Brainscape's Knowledge GenomeTM

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


See full index

TMS > Epigenetics > Flashcards

Epigenetics Flashcards

1
Q

What is epigenetics?

A

Regulation of gene expression mediated through changes in DNA modifications, histone modifications and chromatin structure. These changes are reversible. Does not involve changes of the DNA sequence. Does not change the mRNA sequences or proteins produced, but does change how much of each mRNA is synthesised, and where and when it is synthesised.

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

Describe the mechanism of DNA methylation

A

DNA methyl transferase (DNMT) transfers a methyl group onto carbon 5 of a cytosine residue. The methyl group is taken from S-adenosyl methionine (SAM), leaving behind S-adenosyl homocysteine

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

Where in the genome does DNA methylation occur?

A

On cytosine residues in a 5’CG3’ position (CpG). Sites where there are lots of CpG sequences are known as CpG islands. CpG islands present in 50% of promoter regions.

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

What is the result of DNA methylation?

A

Inhibition of transcription factor binding, either directly or via altered histone acetylation.
Also attracts methyl binding proteins.

Both lead to transcriptional silencing.

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

Describe the group of enzymes that carry out DNA methylation

A

DNMT1 - maintenance methylase, carries out methylation following mitosis using the hemi-methylated DNA strand as a substrate
DNMT2
DNMT3a and DNMT3b - responsible for de novo methylation during ageing and disease processes
DNMT3L

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

Describe the mechanism of active DNA demethylation

A

5mc undergoes hydroxylation by TET enzymes. A hydroxyl group is added onto the methyl group, forming 5hmc. Then undergoes further oxidation forming a carboxylic acid group which is eventually removed.

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

What is the role of 5hmc?

A

Blocks the recruitment of repressive proteins that might otherwise have bee recruited to 5mc. Promotes gene expression, during active demethylation.

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

Where is 5hmc most frequently found?

A

In embryonic stem cells and the brain

In promoter regions, gene bodies and intergenic regions

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

What are the two methods by which DNA can become demethylated?

A

Active demethylation

Passive demethylation - methylation pattern lost following cell division due to errors

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

Name 5 functions of DNA methylation

A

Long term gene silencing for cell differentiation
Silencing of repetitive DNA elements such as transposons
X chromosome inactivation
Establishment and maintenance of gene imprinting
Suppression of viral genes that have incorporated into the host genome

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

Describe the structure of a nucleosome

A

Negatively charged DNA wraps around positively charged histone proteins
8 histones in a nucleosome
2 x (H2A, H2B, H3, H4)
Histone H1 connects nucleosomes to the linker DNA

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

What are the two states that chromatin can be in?

A 
Euchromatin = transcriptionally active
Heterochromatin = tightly compact, transcriptionally inactive
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are the possible histone post translational modifications?

A 
Methylation
Acetylation
Phosphorylation
Ubiquitylation
Biotinylation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How do histone modifications affect gene expression?

A
  1. Histone tails form hydrogen bonds with histone tails on adjacent nucleosomes. Modification of the tails affects how well they can interact, so how tightly the chromatin condenses.
  2. Affects the charge of the histone and therefore how tightly DNA binds to it
  3. Recruitment of transcription factors
  4. Recruitment of histone modification enzymes (positive feedback mechanism)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What are epigenetic regulators?

A

Proteins that ‘read’ and interpret the histone modifications, and put mechanisms in place to either facilitate or block gene transcription

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

What is the histone code?

A

Histone modifications can occur in many combinations, each combination has a different meaning and is read by specific protein complexes

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

On which amino acids can acetylation, methylation and phosphorylation occur?

A

Acetylation - Lysine
Methylation - Arginine (mono or di-methylated) or Lysine (mono, di- or tri-methylated)
Phosphorylation - Serine

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

How does histone acetylation lead to gene expression?

A
  1. Reduced affinity of histone tail for adjacent nucleosomes
  2. Removal of histone positive charge, DNA doesn’t bind as tightly
  3. Recruitment of proteins with bromodomains, such as transcription factors and HAT
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

How does histone methylation lead to gene suppression?

A

Recruitment of silencing or regulatory proteins

Recruitment of proteins with chromodomains

20
Q

What is a topologically associating domain?

A

A genomic region containing DNA sequences that frequently physically interact with eachother, due to the 3D looping nature of chromatin

21
Q

What proteins control chromatin loop structures?

A

CTCF proteins

Cohesion proteins

22
Q

What are the two types of interfering RNAs?

A 
Micro RNA (miRNA)
Small interfering RNA (siRNA)
23
Q

Describe the process of micro RNA synthesis

A 
Pri-miRNA transcribed from DNA
Processed by drosha into pre-miRNA
Exported into the cytoplasm by exportin-5
Processed by dicer
Mature miRNA forms RISC complex
24
Q

How does miRNA regulate gene expression?

A

Complementary base pairing to specific mRNA
Hybridises to a sequence in the 3’UTR
The target mRNA is then destroyed

25
Q

What are some of the functions of epigenetic modifications?

A 
Gene imprinting 
Disorders caused by uniparental disomy
X inactivation
Parental conflict theory
Response to environmental pressures without changing DNA sequence
26
Q

What is gene imprinting and how is it carried out?

A

Certain genes will always be switched off or left switched on depending on if they are inherited maternally or paternally. Means you only have one active allele for that gene. The gene is turned off by DNA methylation in the parental germline, by DNMT1.

27
Q

What is uniparental disomy?

A

Both chromosomes in a homologous chromosome pair are inherited from one parent. If any of the genes on that chromosome are imprinted, you will get either two active or two inactive alleles when there should be one active allele.

28
Q

Describe the process of X inactivation

A

Females have two X chromosomes. At the blastocyst stage either the paternal or maternal X chromosome becomes randomly inactivated in each cell. Inactivation carried out by the Xist gene which initiates histone modifications.

29
Q

What is the parental conflict theory of gene imprinting?

A

Paternally inherited alleles endeavour to use up the mothers resources, as future children may not have his genes (IGF2 gene active, IGF2R gene inactive). Maternally inherited alleles endeavour to limit resource use, to conserve resources for future children (IGF2 gene inactive, IGF2R gene active).

Ligers grow very large due to incompatible gene imprinting patterns from the lion father and tiger mother.

30
Q

How can environmental pressures lead to long term changes in gene expression?

A

DNA methylation affected by environment
Highly sensitive during embryogenesis and perinatal period
Early epigenetic modifications inherited mitotically down somatic cell lineages

31
Q

Name some environmental factors that can have epigenetic effects

A 
Diet
Medications
Recreational drugs
Toxins
Radiation exposure
Climate 
Hormones
32
Q

How can epigenetic processes be involved in cancer?

A

Mutations in epigenetic writers, readers and erasers - particularly DNMT3a and TET are mutated in blood cancers
Mutations in proteins in the chromatin remodelling complex

33
Q

What are the implications of mutations in epigenetic proteins?

A

Global DNA hypomethylation can lead to activation of proto-oncogenes and genomic instability
Promoter hypermethylation can lead to silencing of tumour suppressor genes
Methylated cytosines can become deaminated into guanine - major DNA sequence change

34
Q

Describe an example of where mutations in an epigenetic protein is implicated in cancer

A

Mutations in DNMT3a can lead to AML. Mutated DNMT3a acts dominantly over the wildtype gene allele. Reduced de novo methylation by methyltransferase.

35
Q

How can non coding RNAs be implicated in cancer?

A 
Suppression of tumour suppressor gene mRNA
Promotion of metastasis 
Used in cancer diagnosis 
Confer susceptibility to cancer
Regulation of epigenetic proteins
36
Q

What is a CpG island methylator phenotype?

A

Cancers with high degrees of methylation. Hypermethylation sillences tumour suppressor genes, leading to accumulation of more mutations. Documented in glioma, breast cancer and leukaemia.

37
Q

Why is DNA methylation a good biomarker of cancer?

A

Very commonly accompanies carcinogenesis
Can be detected non invasively (cell free circulation DNA in body fluid samples)
Can be detected to a high degree of sensitivity
More stable than RNA or protein based markers

38
Q

Why is DNA methylation not a good biomarker of cancer?

A

DNA methylation of a certain gene is not specific to one cancer type, cannot be used to diagnose what type of cancer
Assays for DNA methylation sometimes have low sensitivity

39
Q

Name two types of epigenetic therapy that may be used to treat cancer

A

DNA hypomethylating agents (DNMTi’s), such as 5-azacytidine

Histone deacetylase inhibitors (HDACi’s), such as Vorinostat

40
Q

Describe how DNA hypomethylating agents work

A

They are nucleotide analogues that become incorporated into the DNA during DNA replication, and irreversibly bind DNMT1/DNMT3a/DNMT3b to inhibit their activity in further rounds of DNA replication.

Can increase gene transcription of genome protective genes such as p15 and p16, leads to cell cycle arrest and apoptosis of cancer cells

41
Q

What are the limitations of DNA hypomethylating agents

A

Lack of specificity for which genes they target
Development of resistance is common
Not effective at treating solid tumours

42
Q

Describe how histone deacetylase inhibitors work

A

Prevention of histone deacetylation leads to increased transcription of genome protective genes such as p21 and p53, leads to cell cycle arrest and apoptosis of cancer cells

43
Q

Name some of the lab techniques that are used to study epigenetic modifications

A

Methylated DNA immuno precipitation
Sodium bisulfite conversion to detect DNA methylation
Pyrosequencing and Whole genome bisulfite sequencing to analyse DNA produced by sodium bisulfite conversion
Chromatin remodelling assays such as ATAC-SEQ

44
Q

What is methylated DNA immunoprecipitation? Name 1 pro and 1 con

A

Antibodies used to detect presence of 5mc
The method can be adapted to be specific for different residues (e.g. 5hmc)
No base-pair resolution - cannot tell specifically which base pair is methylated

45
Q

How does sodium bisulfite conversion work?

A

Bisulfite applied to DNA
Cytosine residues change into uracil but ones ‘protected’ by a methyl group do not
Following PCR, uracil residues become thymine
Levels of cytosine conversion to thymine inversely correlate with levels of methylated cytosines

46
Q

What is pyrosequencing? Name 1 pro and 1 con

A

Sequences DNA by addition of nucleotides, as they become incorporated there is release of pyrophosphate which initiates an enzyme substrate cascade and emits light

Quick and cost effective, but low throughput and can only be used to analyse short fragments

47
Q

Name 1 pro and 1 con of whole genome bisulfite sequencing

A

Can sequence long DNA sequences
Produces lots of redundant information if you are only interested in one area
Very costly

TMS (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions