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(ANDREW) Epigenetics in Development and Disease > Lecture 5 > Flashcards

Lecture 5 Flashcards

1
Q

What is genomic imprinting?

A

A form of epigenetic regulation that results in mono-allelic expression in a parent-of-origin-dependent manner

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2
Q

How imprinted genes are there? Where in the genome are they found?
How are they regulated?

A

~90 imprinted genes
Often found in large clusters
Regulated by an Imprinting control region (ICR) for each cluster, as well as non-coding RNAs and differential DNA methylation

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3
Q

What is imprinting established?

A

During gametogenesis and not removed during global erasure after fertilisation

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4
Q

Which protein has been implicated in protecting these genes?

A

PGC7/Stella

As seen in protecting maternal non-imprinted genes from active de-methylation

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5
Q

When is the methylation pattern of the primordial germ cell precursors erased?

A

Whilst migrating through the embryo to the gonad’s

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6
Q

When is parental imprinting put down?

A

Before birth and maintained through the meiotic divisions that give rise to sperm cells

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7
Q

When is maternal imprinting put down?

A

Post birth during the oocyte maturation

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8
Q

What happens if both pronuclei are from the same sex?

A

Nuclear transfer of pronuclei to create all combinations showed that pronuclei from the same sex could not create a fully formed embryo or extra-embryonic tissue
Two female nuclei= trophoblast undergrowth, and small embryo
Two male nuclei= trophoblast overgrowth, and deformed embryo

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9
Q

How is H19-Igf2 imprinted differently between maternal and paternal?
What is each protein for?

A

Maternal chromosome has active H19 and inactive Igf2, and the inverse in paternal. H19 is a non-coding RNA and Igf2 encodes a protein that promotes embryonic and placenta growth.

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10
Q

What causes the difference in imprinted H19-Igf2 between maternal and paternal?

A

The two genes are separated by an imprinting control region (ICR). In females the ICR is not methylated and bound by CTCF (an insulator), blocking enhancers down stream from causing Igf2 expression and instead H19 is expressed . In males the ICR is methylated and CTCF cannot bind so enhancer cause expression of Igf2.

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11
Q

What was shown about H19-Igf2 in mice experiments?

A

Igf2 mutant female crossed with normal male= normal offspring
Normal female crossed with Igf2 male= small off-spring

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12
Q

What pair of imprinting disorders are associated with the H19-Igf2 cluster?

A

Beckwith-Wiedemann (BWS) and Silver-Russel (SRS) syndrome

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13
Q

What epigenetically causes BWS and SRS and what are the phenotypes?

A 
BWS= Gain of methylation on the maternal ICR, and Igf2 is expressed from both alleles. Causes overgrowth disease
SRS= Loss of DNA methylation of paternal ICR, and H19 expressed in both alleles. Causes growth retardation
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14
Q

What controls the Igf2R-Air cluster?

A

Anti-sense transcription and differential DNA methylation

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15
Q

Which is expressed in which sex’s gamete?

A

IGF2R in maternal and Air in Paternal

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16
Q

How is expression of the Igf2R-Air cluster controlled between the sexes?

A

In maternal, methylation of Air ICR switches off AIR and allows Igf2R
In paternal, lack of methylation of Air ICR allow its expression, which turns off Igf2R, due to Air being antisense to Igf2R

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17
Q

What is the common pattern in effect on growth of alleles from the sexes?

A

Maternal allele is trying to suppress growth and paternal allele is trying to encourage growth

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18
Q

How is epigenetics different in plants?

A
  • Cytosine methylation in all sequence contexts in all tissues
  • Changes in DNA methylation can be transmitted through multiple generations
  • Plant cells can switch cell fate
19
Q

What type of DNA methylation pattern is seen in plants?

A

Mosaic - some gene body methylation mainly of CG dinucleotides and methylation of all repetitive sequences, CG, CGH or CHH, to maintain heterochromatin and suppress transposable elements

20
Q

What plant is mainly used to study?

A

Arabidopsis

21
Q

Which methyltransferase do plants have for de novo?

A

Drm2

22
Q

Which methyltransferases do plants have for maintenance?

A

Met1 and Cmt3

23
Q

What is DDM1?

A

A chromatin remodelling factor is is required for maintainance of DNA methylation

24
Q

How was DDM1 used by Katuatni to investigate role of DNA methylation in plants?

A

Self crossing ddm1 muatnt six times causes loss of methylation and affects plants development (different few phenotypes seen due to which transposons start moving first?)

25
Q

Why is the methylation pattern passed on through generations of plants?

A

Plants do not carry out the global erasure seen in mammalian development post-fertilisation

26
Q

Why might plants not want to carry out the erasure?

A

Epigenetic changes due to environmental information may be useful for next generations being able to survive

27
Q

How was stress memory in progeny shown by Boyko?

A

Plants grown on increasing concentration of NaCl2 and their germination rate measured. Progeny of plants who had been grown on high salt had higher germination rates. DNA methylation has also shown to be different between progeny of stress and control parent plants

28
Q

What did Teixeria show about ddm1 mutants?

A

Crossing back to wild type to restore DDM1 to normal levels cannot fully restore DNA methylation of gene bodies but can restore DNA methylation of transposable elements and repeats

29
Q

What is commonly seen accumulating in areas of high transposable element methylation?

A

sRNAs

30
Q

Which area of plant genomes are common targets for RNA silencing lead methylation?

A

Transposable elements and repeats

31
Q

What type of RNAs do animals use to epigenetically silence transposons?
Where does this process happen most?

A

piRNA’s

In germ cells - to ensure that the transposable elements are off in the offspring

32
Q

What are the key post embryonic developmental stages of plants?
What proteins control gene expression through these stages?

A

1) Fertilization
2) Seed development
3) Transition to flowering
4) Flower organogeneis
Controlled by Polycomb and trithorax

33
Q

Which polycomb complex does the plant have versions of?

A

PRC2 - versions; FIS, EMF and VRN

34
Q

What is vernalization?

A

Acceleration of flowering by prolonger cold is known as vernilization (quite long period of time)

35
Q

How floral transition inhibited?

A

Transcription favtor FLC represses SOC1 and FT. With FT being the flower transition gene

36
Q

How is FLC epigenetically controlled?

A

In cold VRN complex, which was already associated with the FLC gene, forms complex with VIN3, VEL1 and VRN5. VIN3 only turned on in cold and is main driver for complex formation. The complex spreads across the FLC gene in prlonged cold. When warm temperatures return, VIN3 turned off but VRN5 and VEL1 stay associated with the VRN complex and keep FLC off. This is then reset in offspring.

37
Q

Outline how is VIN3 turned on

A

Some unknown tirgger of cold causes to be turned on. Removal of some PRC2 and repressive marks and gain some of Trithorax complex and active marks (bivalent) In warm temperature returns back to only PRC2 marks.

38
Q

What type of cells are found in maternal gametophyte?

A

Central cell which is diploid and forms the endosperm and the embryo cell which is haploid and forms the embryo

39
Q

What type of cells are found in paternal gametophyte?

A

2 haploid sperm cells

40
Q

What happens in flower plant fertilisation?

A

Sperm cells fertilises the embryo cell to from diploid and the other sperm cell fertilises the central cell to produce a triploid

41
Q

Where does imprinting occur in the flowering plants?

A

Primarily in the endosperm

42
Q

What controls endosperm growth before fertilisation?

A

The PRC2 complex, FIS

43
Q

How are the FIS components turned on the endosperm?

A

DEMETER DNA glycolsylase removes methlyation from the genes activating them

44
Q

What roles does FIS play after fertilistion?

A

Acts to keeps maternal FIS genes active, while repressing paternal FIS genes. Inhibits maternal PHE1 but keeps the paternal PHE1 on. Ensures optimal growth of endosperm

(ANDREW) Epigenetics in Development and Disease (8 decks)

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