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Genomics > The Epigenome > Flashcards

The Epigenome Flashcards

1
Q

What is the genome?

A

The complete set of genetic material in a cell

The DNA sequence that is present in a single full set of chromosomes

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2
Q

How is the genome organised within cells?

A

The genome exists in a cell as an organised structure made up of a number of macromolecules with DNA as the primary building block

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3
Q

What is the role of histones in genome packaging?

A

Histones and other proteins provide a support around which the DNA is wound

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4
Q

How are histones packed into cells?

A

These structures are then organised in 3D to form fibres and ultimately, chromosomes

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5
Q

What is a nucleosome?

A

The first level of packing consisting of histone proteins and DNA

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6
Q

What is chromatin?

A

The genetic material composed of DNA and proteins condensed to form chromosomes during eukaryotic cell division

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7
Q

What are the two types of chromatin?

A

Euchromatin

Heterochromatin

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8
Q

Describe the features of euchromatin

A
  • gene rich
  • transcriptionally active
  • dispersed appearance
  • unique DNA sequences
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9
Q

Outline the features of heterochromatin

A
  • gene poor
  • less transcriptionally active
  • condensed appearance
  • repetitive DNA sequences
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10
Q

Outline the packing solution

A

Nucleosomes are wound up to form 30nm fibres

Fibres are then wound up further with scaffold proteins to generate higher-order structures

Chromosomes are the most densely packed form of genomic DNA

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11
Q

What is the epigenome?

A

The sum of all the (heritable) changes in the genome that do not occur in the primary DNA sequence and that affect gene expression

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12
Q

Describe the effect of an epigenetic change

A

An epigenetic change results in “A change in phenotype but not in genotype”

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13
Q

Outline some epigenetic mechanisms

A
  • DNA Methylation
  • Histone modification
  • X-inactivation
  • Genomic Imprinting
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14
Q

What is DNA methylation?

A

DNA methylation in humans is the addition of a methyl group in the 5’ position of a Cytosine

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15
Q

How is DNA methylation catalysed?

A

This is catalysed by DNA methyltransferase enzymes

DNMT1, DNMT3a and DNMT3b

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16
Q

Where is the methyl group added from in methylation?

A

It requires S-Adenosyl Methionine to provide the methyl group
In differentiated cells it occurs in CpG dinucleotides

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17
Q

What happend to the S-Adenosyl Methionine once it gives up its methyl group?

A

SAM = S-Adenosyl Methionine
becomes
SAH = S-Adenosyl Homocysteine

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18
Q

What enzymes are involved in DNA demethylation?

A
  1. TET = Ten-Eleven Translocation enzyme
  2. TDG = Thymidine DNA glycosylase
    BER = Base Excision Repair
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19
Q

When does passive demethylation occur?

A

Passive demethylation occurs during replication

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20
Q

How does methylation affect transcription?

A

DNA Methylation turns transcription off by preventing the binding of transcription factors

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21
Q

What role does methylation have on gene expression?

A

DNA methylation patterns change during development and are an important mechanism for controlling gene expression

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22
Q

What is histone modification?

A

This is the addition of chemical groups to the proteins that make up the nucleosome

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23
Q

How many histone modifications are there?

A

There are a large number of known histone modifications (>100) and many are of unknown function

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24
Q

What are the common known histone modifications?

A

Common modifications include
acetylation
methylation

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25
How are histone modifications catalysed?
Large range of enzymes catalyse modification
26
How are histone modifications named?
Modifications are named based on the histone, the amino acid and the actual modification For example, H3K4Me3 means that on Histone 3, the Lysine at position 4 is tri-methylated
27
Give examples of common modification names
``` Ac = Acetyl Me = Methyl Ub = Ubiquitinyl ```
28
What are the different types of histone modifiers?
writers erasers readers
29
What is the role of histone writers modifiers?
Enzymes that add histone modifications
30
Name examples of writers
Histone Acetyltransferase - HAT1 | Histone Methyltransferase - EHMT1
31
What is the role of erasers?
Enzymes that remove histone modifications
32
Name examples of histone modification erasers
Histone Deacetylase - HDAC1 | Histone Demethylase - KDM1
33
What are histone modification readers?
Proteins that bind to histone modifications and alter gene activity and protein production
34
Give named examples of histone modification readers
Bromodomain and extra-terminal (BET) proteins – BRD2 | Chromodomain proteins – CBX1
35
What is the role of histone acetylation?
At Lysine residues relaxes the chromatin structure and makes it accessible for transcription factors
36
What is the purpose of histone methylation?
More complex and can repress or activate transcription depending on where it occurs
37
How do different histone modifications relate to one another?
Histone modifications can occur concurrently and so their effects can interact or modify each other
38
What is X-inactivation?
This is the inactivation of one of the two X chromosomes in every somatic cell in females
39
What is the role of X-inactivation?
Y chromosome has virtually no genes, so only one copy of each X chromosome gene in males (hemizygosity) X-inactivation ensures that every somatic cell in all humans has same number of active copies of every gene
40
How does X-inactivation ensure there is the correct number of gene copies across the genome?
The Xist gene is transcribed as a long noncoding RNA (lncRNA) from the X-inactivation centre (Xic) and binds all over the X-chromosome
41
What is meant by barr body?
a small, densely staining structure in the cell nuclei of females, consisting of a condensed, inactive X chromosome. It is regarded as diagnostic of genetic femaleness
42
What is the role of histone modification in X-inactivation?
Histone acetylation removed and histone and DNA methylation occurs Inactive X-chromosome is heterochromatic – Barr body
43
What is Tsix?
Tsix is a non-coding RNA gene that is antisense to the Xist RNA
44
How does Tsix arise?
Tsix is derived by transcription in the opposite direction and antagonises Xist RNA to keep one X active
45
What is genetic imprinting?
Imprinting is the selective expression of genes related to the parental origin of the gene copy
46
Describe an autosomal gene
Every autosomal gene has one paternal and one maternal copy
47
Where are imprinted genes found?
Imprinted genes tend to be found in clusters | There are very few imprinted genes (~250)
48
How is imprinting regulated?
Imprinting is mediated by imprinting control regions (ICRs)
49
What effect does imprinting have on gene expression?
Imprinted genes are genes whose expression is determined by the parent that contributed them. Imprinted genes violate the usual rule of inheritance that both alleles in a heterozygote are equally expressed
50
How does imprinting occur?
One copy is silenced by DNA methylation catalysed by DMNT3a and histone methylation leading to inactivation LncRNAs are essential to the process
51
What are LncRNAs?
LncRNAs - long non-coding RNAs, Xist is one example
52
When are imprinting patterns altered?
Imprinting patterns are reset during gamete formation
53
What is ADME?
ADME is absorption, distribution, metabolism, and excretion of drugs
54
What is the significance of cancer epigenetics?
Global DNA methylation has long been known to be altered in tumour cells
55
How does altered DNA methylation lead to cancer?
- Hypermethylation of tumour suppressor genes | - Hypomethylation of tumour activating genes
56
Name some epigenetic enzymes?
``` DNMT3A and TET1/2 Histone Acetyltransferases Histone Methyltransferases Histone Kinases Histone Readers (acetyl/methyl/phosphoryl) Histone Demethylases ```
57
What role do epigenetic enzymes have in cancer?
Epigenetic enzymes are often mutated in tumour cells
58
What Pharamco eoigenetic drugs are currently available?
DNA Methyl Transferase Inhibitors | Histone Deacetylase Inhibitors
59
Name 2 examples of Histone Deacetylase Inhibitors
- Romidepsin (Istodax) | - Cutaneous T-cell lymphoma
60
Name 2 examples of DNA Methyl Transferase Inhibitors
- 5-Azacytidine (Vidaza) | - Myelodysplastic syndrome

Genomics (20 decks)

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