Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Genomics > The Epigenome > Flashcards

The Epigenome Flashcards

1
Q

What is the genome?

A

The complete set of genetic material in a cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How is the genome organised?

A

It exists in a cell as an organised structure made up of a number of macromolecules with DNA as the primary building block. Histones and other proteins provide a support around which the DNA is wound. These structures are then organised in 3D to form fibres and ultimately chromosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is a nucleosome?

A

Histone proteins and DNA that forms the first level of packaging

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How is DNA packaged?

A
  • Nucleosomes are wound to form 30nm fibres
  • Fibres are wound up further with scaffold proteins to generate higher-order structures
  • Chromosomes are the most densely packed form of genomic DNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
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 effect gene expression.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is an epigenetic change?

A

A change in phenotype but not in genotype

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the epigenetic mechanisms?

A

DNA methylation
Histone modification
X-inactivation
Genomic imprinting

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is DNA methylation?

A

It is the addition of a methyl group in the 5’ position of a cytosine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What catalyses DNA methylation?

A

DNA methyltransferase enzymes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are the DNA methyltransferase enzymes?

A

DNMT1, DNMT3a and DNMT3b

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What provides the methyl group in DNA methylation?

A

S-Adenosyl Methionine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How does DNA methylation occur in differentiated cells?

A

It occurs in CpG dinucleotides

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How is DNA demethylated?

A

Through a series of steps:
1. 5-methylcytosine is converted via TET into 5-hydroxymethylcytosine as there is an addition of an OH onto the 5th carbon.

  1. Then TET converts this into 5-formylcytosine (an aldehyde).
  2. Then TET converts this into 5- carboxycytosine as an COOH group is added.
  3. TDG and BER occur to convert 5-carboxycytosine, 5-formylcytosine or 5-hydroxycytosine back into cytosine through passive demethylation.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is TET?

A

It is Ten-Eleven Translocation enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is TDG?

A

Thymidine DNA glycosylase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is BER?

A

Base Excision Repair

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

When does passive demethylation occur?

A

It occurs during replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is the importance of DNA Methylation?

A
  • Turns off transcription by preventing binding of the transcription factors.
  • Patterns change during development and are an important mechanism for controlling gene expression
19
Q

What is histone modification?

A
  • The addition of chemical groups to the proteins that make up the nucleosome.
20
Q

How many histone modifications are there and what is there function?

A

About 100 modifications and many are of unknown functino

21
Q

What are the common histone modifications?

A

Acetylation and Methylation

22
Q

How are histone modifications named?

A

Based on the histone, the amino acid and the actual modification. For example, H3K4Me3 means on histone 3, the lysine at position 4 and it is tri-methylated

23
Q

What are histone writers? Give examples

A

Enzymes that add histone modifications. For example - Histone Acetyltransferase - HAT1
- Histone Methyltransferase - EHMT1

24
Q

What are histone erasers? Give examples

A

Enzymes that remove histone modifications.
For example:
- Histone deactylase HDAC1
- Histone demethylase KDM1

25
What are histone readers? Give examples
Proteins that bind to the histone modification and alter gene activity and protein production. For example: - Bromodomain and extra-terminal (BET) proteins - BRD2 - Chromodomain proteins - CBX1
26
Function of histone acetylation at lysine
At lysine residues, it relaxes the chromatin structure and makes it accessible for transcription factors
27
Function of histone methylation
More complex than acetylation. Can repress or activate transcription depending on where it occurs
28
What does the concurrence of histone modifications mean?
They can interact or modify each other
29
What is X-inactivation?
Inactivation of one of the two X chromosomes in every somatic cell in females
30
Why is X-inactivation required?
This is needed as the Y chromosome has virtually no genes, so there is only one copy of each X chromosome gene in males but in females, it is needed to make sure there is the same number of active copies of every gene in each somatic cell.
31
How does X-inactivation occur?
- The Xist gene is transcribed as a long non-coding RNA (IncRNA) from the X-inactivation centre (Xic) and binds all over the X-chromosome. - Histone acetylation removed and histone and DNA methylation occurs - The inactive X-chromosome is heterochromatic - Barr body. - Tsix is derived by transcription in the opposite direction and antagonises Xist RNA to keep one X active.
32
Give an example of an animal that has undergone X-inactivation
All tortiseshell cats are female. This is because they have one X with an active orange fur allele and one X with an active black fur allele. Random X-inactivation results in patches of orange and black fur.
33
What is genomic imprinting?
Imprinting is the selective expression of genes related to the parental origin of the gene copy.
34
How are imprinted genes found together?
In clusters.
35
How many imprinted genes are there?
Very few imprinted genes - approximately 250
36
What mediates gene imprinting?
The imprinting control regions (ICRs)
37
How is one gene silenced in imprinting?
One copy is silenced by DNA methylation catalysed by DMNT3a and histone methylation leading to inactivation. LncRNAs are essential to the process.
38
When is imprinting patterns reset?
They are reset during gamete formation
39
Why is pharmacoepigenetics studied?
It is known to cause epigenetic regulation of genes or epigenetic effects of drugs.
40
Why is it important to study the epigentic regulation of genes?
Information can be used to increase the efficacy of drug treatment
41
Why is it important to study the epigenetic effects of drugs?
New paradigms for the drug treatment
42
How is global methylation effected in cancer?
Known that global DNA methylation is altered in tumour cells. This causes: - Hypermethylation of tumour suppressor genes - Hypomethylation of tumour activating genes
43
Which enzymes are affected in tumour cells
- DNMT3A and TET1/2 - Histone Acetyltransferases - Histone Methyltransferases - Histone Kinases - Histone Readers - Histone Demethylases These are often mutated in tumour cells
44
What is an example of a pharmacoepigenetic drug?
DNA methyl transferase inhibitors - 5-Azacytidine (Vidaza) - Myelodysplastic syndrome - Histone deactylase inhibitors - Romidepsin (Istodax) - Cutaneous T-cell lymphoma

Genomics (19 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions