Epigenetics in health and disease Flashcards
1
Q
What is epigenetics
A
reversible regulation of gene expression by alteration to DNA methylation and chromatin structure occurring independent of the DNA structure
2
Q
What is the difference between gene expression by DNA and epigenetics
A
- DNA sequence mediates what specific mRNA molecules are synthesised
- Epigenetic modifications mediate how much of a specific mRNA is made and when are where it’s synthesised
3
Q
Why are epigenetics important
A
- imp for cell differentiation
4
Q
Name some types of epigenetic modifications
A
- DNA methylation
- Nucleosome positioning
- histone modification
- DNAse hypersensitive site
- 3D chromatin architecture
- smRNA and lncRNA (non-coding)
5
Q
What does DNA methylation consist of
A
- addition of methyl group to C5 position of cytosine
- most methylation occurs in sequence context 5’-CG-3’
- occurs almost exclusively at cytosines followed immediately by guanine CpG dinucleotide
6
Q
What is CpG
A
- Cytosine-guanine dinucleotides
- primary targets for DNA methylation
- interspersed throughout DNA
- A hotspot for CpGs is called a CpG island
7
Q
How does DNA methylation affect gene expression
A
- ~50% of human genes have a CpG island in the promoter region
- methylation of CpG in promoter region is related to transcriptional silencing
- methylation inhibits transcription binding either directly or via altered histone acetylation
8
Q
What is the mechanism of action of DNA methylation
A
- DNMTs add methyl groups derived from SAM to the CpG islands to methylate them
9
Q
Name the different types of mammalian DNMTs
A
1, 2, 3a, 3b, 3L
10
Q
What roles do the different types of DNMTs play
A
- DNMT1: maintains methylation during DNA replication, requires hemi-methylated DNA substrate and reproduces pattern of DNA methylation on newly synthesised DNA strand
- DNMT3a and 3b: de novo methylases, add methyl group to previous unmethylated CgP nucleotides, re-establish methylation pattern
11
Q
Name a factor of DNA methylation and what role does it play
A
- 5hmC
- found abundantly in embryonic cells and in the brain
- positively correlated to gene expression
- plays a role in active demthylation to promote gene expression
- conversion of 5mC to 5hmc by TET blocks repressive proteins that typically would’ve been recruited to 5mC
12
Q
What is passive demethylation
A
- demtheylation occurring during cell differentiation and mammalian development
13
Q
What roles does DNA methylation play
A
- long-term silencing of genes
- silencing of repetitive elements (like transposons)
- inactivation of X chromosome
- expression and establishment of imprinted genes
- suppression of viral genes and other deleterious elements which are a part of the host genome
- carcinogenesis
14
Q
Summarise the functioning of DNA methylation
A
- displaces transcription factors
- attracts methyl binding proteins
15
Q
How does DNA methylation inhibit transcription?
A
- alters the shape of the response element that the transcription factor binds to
- Methyl-binding proteins recruit different co-repressor complexes
16
Q
What is chromatin
A
- In a non-dividing cell, nucleus is filled with thin packing material called chromatin
- chromatin provides scaffolding for the entire packaging of our genome
- chromatin is made up of DNA, proteins (mainly histones and some non-histone proteins) and RNA
- Chromatin also regulates accessibility to DNA by modifications in chromatin structure
17
Q
What forms is chromatin found in
A
- Heterochromatin: compact, generally not active
- Euchromatin: less compact generally active
18
Q
What is a histone
A
- part of chromatin
- assembles into octameric complexes
- highly conserved
19
Q
What is a nucleosome
A
DNA wraps around histones to form nucleosomes
- nucleosomes are the building blocks of chromatin
20
Q
What is a nucleosome made up of
A
2 copies each of 4 histones(H2A, H2B, H3, H4)
21
Q
What is the function of the nucleosome
A
- as a signalling hub by providing a scaffold for the binding of chromatin enzymes
- displays PTMs which:
- regulate recruitment of chromatin enzymes
- tunes both nucleosome stability and higher order compaction of chromatin
22
Q
Describe possible histone modifications
A
- Acetylation (HAT/HDAC): reduces affinity for adjacent nucleosomes and relaxes overall high order chromatin structure, increasing access to DNA
- Methylation (DNMTs): recruit silencing or regulatory proteins that bind methylated histones
23
Q
Give an example of how gene silencing works
A
- H3K27ac is an enhancer marker that can be used to distinguish between active and poised enhancer elements
- H3K4 = activation, whether it’s methylated or acetylated
- H3K9ac =activation
- When H3K27 is trimethylated, it is tightly associated with inactive gene promoters
- H3K9me =silenced
24
Q
What is uniparental disomy
A
- when both copies of chromosomes come from one parent
- have loss of expression of some genes and increased expression of others
- causes diseases due to changes in epigenotype and disruption of genomic imprinting
25
What is genomic imprinting
- one copy of a gene is silenced due to its parental origin
- some genes are normally
active only when they are inherited from a person’s father; others are active only
when inherited from a person’s mother
- Imprinting is achieved by DNA methylation
- Prader-Willi Syndrome – cognitive and sexual deficiencies as well as obesity and excessive hunger
- Angelman Syndrome: sleep, mental and developmental deficiencies and uncontrollable laughter
26
Give a real life example of genomic imprinting
- Ligers and tiglons
| - changes in appearance and size depending on different imprinted genes from mother or father
27
What environmental factors can affect the epigenome
- epigenome is particularly susceptible to deregulation during embryogenesis and the perinatal period
28
Why is the epigenome sensitive during the perinatal period and embryogenesis
- DNA synthesis rate is high
- Time when elaborate DNA methylation patterns and chromatin structure required for normal tissue development are established
29
Give an example of how epigenetics has been observed in animal models
- Difference caused by DNA methylation at the agouti viable yellow (Avy) gene
- yellow mouse has High risk cancer, diabetes, obesity
Reduced lifespan
- with maternal supplements like zinc and choline the agouti mouse is brown in colour and has Lower risk of cancer, diabetes, obesity and a Prolonged life
30
Name some factors that can affect the epigenome of a baby during neonatal periods
- diet
- toxins/pollutants
- drugs/alcohol
- radiation
- psychosocial factors
- climate
- hormones
- medication
31
What is Lamarckism
the idea that an organism can pass on characteristics that it acquired during its lifetime to its offspring (also known as heritability of acquired characteristics or soft inheritance)
32
How can a gene reset its epigenome
- erase epigenetic marks of somatic cells
- establish those of germ cells
- on fertilisation, erase marks of germ cells and
- establish those of totipotency / development
33
How are transgenerational effects inherited
Transgenerational effects are inherited via paternal gametes.
34
What genes are frequently mutated in cancer
- genes that regulate epigenomic regulatory factors
35
Name two recognised genes mutated in hematopoietic malignancies
- DNMT3a and TET2
36
What is the role of DNA methylation in cancer
- Hypermethylation (Promoter silencing of tumour suppressing genes)
- Hypomethylation (genetic instability, activation of proto-oncogenes)
- Deamination (mutation)
37
Name a tumour suppressor gene that has been implicated in cancer
- MLH1: mismatch gene, frequently mutated in colon cancer
- Micro-satellite instability phenotype (characterised by multiple genetic alterations)
- 10-15% of non-familial colon cancer have a similar phenotype
- Majority of these cancers harbour epigenetic silencing of a non-mutated MLH1 gene
38
Name some mutations linked with acute myeloid leukemia
DNMT3A
| TET2
39
What is the hypothesis about methylator phenotype
- DNA methylation is an alternative model of tumorigenesis
- DNA hypermethylation silences tumour suppressor genes, which causes the accruement of mutations that inevitably lead to cancer
- CGP island methylator (CIMP) phenotype has been associated with several types of cancers
40
How can you screen for novel genes epigenetically silenced in cancer
- Identify novel cancer-related differentially methylated genes
- Validated using standard techniques such as QMSP; Pyrosequencing
41
What is the role of DNA methylation of tumour progression
- aids invasion of carcinogenic cells
42
Why is DNA methylation a good potential biomarker
- DNA methylation changes are a common event in carcinogenesis
- easy to detect and with a high degree of sensitivity
- DNA methylation is more stable than RNA or Protein based markers
43
Give some examples of DNA methylation cancer screening marker
- Prostate cancer (GSTP1)
- Lung cancer (SHOX2)
- Colorectal cancer (Sept9)
44
What aspect of epigenetics is being tested as a possible biomarker
- circDNA
| - molecular alterations found in tumour cells is reflected in circDNA released from tumour into the blood
45
Describe a technique that's used to interrogate the epigenome
- Bisulphite conversion
- Use sodium bisulfite to differentially convert unmethylated cytosine residues to
uracil + methylated cytosines are unmodified
- Identify methylated cytosine via various downstream nucleic acid analysis e.g. PCR,
qPCR and sequencing
- Can identify individual methylation sites and quantify the level of methylation
46
Name some target-specific epigenomic lab techniques and some genome wise ones
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Targeted
- Direct sequencing
- Cloned Bisulfite PCR
- Bisulfite-pyrosequencin
NGS
- MethylC-seq
- RRBS
- Target Capture
- Affinity Based
- MeDIP
- MIRA
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