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MCB1 Block 4 > Epigenetics & Genomic Imprinting > Flashcards

Epigenetics & Genomic Imprinting Flashcards

1
Q

what is epigenetics

A

gene regulatory mechanisms that do not directly involve DNA sequence
So it involves chromatin structure

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2
Q

how does epigenetics control gene regulatory mechanism

A

via chromatin structures - euchromatin and heterochromatin

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3
Q

what is euchromatin

A

open, available for transcription

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4
Q

what is heterochromatin

A

closed, unavailable for transcription

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5
Q

epigenetic effects can be: (list 4 things)

A

dynamic
stable through life of a cell
stable through mitosis and be passed onto daughter cells after division
stable through meiosis and be passed from a parent to an offspring

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6
Q

what is an epigenetic mark

A

modification occuring that controls chromatin structure

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7
Q

can the enviornment affect epigenetic marks

A

yes

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8
Q

what can lead to obesity regarding this subject

A

epigenetics - if parents are obese they can change thei way their genes are expressed and passed that to their children

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9
Q

DNA methylation is involved in what

A

gene silencing

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10
Q

histone modification is what

A

histone acetylation -activation

histone methylation - variable

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11
Q

ATP-Dependent Chromatin Remodeling - is what

A

Si/Snf can activetly change the structure, can open or close the chromatin

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12
Q

What are variant histones

A

Like H2A, H2A.Z, just different histones that have different affects on chromatin structure

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13
Q

dpeneding on which variant is in nucleosome means what

A

greater propensity for euchromatin or heterochromatin

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14
Q

noncoding RNA h-how do they affect epigenetics

A

miRNA, siRNA, IncRNA

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15
Q

what is imprinting

A

one parent has epigeneitc mark that gets inherited by child

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16
Q

what is x chromosome inactivation related to epigenetics

A

balances gene expression b/w males and females

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17
Q

how does DNA hypermethylation affect cancer

A

silencing of tumour suppressor and other genes

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18
Q

explain general process that needs to happen to clone mammal

A

differentiated cell (like skin cell), want to make it pleuripotent, have to erase all the specific epigentic marks and then reestablish epigenetic marks consistent with pluripotent cells

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19
Q

What is SCNT

A

somatic cell nuclear transfer

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20
Q

what happens to somatic cell nuclear DNA when it gets put into egg cell

A

it turns pleuripotent

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21
Q

DNA methyltation is an example of what

A

epigenetic control method

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22
Q

where does DNA methylation happen

A

on cytosines when they are in CpG sequence

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23
Q

If template strand is methylated what happens to the other coding strand

A

it is also methylated, it would also have CpG in the other direction

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24
Q

Large amounts of CpG islands means what

A

high frequency of CGg, hypermethylation and strong silencing

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25
Q

spontaneous deamination of C leads to what

A

U

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26
Q

Because uracil is not a normal base in DNA what happens

A

mistmatch repair, it ultimately makes thymine

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27
Q

What is the ulatimate result of spontaneous deamination of C

A

mismatch repair may happen, which could ultimately change the DNA sequence depending on which strand is repaired

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28
Q

What disease has one of the most frequently mutated bases in the humane genome

A

Achondroplasia:

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29
Q

when cytosines are methylated it promotes what

A

heterochromatin structure

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30
Q

What methylate the cyosines

A

DNA methyltransferases

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31
Q

Once DNA is methylated what binds to methyl groups and binds

A

methyl-binding domain proteins like MeCP2

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32
Q

CG dinucleotides are underrepresented, why?

A

because spontaneous deamination of C happens so often, mismatch repair: C → T (deamination of Me-C) and G → A (mismatch repair)

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33
Q

What does DNA hypomethylation do?

A

activates oncogenes, resulting in chromosome instability & activates transposons

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34
Q

What do mutations at methylated cytosines do?

A

results in inappropriate gene expression

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35
Q

What do imprinting defects result in?

A

loss of parental identity

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36
Q

Once DNA becomes methylated, what happens to it

A

it stays methylated

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37
Q

If DNA is methylated what happens to it once it goes through mitosis

A

daughter cells will be methylated and it stays methylated

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38
Q

What is the majority of methylation used for

A

through development as genes are no longer needed they are silenced via methylation

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39
Q

Do primoridal cells have a lot of methylation?

A

no - very low levels of methylation

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40
Q

describe methylation levels of sperm and egg

A

sperm has more methyation than egg, they both have higher methylation than primordial germ cells

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41
Q

immediately after fertilization what happens regarding methylation

A

demethylation until the blastocyst stage

42
Q

Describe genomic imprinting

A

alleles inherited from father may always be inactivated or inherited
certain autosomal genes are expressed only from the allele found on the chromosome from a specific parent

43
Q

What is imprinting mediated by

A

DNA methylation

44
Q

the inactive allele inherited from parent is what

A

imprinted

45
Q

AD glomus tumors is now called what

A

Autosomal Dominant Paraganglioma

46
Q

silently growing, mostly benign tumors of parasympathetic ganglia, usually in the head and neck region is what disease?

A

AD Paraganglioma

47
Q

How is AD paraganglioma inherited

A

only from the father

48
Q

how is AD paraganglioma imprinted and expressed

A

maternally imprinted

paternally expressed

49
Q

the disease only presents if the disease is on which chromosome regarding imprinting

A

the active chromosome, so the one not imprinted

50
Q

What does BWS stand for

A

Beckwith-Weidman Syndrome

51
Q

What is MOI of BWS

A

AD

52
Q

How is BWS imprinted and expressed

A

paternally imprinted, maternally expressed

53
Q

Overgrowth syndrome, infants larger than normal, growth asymmetric is what disease

A

BWS

54
Q

How is BWS inherited

A

from mother

55
Q

Why does imprinting happen?

A

They THINK:

it has somethign to do with limiting an allele for the function of a gene

56
Q

Describe monoallelic vs. biallelic expression

A

most genes are biallelic expression

when imprinting happens the allele is monoallelic expressed

57
Q

a defect in imprinting will lead to what

A

developmental problems

58
Q

if imprinting doesn’t work what will happent o parent of origin affect

A

there will be no parent of origin affect

59
Q

if there is a mutation on an imprinted gene, what will be phenotype

A

no phenotype, imprinted is not expressed, the only way it would have phenotype if its on chromosome that is exprsesed

60
Q

most of the time impritning affects all cells in body, sometimes it is:

A

cell-type specific

61
Q

what happens to imprinted genes during gametogenesis

A

they are reset

62
Q

explain resetting imprints

A

during spermatogenesis or oogenesis, the imprints are reset so that a sperm would only have male specific imprints and female would only have female specific imprinting patterns

63
Q

If during spermatogeneiss a gene is mutated that is paternally imprinted, what is result

A

it will be hidden b/c if it’s from father it is imprinted (off)

64
Q

What does PWS stand for

A

parader-willi syndrome

65
Q

What chromosome is affected in AS

A

15q11-13

66
Q

what does AS stand for

A

angelman syndrome

67
Q

What is the most important gene in AS

A

UBE3A

68
Q

The contribution of what leads to AS

A

lack of maternal contribution

69
Q

What is UBE3A

A

important in brain

brain-specific ubiquitin ligase

70
Q

severe intellectual disability, seizures, happy demeanor, lack of speech is what disease

A

AS

71
Q

poor feeding when born, hyperphagia and obesity, hypopigmentation, mental retardation is what disease

A

prader-willi syndrome

72
Q

the contribution of what leads to PWS

A

lack of paternal contribution

73
Q

what chromosome is important in PWS

A

15q11-13

74
Q

What important genes are involved in pWS

A

SNRPN

sometimes OCA2

75
Q

What is SNRPN involved in

A

assembly of SnoRNA

76
Q

SNRPN - how is it usually inherited

A

paternally expressed, maternally imprinted

77
Q

UBE3A - how is it usually inherited

A

maternally expressed, paternally imprinted

78
Q

If one allele is turned off by imprinting and the other allele carries loss of function mutation, what happens

A

disease will present

79
Q

what is uniparental disomy (UPD)

A

two chromosomes from same parent

80
Q

go over mechanisms on the basis of PWS & AS

A

pg 42

81
Q

how does trisomy occur

A

via meiotic nondisjunction

82
Q

what happens if there is mitotic nondisjunction

A

tetrasomic and disomic daughter cells

83
Q

if there is mitotic nondisjunction, what will happen to tetrasomic cells

A

they will die- only the disomic cells will develop into baby

84
Q

what is the danger in mitotic nondisjunction

A

if there is unequal passing of maternal/paternal alleles via the mitotic nondisjunction

85
Q

what is the chance a child will have uniparental disomy if there is mitotic nondisjunction

A

1/3

86
Q

what is chance a child will be normal if there is mitotic nondisjunction

A

2/3

87
Q

what is idiosomy

A

resulting cell will have both alleles from same parent

88
Q

when does idiosomy occur

A

through disomic amete from non-disjunction in meiosis II

89
Q

what is a danger phenotypically with idiosomy

A

if the allele inherited carried recessive allele, the child could have AR disease

90
Q

What is heterodisomy

A

two different alleles but both from same parent - baby only has contribution from one parent

91
Q

how do you diagnose PWS or AS

A

southern blot

92
Q

what is the probe for PWS or AS when doing southern blot

A

SNRPN probe

93
Q

Why is NotI used to detect PWS

A

to detect the allele being expressed

94
Q

How does NotI work?

A

will not cut methylated DNA (imprinted) but will cut non-methylated DNA - so it only cuts what is expressed

95
Q

Are genes inherently paternal or maternal?

A

no

96
Q

what do imprinting patterns refer to when we say they are paternal or maternal

A

if they most recently came from sperm or egg - for example the father could pass on a paternal imprint allele that he got from his mother.

97
Q

How does Xbal work?

A

restriction enzyme that cuts either allele, it isn’t sensitive to methylation

98
Q

Where is mutation in Albinism Type 2

A

OCA2

99
Q

What is MOI of Albinism Type 2

A

AR

100
Q

OCA2 gene for albinism is in same region as what

A

SNRPM - (in same region that both angelman and PWS is)

MCB1 Block 4 (17 decks)

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