Epigenetics

Question 1

what is epigenetics?

Answer 1

changes in organisms caused by modification of gene expression rather than alteration of the genetic code

(not modifying DNA, but modifying which genes are switched on / off)

Question 2

what is genome and what is epigenome?

Answer 2

genome: complete set of genes / genetic material present in a cell or organism. 3 billion bp in human. static.

epigenome: bits of the genome that are switched on / off. flexible - can change with age and environment ( the epigenome describes modifications to the genome that do not affect the DNA sequence but determine whether genes are switched on or off where and when they are needed.)

Question 3

what are epigenetic influences?

Answer 3

1. environment (e.g. state of mind, diet, social contact, state of gut, exercise, chemicals - drugs, smoking, season / circadian rhythm)

Question 4

when is epigenetic life?

why is it difficult to predict what the final outcome of epigenome is going to be?

Answer 4

• changes in epigenome through: pre-conception -> embryo -> infancy -> childhood -> adolescence -> early adult -> adult -> maturity
• cumulative effects makes epigenome difficult to predict what the final outcome will be. also is flexible - so changes

Question 5

what is epigenetic drift?

Answer 5

• environmental exposure to different epigenetical determines epigenetic drift. epigenetic drift gets bigger as we get older
• as move through life, environment plays bigger role on epigenome.
• means we have a biological age and chronological age

Question 6

explain how modifying epigenetic environment can increase / decrease liklihood to getting disease?

Answer 6

• everyone has an individual epigenetic predispostion to disease. but acquired epigenetic mutations can make someone meet the threshold for onset of symptoms earlier / later than expected

Question 7

describe how identical twins from same genome and within same amniotic membrane have different outcomes from leukomia cells

Answer 7

• pre-leukaemic cells present in both twins
• only progressed to leukaemia in one twin.
• environment sub. birth = different.

acute lymphoblastic leukaemia often developens spotaneously from fusion of two genes

Question 8

which part of epigenome is inherited?

Answer 8

• DNA methylation is inheritable

Question 9

why is there a difference in epigenome heritabilty between males and females?

Answer 9

females: germ cells are produced in developing fetus -> affects F1 and F2 directly, F3 indirectly (grandmother can effect grandchildren epigeneticlly).

e.g. granny smokes when pregnent - effects mother. But within mother, she produces oocytes that produces grandchild. oocytes were already formed when she was in-utero in granny- affects granchild

males:

Question 10

describe which progeny are mutltigenerationally and transgenerationally epigenetically affected from changes to male / female?

Answer 10

multigenerational (directly exposed) - female: = F1 and F2. male: F1

transgenerational (no direct exposure) - female: F3. male: F2

Question 11

what is the Barker hypothesis?

Answer 11

thrifty phenotype - if a baby in-utero is subject to poor nutrients (because of bad maternal diet), the epigenome is programmed to expect this environment post-natally. means there are developmental changes in cellular energy metabolism, such as: glucose handling, lipid metabolism and mt biogenesis. if exposed to nutrient poor environment postnally: means pre-disposed to have a survival offspring.

BUT

if born and given a nutrient rich environment -> get increased risk of susceptibility to metabolic disease, such as type 2 diabetes, obesity and CHD

Question 13

what are the risk factors that are increased bc of Barker Hypothesis? what diseases do they lead to?

Answer 13

• increased adipose tissue, increased lipid accumulation in muscles: type 2 diabetes
• impaired glucose sensing: hyperinsulinemia (means the amount of insulin in your blood is higher than what’s considered normal. )
• leptin resistance in brain (think always hungry): obesity
• lipid accumulation in CV system: CVD

Question 14

what are the epigenetic mechanisms / regulators of epigenome

Answer 14

1. DNA methylation-cytosines

2. micro and small RNAs

3. Histone modification - histones

4. chromatin architecture

Question 15

what are histones?

how do they influence DNA structure?

Answer 15

Histones are a family of basic proteins that associate with DNA in the nucleus and help condense it into chromatin.

• 8 histones (octamer of core histones) make one nucleosome. histone H1 keeps the keeps the DNA attached to the histones

histone strings are wrapped into helical fibre -> further coils -> compact af!

Question 16

how does DNA packing prevent gene expression?

Answer 16

When the DNA is bound more tightly to the histones, however, it is more difficult for transcription factors and RNA polymerase to bind to the DNA, making it more likely that those genes will be turned off.

Question 17

describe how chromatin architecture is changed (a factor than influences epigenome mechanism)

Answer 17

chromatin architecture modifcations

• changes shape of histone / DNA complex

- ATP-depending remodelling:

• complex of proteins sits on the histone nucleosomes. uses ATP. alters:
  1. the contact between DNA and histones,
  2. the path of DNA wound around histones,
  3. the structure of nucleosomes.

normally an immediate effect

Question 18

explain how histone modifications occurs (a factor than influences epigenome)

where do most modifications occur?

which enzymes used?

Answer 18

histone modifications

• post-translational modification of histone proteins: acetylation (acetyl functional group added), methylation M (addition of methyl group) , phosphorylation P, ubiquitylation (U)
• most of modifications are on lysine (K) and serine a.a. -> can make active genes by doing this. e.g. H3K4me3 (this is 3 methyl groups on K) OR make genes repressed (e.g. H3K27me3- adding 3 methyl groups to K)

can change histone modifcations using enzymes:

a) histone acetylase (HAT): opens DNA to make it accessible
b) Histone deactylase (HDAC) associated with closing DNA to make it inaccessible

Question 19

what does DNA methylation usually cause to happen?

Answer 19

represses gene transcription -> gene silencing

Question 20

how are HDAC inhibitors used in therapy?

*double check this*

Answer 20

HDAC inhibitors increase gene transcription because they keep chromatin relaxed -> opens up the DNA.

Question 21

explain DNA methylation (a factor than influences epigenome / regulates epigenome)

• where does it often occur?
• what enzyme used?
• which base is methyl added to / what does it make?

Answer 21

- methyl groups can be added / removed from cytosine (the nucleotide base)

• methylation interferes with binding of transcriptional activators -> causes gene inactivation
• occurs when you get areas of DNA where cytosine and guanine are adjacent and repeated (CGCG / CpG islands). found in promoter regions.

- DNA methyltransferase (DNMT) is the enzyme

• methyl is added to cytosine to make 5-methylcytosine.

Question 22

which a factor that influences epigenome / regulates epigenome is inheritable?

Answer 22

DNA methylation

Question 23

what happens to DNA methlyation with age?

Answer 23

changes with age:

• DNA methylation decreases in the zygote
• after implantation and development and have embryo, degree of methlyation increases, as more genes are swithed off

Question 24

how does hypomethylation and hypomethylation change with ageing and how does this influence chance of cancer?

Answer 24

- normal genome is usally hypermethylated and stable (dont need them all genes activated)

• BUT with increased ageing, get genome wide hypomethylation, leads to tumorigenesis
• at tumour suppressor genes, CpG-islands become hypermethylised: locks into an inactive state

Question 25

how can you predict the prognosis of developed cancer from methylation?

Answer 25

hypermethylation is associated with inactivation of tumour suppression.

IN ADDITION TO THIS CANCER, IF YOU HAVE

• hypermethylation of ECM or growth factor proteins -> causes poorer prognosis
• hypomethylation of ECM or growth factor proteins -> improved prognosis

Question 26

explain non-coding RNAs

(a factor than influences epigenome / regulates epigenome):

what is non-coding RNA?

how stop proteins being made?

Answer 26

(how can we prevent RNA from being translated into proteins? use:)

-non-coding RNA (ncRNA). functional, but not translated into proteins = called interfering RNA.

• this ncRNA interferes with gene expression at transcriptional and post-transcriptional level. combine to RNA and prevent it from being translated. (involved in splicing, editing and mRNA stability)
• get different sizes of epigenetic ncRNA (in increasing order): miRNA, siRNA, piRNA, IncRNA

Question 27

what is genomic imprinting?

use igf2 / igf2 receptor in mouse model to explain

Answer 27

(might only want one gene expressed - but this is found on only one of maternal or paternal allele. so have genomic imprinting:

a developmental process called genomic imprinting sometimes leads to the exclusive expression of specific genes from only one parent. imprinting works, rather than looking at the entire genome, consider the effect of this process on smaller chromosomal regions and single genes

. For many diploid genes, even if the copy you inherited from one parent is defective, you have a substitute allele from your other parent. However, in the case of imprinting, even though there are two copies of the gene, it is as if you are haploid for this gene because only one copy is expressed. In other words, there is no substitute allele, which makes imprinted genes more vulnerable to the negative effects of mutations. Additionally, genes and mutations that might normally be recessive can be expressed if a gene is imprinted and the dominant allele is silenced (Jirtle & Weidman, 2007).

)

• differential DNA methylation and histone methylation and acetylation of paternal or maternal allele
• growth factor igf2 from father. igf2 receptor - from mother. (father wants as many offspring as poss. mother wants not too big so shes safe and doesnt lack own nutrients). they cancel each other out
• if lacking in igf2 receptor -> offspring v large OR if ifg2 gene not on -> too small

Question 28

name and explain two imprinting syndromes?

Answer 28

Prader-Willi / Angelman syndrome

both produced by same genetic mutation. but phenotype is different depending if on male / female

Prader-Willi: (autosomal). deletion is on fathers copy of Chr. 15. region: 15q11-q13. excess weight gain. development delays

Angelman syndrome: deletion of maternal copy Chr. 15. happy demeanour, severe mental b

Question 29

name 4 epigenetic therapies

Answer 29

• HDAC inhibitors -> vorinosat for acute myeloid leukaemia (phase 3 trial).
• DNMT inhibitors (5-azacytidine. inhibits DNA methylation)
• Non-coding RNA (difficult to deliver into humans)

- Osteopathic manipulation (changes to diet / exercise)

Question 30

how does diet restriction slow age related epigenetic changes?

Answer 30

CR: maintaining degree of methylation and preventing methylation drift. stops hypomethylation