Chromatin & Epigenetics

Question 1

What is epigentic inheritence?

Answer 1

The ability of a daughter cell to retain memory of the gene expression patterns that were present in the parent cell.

Question 2

E.g - female cats can have patchy coloured fur, what is this a result of?

Answer 2

Random X-inactivation. Two alleles, one is suppressed whilst the other is expressed.

Question 3

What did Mary Frances Lyon hypothesise?

Answer 3

She said that X-inactivation is to prevent XX female cells from expressing twice as many X-linked gene products as XY male cells.

Question 4

X- chromosome inactivation - early development - random inactivation - heritable in somatic cells

Question 5

What is dosage compensation?

Answer 5

Transcriptional X-inactivation in female somatic cells

Question 6

How does X-inactivation arise and what does it lead to?

Answer 6

The cells in the early embryo have a condensation of RANDOMLY SELECTED X chromosome during embryonic development - silenced. The future cells memorise which X chromosome is silenced. This leads to mosaicism.

Question 7

What does Xist stand for and what is it?

Answer 7

X-inactive specific transcript and is a lncRNA

Question 8

How does Xist lead to inactivation of an X chromosome?

Answer 8

Both X chromosomes during ES Cell development express Xist but one will express it more than the other. Xist RNA will ‘coat’ the Xi (inactive X). Xist RNA coating enables the complementarity with transcriptional repression complexes and chromatin modifiers leading to heterochromatinisation.

Question 9

What is the Xi now known as?

Answer 9

Barr body

Question 10

Where is Xist located on the X chromosome?

Answer 10

X-chromosome Inactivation Center (XIC)

Question 11

Where does the Barr body reside within the nucleus?

Answer 11

Localised close to the nuclear periphery 65%-80% of interphase cells.

Question 12

What is a nucleosome?

Answer 12

It is an octamer of histones. 147 base pairs wrapped around 8 histones.

Question 13

What are the histones?

Answer 13

Two copies of each H2A, H2B, H3, and H4

Question 14

Histone tails extend beyond the DNA

Question 15

What do the units of TADs (spatial organisation of chromatin in 3D space within the nucleus) represent?

Answer 15

Segregation of chromatin into active and inactive domains

Question 16

What are some covalent modifications the N-terminal tail can undergo?

Answer 16

Methylation, ubiquitylation, phosphorylation, biotinylation, acetylation, and more.

Question 17

Are these modifications reversible?

Answer 17

Yes

Question 18

Each particular histone modification is created by a specific enzyme. E.g - histone acetyl transferases (HATs) and histone deacetylase complexes (HDACs).

Question 19

Two forms of chromatin

Answer 19

Euchromatin & Heterochromatin. Either being transcriptionally active/inactive.

Question 20

What recognises the specific marks found on the histones?

Answer 20

Transcription factors

Question 21

What causes androgenetic lethality?

Answer 21

Two paternal chromosomes leads to failure of embryonic development

Question 22

What causes gynogenetic lethality?

Answer 22

Two maternal chromosomes leads to failure of extraembryonic development

Question 23

What do these show?

Answer 23

Chromosomes can carry parent-specific memories (imprints)

Question 24

What is the timeline of imprinting?

Answer 24

• 1st generation imprints in maternal and paternal parents before fertilisation
• Imprinting erasure precedes sex determination in gonads of developing embryo
• 2nd generation imprints acquired in oocytes/sperm

Question 25

When should imprinting be stable and not erased?

Answer 25

Once established, the imprint must remain on the same chromosome after fertilisation and be resistant to post-fertilisation reprogramming.

Question 26

When should imprinting be erasable?

Answer 26

During the reprogramming of germline cells

Question 27

What donates a methyl group to a DNMT for it to be donated to a cytosine?

Answer 27

S-adenosyl-L-methionine (SAM)

Question 28

Where are the predominant sites of methylation?

Answer 28

CpG dinucleotides (C in front of the G)

Question 29

Which enzymes are responsible for de novo methylation?

Answer 29

DNA methyltransferases - DNMT3A & DNMT3B

Question 30

Which enzyme is responsible for maintenance methylation?

Answer 30

DNMT1

Question 31

What are usually unmethylated and why?

Answer 31

CpG islands because they contain promoters

Question 32

Transposable elements are usually methylated to remain inactive

Question 33

Demethylation occurs after fertilisation for most genes, which genes do not get methylated during the first wave of demethylation?

Answer 33

Imprinted genes are not demethylated.

Question 34

When do they undergo demethylation and why?

Answer 34

During the production of PGCs so that new sex-specific imprints can be established depending on whether the embryo is male or female.

Question 35

Which enzymes remove methyl groups from the cytosine and what is the pathway after this? (active demethylation)

Answer 35

Tet enzymes oxidise the 5mC
- 5mC (5 methyl cytosine)
- 5hmC (5 hydroxymethyl cytosine)
- 5caC (5 carboxyl cytosine)
- 5fC (5 formyl cytosine)

Question 36

What are two mechanisms of passive demethylation?

Answer 36

1. DNMT1 fails to recognise 5hmC
2. DNMT1 is absent or inhibited

Question 37

What are four processes associated with DNA methylation in mammals?

Answer 37

1. Genomic imprinting
2. X-chromosome inactivation
3. Repression of TEs
4. Ageing

Question 38

Most imprinted genes appear in clusters, what are they controlled by?

Answer 38

Imprint Control Element (ICE)