2.8 Epigenetics

Question 1

Answer 1

Question 2

What is epigenetics?

Answer 2

Epigenetics is the study of changes in gene expression that occur without changes in DNA sequence.

Epigenetic changes are mitotically heritable

Question 3

In what way can epigenetic modifications be reset?

Answer 3

• Some epigenetic marks around implantation will persist for the entire lifetime
• Germ cell and early embryonic development is where epigenetic marks are removed (break in the cycle)

Question 4

Name the five epigenetic alterations

Answer 4

1. DNA methylation
2. Post translational histone modification
3. Non coding RNAs
4. Histone Variants
5. Nucleosome remodelling/chromatin remodelling

Question 5

Where does DNA methylation occur

Answer 5

• At CpG dinucleotides in mammals, regions where C is followed by G base
• A 5-methyl group is added

Question 6

How does DNA methylation occur?

Answer 6

• DNA methylation is laid down by de novo methyltransferases, DNMT3A and DNMT3B in mammals

Question 7

How is DNA methylation symmetrical?

Answer 7

• The new daughter strand of DNA (green) is not methylated
• Because it is semi conservative you still have one strand with methylation
• Maintenance DNMT1 lays down methylation on the other strand, recognising hemi methylated DNA

Question 8

Apart from CpG islands where else does DNA methylation occur?

Answer 8

Question 9

What is ICF syndrome?

Answer 9

• Immunodeficiency, Chromosomal instability and Facial Anomolies syndrome
• Very rare, autosomal recessive disorder with variable phenotypes

Question 10

What causes ICF syndrome?

Answer 10

• Mutation in DNA methyltransferase 3B (DNMT3B)
• Hypomethylation of a small amount of the gemone in patients - not enough methylation
  
  • Pericentromeric repeats at centromeres of chromosome 1, 9, 16 related to chromosomal instability
  • Hypomethylation of CpG islands on inactive X chromosome in females, Y chromosome in males
  • Some other genes, related neurogenesis, immune funciton, craniofacial patterning, which all relate to phenotypes in patients

Question 11

When does DNA demethylation happen?

Answer 11

• It is mitotically heritable, due to action of maintenance methyltransferase DNMT1
• DNA demethylation is shown to occur in early development, in primordial germ cell development and at later specific stages of differentiation

Question 12

How is DNA demethylation achieved?

Answer 12

Question 13

In what ways can DNA methylation cause silencing?

Answer 13

• It can interfere with transcription factor binding
• Result in the binding of methyl-CpG binding proteins which recruit other factors that alter chromatin state

Question 14

Where do histone tail modifications occur?

Answer 14

Question 15

What is histone acetylation?

Answer 15

• Acetylation is correlated with gene activity, partly due to reduced positive charge of histone.
• Not mitotically heritablem not strictly epigenetic, chromatin mark

Question 16

What is histone methylation?

Answer 16

• Histone methylation does not alter the charge of the histone
• It can correlate either with transcriptional activity or inactivity, depending on which histone tail residue is methylated
• Mono, di and tri methylation exist

Question 17

Why do histone tail modifications correlate with different chromatin states?

Answer 17

• Histone tail modifications are “read” by other chromatin proteins
• The interacting chromatin proteins may alter chromatin packaging or bring about other histone modifications
• They don’t cause altered gene expression but instead mark euchromatin or heterochromatin to be bound by other factors that themselves can alter accessibiility

Question 18

What is the role of histone tails and chromatin proteins?

Answer 18

• Modified histone tails act as docking sites for other chromatin proteins
• Proteins that bind Me or Ac at specific residues alter chromatin packaging or bring about additional epigenetic charges

Question 19

What are 3 examples of chromodomain proteins?

Answer 19

1. CHD1 - ATP dependent chromatin remodeller
2. HP1 - essential heterochromatin protein, can recruit DNA methyltransferase 1
3. CBX2 - part of polycomb repressive complex that lays down H2AK119ub, another epigenetic mark

Question 20

Answer 20

Question 21

What are two examples of long non coding RNAs?

Answer 21

• X inactivation (e.g. Xist)
• Genomic imprinting (e.g. Kcnq1OT1, Snrpn, Airn)

Question 22

What are some of the possible mechanisms for long non coding RNAs?

Answer 22

The common feature is that there is the formation of RNA - protein complexes that influence the regulation of gene expression

Question 23

How do long non coding RNAs guide epigenetic complexes of proteins?

Answer 23

• Sequence complementarity allows the lncRNA to guide the epigenetic modifier complex to a specific location in the DNA

Question 24

What is X Chromosome inactivation?

Answer 24

• X inactivation is an epigenetic dosage compensation mechanism in mammals, so that males and females have the same dose of genes on the X chromosome.
• Random X inactivation occurs at gastrulation in the embryo, then this epigenetic state is mitotically inherited by each daughter cell

Question 25

How does X inactivation manifest visually in cats?

Answer 25

* There is a ginger colour gene G, and the null allele giving a black coat (g) * Additional coat colour genes for white bellies * Coat colour patches and X inactivation maintained for the lifetime of the female mammal, due to mitotic heritability of epigenetic marks on the inactive X

Question 26

What epigenetic marks are needed for the inactive X chromosome?

Answer 26

* Xist long non coding RNA bound * Low levels of histone acetylation * Accumulation of H3K27me and H3K9me * DNA methylation of inactivated CpG islands

Question 27

What is Xist?

Answer 27

* Xist is aa 17kb long non-coding RNA that is critical for X inactivation * Xist expression from one of the X chromosomes is the first detectable event of X inactivation * Xist is expressed from the chromosoem that will become the inactive X * Xist RNA coats the inactive X elect *in cis*

Question 28

How does Xist influence epigenetic silencing?

Answer 28

* Xist RNA binds Hnrnpk, which then recruits polycomb repressive complex 1, which imparts H2AK119ub * H2AK119ub recruits polycomb repressive complex 2, which imparts H3K27me

Question 29

In 2015 what extra step of Xist X inactivation method was discovered?

Answer 29

Xist binds Spen. Spen may activate Hdac3 to enable deacetylation

Question 30

How heritable is X inactivation?

Answer 30

X inactivation status is stable and mitotically heritable. If paternal X was inactivated in the founder cell, all daughter cells will also have the paternal X chromosome inactivated

Question 31

What is Rett Syndrome?

Answer 31

* X-linked neurodevelopmental syndrome caused by mutations in a methyl binding domain protein MeCP2 * MeCP2 is encoded on the X chromosome * Lethal in males before birth (hemizygous) * Heterozygous females survive because they are mosaics

Question 32

What happens in there is XCI skewing with Rett Syndrome?

Answer 32

* X inactivation skewing is where is is usually an equal chance of either X chromosome being inactive, but can have uneven split * X^mutX: if skewing is such that X^mut is silenced 80% of the time it is less severe. If skewed so X is silenced 80% of the time then more severe

Question 33

How could Rett Syndrome possible be treated?

Answer 33

* Try to switch on the inactive X in the brain of Rett patients, meaning wild type copy of MeCP2 was made to bring about normal function. * This requires removing many epigenetic marks on the inactive X. the large number of redundant epigenetic marks results in vary stable silencing