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GENE3340 MOLECULAR GENETICS > Epigenetics > Flashcards

Epigenetics Flashcards

1
Q

Define epigenetics

A

The study of reversible heritable changes in gene function that occur without a change in the sequence of DNA

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2
Q

What did Bird propose?

A

A modern definition that avoids the requirement for heritability in epigenetics

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3
Q

What are the mechanisms of epigenetics?

A
  • histone modification and chromatin remodelling
  • DNA methylation
  • Non-coding RNA mediated regulation
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4
Q

Which nucleotides are purines?

A

A and G

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5
Q

Which nucleotides are pyrimidines?

A

T and C

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6
Q

What is an epigenetic landscape?

A

A metaphor in which valleys and ridges illustrate the epigenetic landscape that guides a pluripotent cell to a differentiated state, represented by a ball rolling down the landscape

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7
Q

What are some examples epigenetics play roles in?

A

Developmental process, whereby an undifferentiated cell undergoes differentiation towards it final state.

E.G. lymphoid/myeloid development, T-helper, neural stem cells and muscle differentiation

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8
Q

What is the histone code hypothesis?

A

Modifications of histone tails act as epigenetic marks that control the expression or replication of chromosomal regions

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9
Q

What does DNMT1 do? What does DNA demethylase do?

A

Follows the replication fork adding methylation marks to newly synthesized DNA - re-established histone modifications.

DNA demethylase takes off replication marks

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10
Q

What is DNA methylation?

A

An epigenetic gene regulation.

In vertebrates, 5-methylC residues within the CpG dinucleotide. 5-hyrdomethylC, 5-formylC and 5-carboxylC appear as intermediates of active DNA methylation during embryogenesis

In plants CpG, CpNpG and CpHpH methylation common

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11
Q

What processes is methylation involved in?

A
  • embryonic development
  • X chromosome inactivation
  • Imprinting
  • gene silencing
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12
Q

What is an example of epigenetic embryonic development?

A

Agouti gene mutation in mice

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13
Q

What does agouti encode for?

A

A paracrine signalling molecule that promotes follicular melanocytes to produce yellow pheomelanin rather than black eumelanin pigment. The mutant is a result of the insertion of a murine IAP transposable element ~100kb upstream of start site of the agouti gene

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14
Q

What happens if the diet is mice with agouti mutation are supplemented vs unsupplemented?

A

While pregnant both mothers fed Bisphenol A (BPA) but different diets:

  • mothers of yellow mice received normal diet
  • mothers of brown were supplemented with choline, folic acid, betaine and vitamin B12
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15
Q

What is X chromosome inactivation?

A

At ~1000 cell stage, cell choose one X chromosome to remain ON. Other is inactivated via XIST (X inactivation specific transcript) an X chromosome encoded LncRNA. XIST coats the X chromosome leading to heterochromatin spreading and methylation

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16
Q

What happens in mammalian X chromosome inactivation?

A

Early female embryo has both X’s active. Methylation patterns are heritable through mitosis, but reset during oogenesis. Fully developed female is a mosaic of different clones

17
Q

What is genomic imprinting?

A

Parent-specific expression or repression of genes or chromosomes in offspring. Only the maternal or paternal allele is expressed.

18
Q

Which allele is said to be imprinted in genomic imprinting?

A

The non-expressed allele

19
Q

What is the evolutionary explanation for genomic imprinting?

A

The explanations remain controversial. The conflict/kinship theory posits that imprinting evolved as a result of different selection pressures on maternally and paternally derived selection pressures on maternally and paternally derived alleles

20
Q

What are imprinted diseases characterized by?

A

By non-mendelian inheritance patterns that exhibit parental-origin effects. Symptoms suggest a role of imprinted genes in growth regulation during embryonic and postnatal development, brain function and behaviour

21
Q

What are some examples of imprinted diseases?

A
  • Beckwith-wiedemann syndrome
  • prader-Willi syndrome
  • angelman syndrome
  • wilms tumour
  • fragile X syndrome
  • myotonic dystrophy
22
Q

What 2 diseases both involving imprinting defects at 15q11-q13?

A

Angelman syndrome and Prader-Willi syndrome

23
Q

What is Angelman syndrome?

A

Severe mental retardation, microcephaly, lack of speech, frequent laughter. Result of deletion of maternal 15q11-q13 (loss or inactivation of maternal UBE3A gene)

24
Q

What is Prader-Willi syndrome?

A

Mild mental retardation, obesity, short stature. Result of deletion of paternal 15q11-q13 (loss or inactivation of maternal UBE3A gene)

25
Q

What is Beckwith-Wiedemann syndrome?

A

Embryonic and placental overgrowth, predisposition to childhood tumours. Caused by increased expression of IGF2 and suppression of CDKNIC

26
Q

What are conditions caused by many contributing factors called?

A

Complex or multifactorial disorders

27
Q

How many participants minium are required for GWAS studies?

A

10,000+ participants

28
Q

Within what variant was obesity associated with?

A

Within FTO form functional long-range connections with IRX3 (intron 1). Influences expression of IRX3/5 via interaction with repression factor ARID5B

29
Q

What are the types of study designs for EWAS?

A
  • Case vs control (many cohorts, can’t easily control genetic/environmental)
  • families (can study potential inheritance; few large cohorts)
  • disease-discordant monozygotic twins (controls for genetics; few large cohorts exist)
  • prospectively sampled, longitudinal (can establish causality; slow and difficult to establish)
30
Q

What would a study using monozygotic twin pairs having immune cells profiled for T1 diabetes entail?

A
  • Can use DMP (differentially methylated position) or DVP (differentially variable position)
  • comparing disease versus healthy cohort
31
Q

What is the relationship between aging and epigenetics?

A

Twin studies show DNA methylation variation is influences by genetics and increasingly diverges with age. Methylation of specific CpG sites as a biological clock. Studies found lifelong progression of methylation loss is a biomarker for cellular aging

32
Q

What are induced pluripotent stem cells (iPS cells)?

A

Type of pluripotent stem cell that can be generated directly from adult cells. Gene editing using CRISPR technology applied to iPS cells to enable repair of disease-causing genetic lesions. Reprogramming induces changes to the DNA methylation pattern throughout the genome to a state that is very similar to embryonic stem cells. Reprogrammed iPS cells retain an epigenetic memory of the cell of origin which may limit differentiation and therapeutic capacity

33
Q

What is the methylation patterns in cancer?

A

Regions that are normally unmethylated (CpG islands) become methylated, and regions that are normally methylated become unmethylated

34
Q

What are some epigenetic regulators that drive cancers?

A

Epigenetic regulatory genes are significantly mutated in many sub-types of solid and haematological cancers. E.g.g MLL-gene rearrangements, DNMT3a, TET2

35
Q

What are the 3 types of epigenetic regulators?

A
  1. Writing: add on
    - acetylases, methylases, phosphorylases
  2. Erasing: taking off
    - deacetylases, demethylates, phosphatases
  3. Reading: bind modified histones
    - bromodomain, chromodomain, PHD finger, WD40 repeat

GENE3340 MOLECULAR GENETICS (20 decks)

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