Epigenetics 20/10/22

Question 1

How much do our epigenetics influence our environment?

Answer 1

Epigenetics can determine 30-40% of our mental health, it can play a role in how we respond to drugs, disease exposure, toxic chemicals, and can influence our social interactions and exercise. Early life stress can change genes through epigenetics.

Question 2

How does epigenetics explain differences in identical twins?

Answer 2

Depending on environmental factors epigenetics can change the expression and regulation of different genes and this can explain certain differences seen in individuals that are identical.

Question 3

How might genetically identical cells differ?

Answer 3

Aging
Environment (exercise)
Diet (high fat)
Sex (male/female)
Neonatal influences
Disease

Question 4

How are ants an example of epigenetics?

Answer 4

Ants in the same colony will have the same genetics but because of eating something different one ant will grow up to be a massive ant and become a protector and the other ants will remain small and scavenge for food.

Question 5

What is epigenetics?

Answer 5

Epigenetics does not change the DNA sequence and is not DNA, but epigenetics needs DNA to work, epigenetics is heritable, and can affect gene function.

Question 6

What does epigenetics do?

Answer 6

Epigenetics can change the gene expression without changing the DNA by regulating DNA.

Question 7

How many genes are active in a cell?

Answer 7

Only 10-20% of genes are active in any cell and epigenetics prevents one cell type from being expressed in another. For example, genes from muscles are turned on in muscles but are turned off in neuron cells.

Question 8

How do epigenetics work in totipotent stem cells?

Answer 8

Totipotent stem cells can differentiate into any type of cell and therefore epigenetics haven’t turned off specific genes yet.

Question 9

How do epigeneitcs work in pluripotent stem cells?

Answer 9

Pluripotent stem cells have differentiated into more specialised cell types such as nerve cells or muscle cells, therefore these cells have certain genes turned off, but they can still differentiate within that cell type.

Question 10

What is DNA methylation?

Answer 10

This is where a methyl group is added or removed to a DNA group, particularly on a cytosine or in a CGCG sequence (CpG dinucleotides). This alters the activity of the DNA/gene.

Question 11

What is a histone modification?

Answer 11

Histones can also be modified so they can change how tightly packed together DNA is to modify how active that DNA/gene is.

Question 12

Where are CpG found most?

Answer 12

Found in high concentrations in CpG islands, these are around promotor regions and in the gene body.

Question 13

What does DNMT1 do?

Answer 13

This methylates a CG sequence de novo.

Question 14

What does DNMT3 do?

Answer 14

This will methylate the opposite strand of the CG sequence that was methylated by DNMT1, this is why the area that is methylated typically has a CG on both strands in the same place.

Question 15

What does TET do?

Answer 15

This demethylated any methylated region.

Question 16

How can you reveal epigenetics in a lab?

Answer 16

Use sodium bisulphite PCR sequencing. If a nucleotide is methylated then the sodium bisulphite wont covert to an uracil, if it isn’t methylated then the nucleotide will convert to an uracil.

Question 17

What analysers are used for bisulphite PCR sequencing?

Answer 17

Pyromark pyrosequencing or IIIumina NextSeq NextGen sequencer.

Question 18

How do these bisulphite sequencing analysers work?

Answer 18

They use a minION and nanopore technology and this is electrically charged, and the DNA is threaded through the nanopore and so a different current will be given out on the computer depending on the nucleotide base and then this can show if a base is methylated or not.

Question 19

What is chromatin?

Answer 19

Chromatin is made up of an octamer of histone proteins (two of each - H2A, H2B, H3, H4) and allows genes to be modified differently (acetylation, methylation, phosphorylation, ubiquitylation, sumoylation) by the histone tails.

Question 20

What do methylation and acetylation do?

Answer 20

Methylation typically means gene silencing. Acetylation typically means gene activation.

Question 21

What are histone modifiers?

Answer 21

HATs - histone acetylases
HDACs - histone deacetylases
HMTs - histone methylases

Question 22

How can you measure histone marks?

Answer 22

Chromatin immunoprecipitation (ChIP).

If you try to take DNA apart to see histone, they will all fall off before you can look at them, therefore, cells are crosslinked with formaldehyde (glues everything together), so histones won’t fall off. Break open the cells and cup DNA into smaller pieces (sonication). Use antibody that will bind to protein/histone and wash the rest away and will leave the protein/histone with the DNA that it was bound to. Reverse the crosslinks to the DNA and proteins/histones separate and then you have all the DNA and proteins that are in the gene. Then PCR analysis.

Question 23

What are regulatory noncoding RNAs?

Answer 23

ncRNA is a functional RNA that is transcribed from DNA but not translated into protein.

~75% genomic DNA is transcribed, ~3% of transcripts encode for proteins, the rest are ncRNAs.

Question 24

What do ncRNAs do?

Answer 24

ncRNAs regulate gene expression at transcriptional and post transcriptional level, histone modification, DNA methylation targeting, and gene silencing.

Question 25

What are the different types of ncRNAs?

Answer 25

miRNA/siRNA - 18-25bp, post transcriptional gene silencing, RNA interference
piRNA/snoRNA - 20-300bp, RNA modification, telomeres, chromatin, transcription
Long ncRNAs - 300-1000bp, X inactivation, DNA imprinting, gene transcription, generating other ncRNAs

Question 26

How to measure miRNA?

Answer 26

miRNA seq
miRNA arrays
miRNA Realtime PCR

Question 27

What are the roles of epigenetics?

Answer 27

X inactivation
Genomic imprinting
Protecting the genome from transposition
Tissue, gene, developmental stage specific expression
Genome-Environment interaction

Question 28

How does X chromosome inactivation work?

Answer 28

Females receive two X chromosomes and so one chromosome is active, and one half of a X chromosome is inactivated through all the previous mechanisms. This means males and females have the same amount of DNA that has the potential to be active.

Question 29

What is genomic imprinting?

Answer 29

Most genes inherit as two working copies, one from mum and one from dad.

Imprinted genes, we inherit only one working copy. Depending on the gene, either the copy from mom or the copy from dad is epigenetically silenced. The epigenetic marks on imprinted genes usually stay put for the life of the organism but are reset during egg and sperm formation.

Question 30

How does imprinting effect donkeys?

Answer 30

Depending on if you breed a horse with a horse or a horse and a donkey due to the genetic imprinting you can get different offspring. For example, two horses will result in a horse, but a donkey and a horse will result in a mule. Same genetics, different imprinting.

Question 31

Why is imprinted needed?

Answer 31

Normally an individual has one active copy of an imprinted gene. Having two active or two inactive copies can lead to severe developmental abnormalities, cancer, and other problems. Prader Willi and Angelman syndrome are two very different disorders linked to the same imprinted region of chromosome 15.

Question 32

What is Prader Willi syndrome?

Answer 32

Prader Willi syndrome results in learning difficulties, short stature, compulsive eating, obesity. Individuals are missing gene activity that normally comes from dad. Contains the paternally expressed SNRPN and NDN and maternally expressed UBE3A. Due to a deletion.

Question 33

What is the parental conflict hypothesis?

Answer 33

The inequality between parental genomes is due to imprinting is a result of the differing interests of each parent in terms of the evolutionary fitness of their genes.

Father wants the growth of his offspring, at the expense of the mother. Mother wants to conserve resources for her own survival while providing sufficient nourishment to current and subsequent litters.

Accordingly, paternally expressed genes tend to be growth promoting whereas maternally expressed genes tend to be growth limiting.

Question 34

What is an example of an imprinted gene?

Answer 34

An example the Igf2 receptor. If the mothers Igf2 are deleted then you get a large offspring (would normally limit growth), if the fathers Igf2 are deleted then you get a small offspring (would normally encourage growth).

Question 35

What is Beckwith Wiedemann Syndrome?

Answer 35

The IGF2 gene (but not the IGF2 RECEPTOR gene) is also maternally imprinted in humans. A DNA mutation or an “epimutation” (missing epigenetic marks) can activate it, resulting in two active copies of the gene. Known as Beckwith Wiedemann Syndrome.

Babies with BWS are born larger than 95% of their peers. Also have an increased risk of cancer, especially during childhood.
BWS incidence ~1 in 15,000 births but may be as high as 1 in 4,000 in babies conceived with help of artificial reproductive technology (ART).

This and other evidence of imprinting errors is prompting some to call for further investigation into the safety of common ART laboratory procedures. Environmental signals can also affect the imprinting process including diet, hormones, and toxins.

Question 36

What is a hydatiform mole?

Answer 36

When a normal sperm cell fertilizes an oocyte, the resulting embryo has only one set of chromosomes because the embryo has no genes from the mother due to mutation, the pregnancy cannot develop normally, resulting in a hydatidiform mole.

Question 37

What is a transposable element?

Answer 37

This is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell’s genetic identity and genome size. They are unstable and need to be methylated.

Question 38

How much DNA is noncoding?

Answer 38

There are 3 billion base pairs of DNA and a small percentage codes protein. Most of the rest is made up of several types of noncoding repeated elements. Interspersed repetitive elements are in single copies and distributed widely throughout genome. Constitute ~45% of genome includes transposons.

Question 39

How much of repetitive elements are methylated?

Answer 39

Repetitive elements are usually methylated to suppress their activity. An active transposon is potentially disastrous, i.e., cancer. This is why ~60 90% of all CpGs are methylated in mammals.

Question 40

How does methylation change with age?

Answer 40

During aging, there is a continuous accumulation of epigenetic changes, which might give rise to multiple age-related pathologies. Monozygotic twins exhibit an increased rate of phenotypic discordance particularly for age related diseases among older siblings. Epigenetic differences increase from young to old twins.

Question 41

What did Steve Horvath do?

Answer 41

Steve Horvath (2013) developed an age predictor based on DNA methylation values of 353 individual CpG sites.

The clock starts ticking early during development where foetal tissues as well as embryonic and induced pluripotent stem cells reveal a DNA methylation age ( DNAm age) between −1 and 0. Epigenetic clocks have been also proposed to measure molecular processes involved in development and tissue homeostasis particularly those affecting stem cell differentiation as well as replenishment of committed cells.

Question 42

What are the epigenetic markers for age-related disease?

Answer 42

DNAm age acceleration is associated with incidence, future onset, and mortality across several types of cancer. DNAm age was reported to be a useful biomarker for predicting physical and mental fitness in elderly individuals (Marioni et al., 2015) and was shown to be associated with cholesterol, insulin, glucose, and triglycerides levels (Levine et al., 2018).

The accelerated ageing disease, Werner syndrome, showed DNAm age acceleration of >6 years. DNAm changes associated with Diabetes, neurodegenerative diseases, heart disease etc.

Question 43

What is the Baker hypothesis?

Answer 43

Hypothesis - multiple factors during pre-pregnancy, pregnancy, and the early postnatal period influence long lasting disease susceptibility in offspring.

Depending on how your childhood was, stressful or not stressful, this can impact how adapted you are in your adult life. For example, a highly stressed child who doesn’t need to be stressed in adulthood will bring that stress from childhood and result in an anxious and stressed adult which can result in mental health problems. This can apply to many environmental factors such as diet, exercise, etc. Early in childhood you have a developmental plasticity, if not adapted correctly then this can result in more health conditions when older.

Question 44

What is the thrifty phenotype hypothesis?

Answer 44

Hales and Barker (1992) - maternal undernutrition could retard the growth of foetal beta cells in utero and subsequently lead to T2DM and metabolic syndrome in adult life. This hypothesis is known as the “thrifty phenotype hypothesis,” because a foetus can be forced to assume its most thrifty phenotype tailored to a
maternally undernourished environment.

Question 45

What is the mismatch theory?

Answer 45

Developmental plasticity attempts to tune gene expression to produce a phenotype best suited to the predicted later environment. When the resulting phenotype is matched to its environment the organism will remain healthy. When there is a mismatch, the individual’s ability to respond to environmental challenges may be inadequate and risk of disease increases. Thus, the degree of the mismatch determines the individual’s susceptibility to chronic disease.

Question 46

What is maternal diabetes and its affects?

Answer 46

Diabetes during pregnancy can have long lasting metabolic effects on offspring. A study in Pima Indians found maternal diabetes increased development of T2DM, higher systolic blood pressure and haemoglobin A1c, and greater rates of obesity in offspring (Dabelea et al. 2000).

Mothers with overweight or obese BMIs (or excessive weight gain) during early pregnancy had children that were significantly more likely to be overweight at 3 years of age (Olson et al. 2009).

Question 47

What effect can maternal undernutrition have?

Answer 47

Hypothesis - energy deprivation retards growth of the specific system that is affected. E.g., since the second trimester is a period of rapid nephron and bronchial development, undernutrition during these periods could lead to negative, organ specific health outcomes in adult offspring such as microalbuminuria or obstructive airway disease (Painter et al. 2005).

Famine exposed foetus’ had lower birth weight associated with CVD and metabolic syndrome later in life. Time specific exposure to famine during late pregnancy was most closely associated with impaired glucose tolerance in offspring. Mid gestation increased incidence of microalbuminuria and obstructive airway disease in offspring. Early gestation increased coronary heart disease and obesity, lipids, and altered clotting later in life.

Question 48

What affect can paternal diet have on offspring?

Answer 48

Paternal and grand paternal diet may lead to both positive and negative phenotypes in offspring. Studies of Swedish birth cohorts found - Fathers who experienced low food availability during their “slow growth period” (defined as ages 9-12 for men) had offspring that showed lower CVD mortality (Kati et al. 2002).

Increased survival if their paternal grandfather experienced low food availability during their slow growth period. Excess food availability had the opposite effect (Bygren et al. 2001).

Additionally, subjects displayed increased diabetes mortality when the paternal grandfather lived through high food availability during their slow growth period. Food restriction can have a very different effect depending on the timing of fathers who were undernourished in gestation due to the Dutch famine
had offspring that were more obese (Veenendaal et al. 2013).

Question 49

What effect can the postnatal diet have on lifespan?

Answer 49

Calorically restricted in mice early life show increase (18%) in median life span. Limiting postnatal growth increases longevity and protects against the life shortening effect of an obesity inducing diet later on. By contrast, lifespan is shortened if the postnatal period of growth is accelerated to make up for reduced growth in utero, and that, in addition, these mice are susceptible to the adverse effects on longevity of an obesity inducing diet after weaning. (Ozane et al. 2004).

Question 50

What affects do environmental toxicants have on offspring?

Answer 50

Prenatal exposures to multiple environmental toxicants pose significant risk to the health of offspring in both mouse models and humans. Correlations have been made between prenatal cigarette smoke exposure and later disease in humans and prenatal cigarette smoke and environmental toxicant exposure and life span decreasing diseases in rodents. Further studies show exposure to toxins during pregnancy can impact the 3rd generation.

Question 51

What affects do polychlorinated Biphenyls?

Answer 51

Polychlorinated biphenyls (PCBs) found in insulating material, plastic softeners, and
electrical equipment. Though banned in the 1970s exposure still continues today due to contaminated groundwater and food supply. Female mice offspring exposed perinatally to endocrine disruptors (PCBs, herbicides etc.) show multigenerational transmission of effects.

Question 52

What affects does stress have on offsrping?

Answer 52

Maternal social stress and mental health during pregnancy on offspring health and disease. Increased levels of stress related behaviours. Greater rates of inflammation in adult offspring independent of adult depression (Plant et al. 2016). Predicts insulin resistance and higher BMI in adult offspring (Entringer et al. 2008).

Question 53

How can the season on birth affect life?

Answer 53

Season of birth has been shown to have an influence on longevity and health e.g., a US study of 1880 1895 born centenarians odds of becoming a centenarian increased if the month of birth was in the second half of the year (especially September November) as opposed to the first half of the year (Specifically March).

Question 54

How does prenatal exercise affect offspring?

Answer 54

Studies suggest prenatal exercise can lower the risk for age related diseases which could increase life expectancy. Maternal exercise (voluntary wheel running vs. sedentary) significantly improves both insulin sensitivity and glucose homeostasis in offspring. In humans, maternal exercise associated with increased foetal heart rate variability and decreased heart rate, indicative of improved cardiac autonomic control (May et al. 2010). In mice improvements in cancer risk and Alzheimer’s risk in offspring have been observed as well (Herring et al. 2012).