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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
Q

How are histone modifications catalysed?

A

Large range of enzymes catalyse modification

26
Q

How are histone modifications named?

A

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
Q

Give examples of common modification names

A 
Ac = Acetyl
Me = Methyl
Ub = Ubiquitinyl
28
Q

What are the different types of histone modifiers?

A

writers
erasers
readers

29
Q

What is the role of histone writers modifiers?

A

Enzymes that add histone modifications

30
Q

Name examples of writers

A

Histone Acetyltransferase - HAT1

Histone Methyltransferase - EHMT1

31
Q

What is the role of erasers?

A

Enzymes that remove histone modifications

32
Q

Name examples of histone modification erasers

A

Histone Deacetylase - HDAC1

Histone Demethylase - KDM1

33
Q

What are histone modification readers?

A

Proteins that bind to histone modifications and alter gene activity and protein production

34
Q

Give named examples of histone modification readers

A

Bromodomain and extra-terminal (BET) proteins – BRD2

Chromodomain proteins – CBX1

35
Q

What is the role of histone acetylation?

A

At Lysine residues relaxes the chromatin structure and makes it accessible for transcription factors

36
Q

What is the purpose of histone methylation?

A

More complex and can repress or activate transcription depending on where it occurs

37
Q

How do different histone modifications relate to one another?

A

Histone modifications can occur concurrently and so their effects can interact or modify each other

38
Q

What is X-inactivation?

A

This is the inactivation of one of the two X chromosomes in every somatic cell in females

39
Q

What is the role of X-inactivation?

A

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
Q

How does X-inactivation ensure there is the correct number of gene copies across the genome?

A

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
Q

What is meant by barr body?

A

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
Q

What is the role of histone modification in X-inactivation?

A

Histone acetylation removed and histone and DNA methylation occurs
Inactive X-chromosome is heterochromatic – Barr body

43
Q

What is Tsix?

A

Tsix is a non-coding RNA gene that is antisense to the Xist RNA

44
Q

How does Tsix arise?

A

Tsix is derived by transcription in the opposite direction and antagonises Xist RNA to keep one X active

45
Q

What is genetic imprinting?

A

Imprinting is the selective expression of genes related to the parental origin of the gene copy

46
Q

Describe an autosomal gene

A

Every autosomal gene has one paternal and one maternal copy

47
Q

Where are imprinted genes found?

A

Imprinted genes tend to be found in clusters

There are very few imprinted genes (~250)

48
Q

How is imprinting regulated?

A

Imprinting is mediated by imprinting control regions (ICRs)

49
Q

What effect does imprinting have on gene expression?

A

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
Q

How does imprinting occur?

A

One copy is silenced by DNA methylation catalysed by DMNT3a and histone methylation leading to inactivation
LncRNAs are essential to the process

51
Q

What are LncRNAs?

A

LncRNAs - long non-coding RNAs, Xist is one example

52
Q

When are imprinting patterns altered?

A

Imprinting patterns are reset during gamete formation

53
Q

What is ADME?

A

ADME is absorption, distribution, metabolism, and excretion of drugs

54
Q

What is the significance of cancer epigenetics?

A

Global DNA methylation has long been known to be altered in tumour cells

55
Q

How does altered DNA methylation lead to cancer?

A
  • Hypermethylation of tumour suppressor genes

- Hypomethylation of tumour activating genes

56
Q

Name some epigenetic enzymes?

A 
DNMT3A and TET1/2
Histone Acetyltransferases
Histone Methyltransferases
Histone Kinases
Histone Readers (acetyl/methyl/phosphoryl)
Histone Demethylases
57
Q

What role do epigenetic enzymes have in cancer?

A

Epigenetic enzymes are often mutated in tumour cells

58
Q

What Pharamco eoigenetic drugs are currently available?

A

DNA Methyl Transferase Inhibitors

Histone Deacetylase Inhibitors

59
Q

Name 2 examples of Histone Deacetylase Inhibitors

A
  • Romidepsin (Istodax)

- Cutaneous T-cell lymphoma

60
Q

Name 2 examples of DNA Methyl Transferase Inhibitors

A
  • 5-Azacytidine (Vidaza)

- Myelodysplastic syndrome

Genomics (20 decks)

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