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GEN > 18. THE EPIGENOME > Flashcards

18. THE EPIGENOME Flashcards

1
Q

What is the most densely packed form of genomic DNA?

A
  • Chromosomes are the most densely packed form of genomic DNA
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2
Q

What are the two types of chromatin & what compartments of the genome do they correspond to?

A
  1. Euchromatin - Compartment A (transcriptionally active)

2. Heterochromatin - Compartment B (transcriptionally repressive)

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3
Q

What are the properties of euchromatin?

A
  • Euchromatin is:
    1. Gene rich
    2. Unique DNA sequences
    3. Transcriptionally active
    4. Dispersed appearance (decondensed)
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4
Q

What are the properties of heterochromatin?

A
  • Heterochromatin is:
    1. Gene poor
    2. Less transcriptionally active
    3. Contains repetitive DNA
    4. Condensed appearance
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5
Q

What is the epigenome?

A
  • The epigenome is the sum of all the changes in the genome that don’t occur in the primary DNA sequence & affect gene expression.
  • Epigenetic changes are changes to the phenotype but don’t change the genotype
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6
Q

What are the 4 main epigenetic mechanisms?

A
  1. DNA methylation
  2. Histone Modifications
  3. X inactivation
  4. Genome imprinting
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7
Q

What is DNA methylation & how does it occur?

A
  • DNA methylation involves adding a methyl group to the 5’ position of cytosine
  • DNA METHYTRANSFERASE (DNMT) is the enzyme involved in DNA methylation
  • There are three types: DNMT1, DNMT 3a, DNMT 3b
  • S- adenosyl methionine (SAM) provides a methyl group
  • DNA methyl transferase removes the methyl group from SAM and adds it to the 5; cytosine position
  • DNA methylation occurs on CpG sites/dinucleotides in differentiated cells
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8
Q

Which enzyme is responsible for DNA methylation?

A 
DNA METHYTRANSFERASE (DNMT) is the enzyme involved in DNA methylation
- There are three types: DNMT1, DNMT 3a, DNMT 3b
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9
Q

What is the purpose of DNA methylation?

A
  • DNA methylation turns transcription off by preventing the binding of transcription factors so that there’s no gene expression
  • DNA methylation occurs on CpG islands which are enriched with CpG nucleotides mainly located in the promoter region
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10
Q

**What are the 5 steps of DNA demethylation?

A
  • In order for DNA DEMETHYLATION to occur, the DNA needs to be methylated first by DNA methyl transferases
    1. TET (TEN-ELEVEN TRANSLOCATION ENZYME) adds a hydroxyl group to the methyl group so that it becomes hydroxymethyl group
  • 5mC (5’ methyl) -> 5hmC (5’ hydroxymethyl)
    2. TET then changes the hydroxymethyl to formyl group
  • 5hmC –> 5fc
    3. The formyl group is then replaced by a carboxyl group to give 5CaC
    4. Thymine DNA glycosylase removes the formyl or carboxyl group by base excision
    5. The methylated cytosine is removed by leaving the OH, the cytosine can then be added back
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11
Q

What is histone modification?

A
  • Histone modification involves adding chemical groups to the proteins that make up the genome (histones)
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12
Q

What are the 4 common histone modifications?

A
  1. Histone methylation
  2. Histone acetylation
  3. Histone phosphorylation
  4. Histone ubiquitination
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13
Q

How are histone modifications named?

A

Histone modifications are named based on the histone, the AA & the actual modification
- E.g H3K4Me3 MEANS on Histone 3, the K (leucine) is trimethylated

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14
Q

*What are the three classes of proteins involved in histone modification & their roles?

A
  1. WRITERS - add histone modifications
  2. ERASERS - remove histone modifications
  3. READERS - proteins that bind to histone modifications & alter gene activity & protein production
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15
Q

Give two examples of a writer protein

A
  1. Histone methyltransferase

2. Histone acetyltransferase

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16
Q

Give two examples of an eraser protein

A
  1. Histone demethylase

2. Histone deacetylase

17
Q

Give two examples of a reader protein

A
  1. Bromodomain protein - BRD2

2. Chromodomain protein - CBX1

18
Q

What is the purpose of histone modifications such as acetylation & methylation?

A
  • HISTONE ACETYLATION on the lysine residue relaxes the DNA converting it from heterochromatin to euchromatin
  • The DNA becomes decondensed making it accessible to transcription factors, to allow for gene expression
  • It does this by reducing the positive charge on the histones
  • HISTONE METHYLATION is more complex & can either repress or activate gene expression depending on where it occurs
19
Q

What is X-inactivation?

A
  • X-inactivation refers to the inactivation of one copy of the X chromosome in every somatic cell in females. This is so that every human has the same number of active copies of a gene
  • Males only have one copy of an X chromosome & it has virtually no genes
20
Q

*How does X-inactivation occur?

A
  1. The Xist gene is transcribed as long non-coding RNA from the X-inactivation centre
  2. The Xist gene binds all over the X chromosome
  3. Histone acetylation is repressed & DNA & Histone methylation occur
  4. The inactivated X chromosome is heterochromatic (condensed) forming a Barr body
21
Q

What mechanism stops both X-chromosomes being inactivated?

A
  • The Tsix is gene antagonises the Xist RNA to keep one X active
  • Tsix is derived by transcription in the opposite direction
22
Q

Give an example of X-inactivation in cats?

A
  • Almost all tortoise shell cats are female. In tortoise shell cats, one X has the allele for orange fur & the other has the allele for black fur
  • The cats have patches of black & orange fur due to random X-inactivation
23
Q

What is genomic imprinting?

A
  • Genomic imprinting is a type of epigenetic inheritance that leads to the selective expression of genes related to the parental origin
  • Every autosomal gene has a paternal & maternal copy, so one of these needs to be silenced
  • Imprinted genes are found in clusters
24
Q

How does genomic imprinting occur?

A
  • Imprinting is mediated by imprinting control regions (ICRs)
  • One parental copy is silenced by DNA methylation & histone methylation leading to inactivation
  • Imprinting patterns are reset during gamete formation, the sperm imprints are rewritten with the paternal pattern & egg imprints are rewritten with the maternal pattern
25
Q

What is pharmocoepigenetics?

A
  • Pharmacoepigenetics is the study of the epigenetic basis of the variance in the individual’s response to a drug
  • Looks at the epigenetic regulation of disease genes, epigenetic effects of drugs
26
Q

How can cancer be treated by targeting epigenetics?

A
  • DNA methylation is altered in tumour cells.
  • There’s hypermethylation of TUMOUR SUPPRESSOR GENES, inactivating the genes that supress tumours
  • There’s hypomethylation of TUMOUR ACTIVATOR GENS, leading to more activation of the genes that activate tumours
  • Epigenetic modifications can be used to reverse these
27
Q

Give an example of a DNA methyl transferase inhibitor & what it’s used to treat?

A
  • DNA methyl transferase inhibitor prevent DNA methylation to activate genes
  • E.g Vidaza/ 5-Azacytidine
  • Treats Myelodyplastic syndrome
28
Q

Give an example of a Histone deacetylase inhibitor & what it’s used to treat?

A
  • Histone deacetylase inhibitors prevent the removal of histone acetylation, leaving teh DNA accessible
  • E.g Istodax/ Romidepsin
  • Treats T-cell lymphoma

GEN (18 decks)

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