OH)
  
  • results in gene expression
  • de-methylation
    
    • Mutation = cancer in bone marrow
• BER (DNA Repair Pathway) = removes the -OH
  
  • OGG
  • MUTYH

Question 5

What is Genomic Imprinting?

Answer 5

Genomic Imprinting

• Epigenetic modifications = erased in the germline
  
  • re-establishes in the egg & sperm prior to fertilization
• Prevents Parthenogenesis (self-fertilization)

Question 6

What are Histone Modifications?

Answer 6

• Primary Role:
  
  • Organizing DNA inside the nucleus
  • Different histone proteins = make up the octamer
    
    • Modifications = Binding site for large multi-protein complexes
• Structure:
  
  • N-terminus tail = regulation site (junction box)
    
    • H2A & H2B = interact (fall off during chromatin assembly)
    • H3 & H4 = interact (stay on during chromatin assembly)
      
      • Handshake interaction
    • Modifiable residues: K, R, S, T
  • Beads on a string
    
    • octamer = nucleosome
    • Euchromatin + Heterochromatin
• Modifying Enzymes
  
  • HAT = add acetyl group (+ charge elimiated)
    
    • nullifies (+) charge assocated w/ nucleosomes
  • HDAC = remove acetyl group
    
    • add (+) charge back
  • Histone Methyltransferase (KMT) = add methyl
  • Histone Demethylase (KDMT) = remove methyl
  • Kinase/Phosphatase
  • Ub transferase/De-ubiquitnase
    
    • Many more = mass spectroscopy

Question 7

What is the importance of Histone Acetylation?

Answer 7

• HAT = add acetyl group (+ charge elimiated)
  
  • nullifies (+) charge assocated w/ nucleosomes
  • opens up DNA = gene expression
• HDAC = remove acetyl group
  
  • add (+) charge back
  • closes DNA = no gene expression
• HDACI (inhibitor)
  
  • blocks HDAC = keeping activity of gene ON

Question 8

What are the types of Epigenetic Modifying Enzymes?

Answer 8

• Writers
  
  • Establish marks on DNA/chromatin
    
    • ex: HAT/Kinase
• Readers
  
  • Recognize marks & bind to them
    
    • Ex: Bromo/Sant
• Erasers
  
  • Remove epigenetic marks
    
    • Ex: HDAC/PPTase

Question 9

What can Epigenetic Modifications do to gene expression?

Answer 9

Epigenetic Modifications can silence or activate gene expression

• can change as consequence to environmental conditions
• can be fixed/modified
• heritable via mitosis/meiosis

Methylation

• inhibits transcription = gene repression

Demethylation

• allows transcription = gene expression

EXCEPTION: Fixed in place epigenetic regulation

• HOX gene in flies

Question 10

What is an example of Environmental effects that influence Epigenetic Responses?

Answer 10

Resveratrol

• Found in grapes/wine
  
  • affects Sir 2 (HDAC)
    
    • shuts gene off!

Other Enivronmental Influences:

• Hypoxia
• Inflammation
• Nutrients
• Cell density
• Drugs

Question 11

What is the importance of X‐Chromosome inactivation or silencing?

Answer 11

• Dosage compensation
  
  • Barr body
    
    • on silenced chromosome = 15% gene is still active
• Mammalian females = natural genetic mosaics
  
  • inactive X chromosome can vary from cell to cell
• Skewed X‐Chromosome inactivation
  
  • protects from mutation effects on X
  • women as they age = skewing increases

Question 12

What is Lyonization?

Answer 12

Lyonization

• Basics:
  
  • Xist = long noncoding RNA
    
    • expressed in X inactivation center (XIC)
  • Random expression = random X-chromosome silencing
  • Formation of the Barr Body
• Process:
  
  • Xist & Tsix = expressed on inactive X-chromosome
    
    • Xist = draws X chromosome close to XIC
    • X chromosome = inactivated via Xist sequestration & epigenetic modifcations
      
      • forms the Barr Body

lncRNA

• long non-coding RNA
• involved w/ every aspect of Nuclear Metabolism
  
  • gene-gene interaction
  • barr body
  • enhancer/promotor

Question 13

Discuss Epigenetics and disease

Answer 13

• DNA methylation = diagnostic marker
  
  • Nucleosomes = markers for cancer

Examples:

• Mutations in MGMT = linked to small lung carcinoma

Personalized medicine:

• Aggressive Glioblastomas can be resistant to chemotherapeutic agents such as temozolamide.
  
  • Why?
    
    • MGMT gene expressions in the tumor is upregulated –> demethylation
    • Promoter methylation of the MGMT gene = diagnostic marker for drug therapy with temozolamide.