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Genomics > The Epigenome > Flashcards

The Epigenome Flashcards

1
Q

What is the nucleosome made up of?

A

Histone proteins and DNA

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2
Q

What are the features of euchromatin?

A

Gene rich, Transcriptionally active, less wound up and unique DNA sequences

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3
Q

What is another name for euchromatin?

A

Compartment A

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4
Q

What are the features of heterochromatin?

A

Gene poor, less Transcriptionally active, condensed appearance and a repetitive DNA sequence

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5
Q

What is another name for heterochromatin?

A

Compartment B

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6
Q

What is a definition for the epigenome?

A

The sum of all (heritable) changes in the genome that doesn’t occur in the primary DNA sequences and that affect gene expression

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7
Q

What does a change in the epigenome result in?

A

A change in the phenotype, not the genotype

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8
Q

What are the mechanisms that regulate gene expression?

A

DNA methylation and histone modification

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9
Q

What is DNA methylation?

A

Addition of a methyl group in the 5’ position of a cytosine

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10
Q

What is DNA methylation?

A

Addition of a methyl group in the 5’ position of a cytosine

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11
Q

What is DNA methylation catalysed by?

A

DNA methyltransferase enzymes

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12
Q

Which DNA methyltransferase enzymes catalyse DNA methylation?

A

DNMT1, DNMT3a and DNMT3b

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13
Q

What provides the methyl group for DNA methylation?

A

S-adenosyl methionine

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14
Q

Where does DNA methylation occur in differentiated cells?

A

CpG dinucleotides

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15
Q

What does DNA demethylation do?

A

Turns transcription off by preventing the binding of transcription factors

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16
Q

What is histone modification?

A

Addition of chemical groups to the histone

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17
Q

What are the four common modifications?

A

Methylation, acetylation, phosphorylation and ubiquitination

18
Q

How are the modifications named?

A

Based on the histone, amino acid and actual modification

19
Q

What are the three types of histone modifiers?

A

Writers, readers and erasers

20
Q

What are the two examples of writers?

A

Histone acetyltransferases and histone methyltransferases

21
Q

What are the writers?

A

Enzymes that add histone modifications

22
Q

What are the readers?

A

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

23
Q

What are two examples of readers?

A

Bromodomain and extra-terminal proteins and chromodomain proteins

24
Q

What are erasers?

A

Enzymes that remove histone modifications

25
Q

Give some examples of erasers?

A

Histone deacetylase and histone demethylase

26
Q

What does histone acetylation at lysine residues do?

A

Relax the chromatin structure by reducing the positive charge on the histones, making it accessible for transcription factors

27
Q

What can histone methylation do?

A

Can repress or activate transcription depending on where it occurs

28
Q

What is X-inactivation?

A

Inactivation of one of the two chromosomes in every female somatic cell

29
Q

Why is X-inactivation necessary?

A

Needed as the Y chromosome has almost no genes

30
Q

What is the process of X-inactivation?

A

The X-ist gene is transcribed as long non coding RNA from the X-inactivation centre and binds all over the X-chromosome
Histone acetylation is removed and histone and DNA methylation occurs
Inactive X-chromosome is heterochromatic
Tsix is derived by transcription in the opposite direction and antagonises Xist RNA to keep one X active

31
Q

Why are all tortoiseshell cats female?

A

Random X inactivation results in random patches of orange and black fur

32
Q

What is gene imprinting?

A

The selective expression of genes related to the parental origin of the gene copy

33
Q

What are imprinted genes mediated by?

A

Imprinting control regions

34
Q

What are essential to the genetic imprinting process?

A

Long noncoding RNAs

35
Q

When are imprinting patterns reset?

A

During gamete formation

36
Q

How is the non-imprinted gene inactivated?

A

DNA methylation and histone methylation

37
Q

What is pharmacoepigenetics split into?

A

Epigenetic regulation of genes and epigenetic effects of drugs

38
Q

What does the changing the Epigenetic regulation of genes do?

A

Increasing the efficacy of drugs

39
Q

What does changing the epigenetic effects of drugs do?

A

New paradigms for drug treatment

40
Q

What are the epigenetic enzymes that are normally mutated in tumour cells?

A 
DNMT3A and TET1/2
Histone acetyltransferases
Histone methyltransferases
Histone kinases
Histone readers
Histone demethylases
41
Q

Give some examples of pharmacoepigenetic drugs

A

DNA methyltransferase inhibitors and histone deacetylase inhibitors

Genomics (16 decks)

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