GH - Lecture 11 + GLS

Active, inactive, and silent. It tends to switch more between active and inactive, but rarely becomes active again once it is silent.

What are the 3 states of activity chromatin may be in and switch between?

This happens via the epigenome

By what mechanism can chromatin move between states of activity? (general)

During the formation of gametes

What is one major instance where silent chromatin must become active again?

Epigenetics is concerned with the genetic mechanisms which cause changes in phenotype and are not encoded by the GCAT sequence of DNA, but a higher mechanism which controls these

Provide a breif definition of epigenetics

Cell differentiation in the embryo

Name an example of normal epigenetic changes in the human body

The progress of cells from a totipotent state to a pluripotent state as the zygote enters the morula stage with 16-32 cells, abojut 4 days after fertilisation

What is the first epigenetic change in the human body?

This is the final commitment step in cell differentiation in which a cell only expresses genes of its cell type and can no longer replicate and has a set lifespan (eg: myotcyte, osteocyte)

What does terminal differentiation entail?

This is largely determined by extracellular chemical signals such as hormones

How do cells 'know' what epigenetic changes they must undergo in order to become the right type of cell?

Morphogens

What is the term for chemical messengers that control the location, differentiation and fate of surroudning cells

- diffusible molecules

- non-diffusible molecules which bind to extracellular receptors

- direct contact via gap junctions

Name 3 types of chemical cellular messaging

Cells called "organisers" emit these signals and determine the fate of surrounding cells through varying morphogen concentrations

What is a common source of morphogens in embryogenesis?

Histone modification and DNA methylation

What are the two main mechanisms through which cell memory is produced and genes are turned on or off?

N-terminal histone tails

What part of the histone is modified in histone modification?

Yes

Is histone modification hertiable?

On: acetylation

Off: methylation

(In reality more complicated and depending on specific patters of acetylation, phosphorylation, and methylation)

In simplest terms, which molecules are responsible for turning genes on and off respectively for histone modification, as they are added to histone tails?

Methyl groups inactivate genes, demethylation activates them (active genes are not completely free of methyl groups)

Which molecules are responsible for turning genes on and off at the DNA level?

Histone acetylase + Histone deacetylase

Histone methylase + Histone demethylase

DNA methylase + DNA demethylase

Which enzymes are responsible for methylation and acetylation respectively?

5' Carbon of Cytosine when cytosine is followed by a guanine

At which specific point are methyl groups typically added to DNA?

CpG; 5'-C-phosphate-G-3'

What is the common name for a CG doublet?

5-methylcytosine

What is the methylated version of cytosine called?

Initially replicated DNA is hemimethylated (only 1 strand methylated). Methyl groups are then added by DNA methyltransferase 1 (Dnmt1)

How is DNA methylation maintained through replication?

This is done by DNA methyltransferase 3 (Dnmt3)

How are new/de novo methyl groups added?

DIrectly: by repelling transcription factors

Indirectly: by recruiting suppressor proteins which then stop binding of transcription factors

How do methyl groups suppress gene expression?

A region of the gene in which high numbers of CG doublets are found which can be methylated

What is a CpG island?

During gametogenesis, epigenetic tags are removed. These return in the gamete in a patterns that follows the parent of origin for a small number of genes (imprinting). The rest are heritable to a degree and reappear in the same spots where they were in the parents

How do epigenetics affect offspring?

Epigenetic markers are established during gamete formation for both parents. These markers are retained through cell divisions in the conceptus and later determine which genes are expressed or inactive

How does imprinting work?

This happens due to environmentally influenced de novo marking: DNA methylation and histone modification that is adaptive to the environment

How do epigenetics vary between monozygotic twins?

Mouse model: pups which were nurtured more by their mothers expressed more glucocorticoid receptors via demethylation of GR gene. This had an effect on their behvaiour and they were less likely to become stressed and calmer overall

Give an example of how external stimuli can influence epigenetics and how those can in turn influence behaviour

Food high in folic acid, B vitamins, and S-adenosyl methionine are components in the methyl making pathway and hence contribute to methylation patterns

How can diet influence epigenetics inhumans?

BPA consumption of mothers is linked to high rates of obesity in offspring, though maternal nutrient supplementation can suppress this

How can BPA affect offspring of mums who consume it?

Activities of the mother influence her epigenetic apparatus, the foetuses epigenetic apparatus, and the epigenetic apparatus which modifies the forming oocytes in a female foetus - 3 generations are affected epigenetically by 1 environment. Smoking during pregnancy affects not only the daughter but also the grandchild

What is the special epigenetic phenomenon seen in pregnancy?

ONly a small proportion ~70 genes

What proportion of genes are turned on or off via imprinting of the parent of origin?

Homeobox genes are genes which are highly preserved all the way from arthropods to mammals

What are HOX genes?

39

How many HOX genes do mammals have?

In 4 clusters (A,B,C,D) along the genome - these are inherited together

How are HOX genes distributed?

They are transcription factors which control gene expression that controls the body plan

What do HOX proteins do?

Duplication of hox clusters allow for development of additional complexity in the organism. They can also serve as backups

How have HOX clusters contributed to differences between species?

This would cause incorrect segmentation of the body plan

What would happen if HOX genes are not properly activated during prenatal development?

Twice

How often have HOX clusters duplicated through human evolution?

Spacial and temporal regulation of genes (turned on in the right place and turned on at the right time)

In which ways are HOX genes regulated

These are expressed sequentially and control limb development

What is the role of HOX D9- HOX D13

Different mutations will produce different abnormalities, as it is for any gene. Mutations may lead to different types of syndactyly: conjoined fingers

The HOXD13 gene plays an important role in correct finger development. Explain what kind of errors may occur during mutation?

Y chromosome

When it comes to phenotypic sex, which chromosome is 'dominant' over the other?

SRY (sex-determining region of the Y chromosome)

What is the gene that determines sex?

Testis Determining Factor (TDF)

What is the transcription factor produced from the SRY gene, which produces testes?

Near the telomere on the p (short/petite) arm

Where is the SRY gene located on the Y chromosome?

These are regions at which the X and Y chromosome can cross over

What are the pseudoautosomal regions?

1. the SRY region has crossed over to the X chromosome which ended up in another gamete

2. Damage to the telomere and subsequent loss of the SRY region which resides very close to it

3. Duplication of DAX1 on the X-chromosome which antagonises the SRY gene, when duplicated

Explain 3 ways through which you might get an XY female

These are important for formation of the testes. SOX9 is downstream from SRY and DAX1 is found on the X chromosome

What are the normal roles of SOX9 and DAX1? Where are they found?

Dosage-sensitive sex reversal (DSS)

Name the phenomen which occurs when DAX1 is duplicated and antagonises SRY

The SRY region from a Y chromosome may have crossed over to one of the X chromosomes

Explain how an XX male can be produced

Germ cells: oogonia

Coelomic cells: granulosa cells

Mesenchymal cells: Theca cells

What do the following cells of the indifferent gonad become in the absence of SRY:

Germ cells, Coelomic epithelium, Mesenchymal cells

Germ cells: Spermatogonia

Coelomic cells: Sertoli cells

Mesenchymal cells: Leydig cells

What do the following cells of the indifferent gonad become in the presence of SRY:

Germ cells, Coelomic epithelium, Mesenchymal cells

Sertoli cells

Which cells produce Anti mullerian hormone (AMH)/MIH/MIS

Leydig cells

Which cells produce androgens during sex development?

Via downstream gene cascades which are expressed in response to SRY

How does SRY exhibit so many different developmental changes?

Pax6, eyeless (named after mutant)

What is the gene for eye development called in mammals and flies respectively?

A mutation in Pax6 which results in complete loss of the iris

What is aniridia?

Loss of Function/Haploinsufficiency

Of which type of mutation are almost all Pax6 mutations?

Heterozygous, as 2 mutations are mebryonically lethal

What is the genotype for aniridia?

Neural tube formation

What is another VITAL role of Pax6?

Any agent that disrupts normal cellular development during organogenesis (including deficiencies)

Define teratogen

These are specific timeframes during embryonic and foetal development during which certain genes are expressed. During this time the individual is susceptible to teratogens for the affected body part.

What are critical periods?

A mother takes thalidomide during early week 4 of embryo development, when the upper limb forms, but stops very soon as her morning sickness improves. As a result a child with no long bones in the upper limbs, but normal lower limbs is born

Give an example of a teratogen affecting an individual during a critical period

Foetal alcohol syndrome (FAS), part of FASD, can occur when the mother drink alcohol during foetal development. The effects tend to be stronger when the mother drinks more and during critical periods

Name a common birth defect linked to maternal alcohol consumption during pregnancy and explain the relationship between the two

- Microcephaly

- Smooth philtrum

- Epicanthal folds: folds at inside of eye

- Underdeveloped curvature at the top of the ear

- Campodactyly: permanent flexion/contracture of a finger or toe

- Clinodactyly: permanent curving of 5th finger

Name 5 symtoms of FAS