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MCB1 Block 4 > Epigenetics & Genomic Imprinting > Flashcards

Epigenetics & Genomic Imprinting Flashcards

(100 cards)

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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
spontaneous deamination of C leads to what
U
26
Because uracil is not a normal base in DNA what happens
mistmatch repair, it ultimately makes thymine
27
What is the ulatimate result of spontaneous deamination of C
mismatch repair may happen, which could ultimately change the DNA sequence depending on which strand is repaired
28
What disease has one of the most frequently mutated bases in the humane genome
Achondroplasia:
29
when cytosines are methylated it promotes what
heterochromatin structure
30
What methylate the cyosines
DNA methyltransferases
31
Once DNA is methylated what binds to methyl groups and binds
methyl-binding domain proteins like MeCP2
32
CG dinucleotides are underrepresented, why?
because spontaneous deamination of C happens so often, mismatch repair: C → T (deamination of Me-C) and G → A (mismatch repair)
33
What does DNA hypomethylation do?
activates oncogenes, resulting in chromosome instability & activates transposons
34
What do mutations at methylated cytosines do?
results in inappropriate gene expression
35
What do imprinting defects result in?
loss of parental identity
36
Once DNA becomes methylated, what happens to it
it stays methylated
37
If DNA is methylated what happens to it once it goes through mitosis
daughter cells will be methylated and it stays methylated
38
What is the majority of methylation used for
through development as genes are no longer needed they are silenced via methylation
39
Do primoridal cells have a lot of methylation?
no - very low levels of methylation
40
describe methylation levels of sperm and egg
sperm has more methyation than egg, they both have higher methylation than primordial germ cells
41
immediately after fertilization what happens regarding methylation
demethylation until the blastocyst stage
42
Describe genomic imprinting
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
What is imprinting mediated by
DNA methylation
44
the inactive allele inherited from parent is what
imprinted
45
AD glomus tumors is now called what
Autosomal Dominant Paraganglioma
46
silently growing, mostly benign tumors of parasympathetic ganglia, usually in the head and neck region is what disease?
AD Paraganglioma
47
How is AD paraganglioma inherited
only from the father
48
how is AD paraganglioma imprinted and expressed
maternally imprinted | paternally expressed
49
the disease only presents if the disease is on which chromosome regarding imprinting
the active chromosome, so the one not imprinted
50
What does BWS stand for
Beckwith-Weidman Syndrome
51
What is MOI of BWS
AD
52
How is BWS imprinted and expressed
paternally imprinted, maternally expressed
53
Overgrowth syndrome, infants larger than normal, growth asymmetric is what disease
BWS
54
How is BWS inherited
from mother
55
Why does imprinting happen?
They THINK: | it has somethign to do with limiting an allele for the function of a gene
56
Describe monoallelic vs. biallelic expression
most genes are biallelic expression | when imprinting happens the allele is monoallelic expressed
57
a defect in imprinting will lead to what
developmental problems
58
if imprinting doesn't work what will happent o parent of origin affect
there will be no parent of origin affect
59
if there is a mutation on an imprinted gene, what will be phenotype
no phenotype, imprinted is not expressed, the only way it would have phenotype if its on chromosome that is exprsesed
60
most of the time impritning affects all cells in body, sometimes it is:
cell-type specific
61
what happens to imprinted genes during gametogenesis
they are reset
62
explain resetting imprints
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
If during spermatogeneiss a gene is mutated that is paternally imprinted, what is result
it will be hidden b/c if it's from father it is imprinted (off)
64
What does PWS stand for
parader-willi syndrome
65
What chromosome is affected in AS
15q11-13
66
what does AS stand for
angelman syndrome
67
What is the most important gene in AS
UBE3A
68
The contribution of what leads to AS
lack of maternal contribution
69
What is UBE3A
important in brain | brain-specific ubiquitin ligase
70
severe intellectual disability, seizures, happy demeanor, lack of speech is what disease
AS
71
poor feeding when born, hyperphagia and obesity, hypopigmentation, mental retardation is what disease
prader-willi syndrome
72
the contribution of what leads to PWS
lack of paternal contribution
73
what chromosome is important in PWS
15q11-13
74
What important genes are involved in pWS
SNRPN | sometimes OCA2
75
What is SNRPN involved in
assembly of SnoRNA
76
SNRPN - how is it usually inherited
paternally expressed, maternally imprinted
77
UBE3A - how is it usually inherited
maternally expressed, paternally imprinted
78
If one allele is turned off by imprinting and the other allele carries loss of function mutation, what happens
disease will present
79
what is uniparental disomy (UPD)
two chromosomes from same parent
80
go over mechanisms on the basis of PWS & AS
pg 42
81
how does trisomy occur
via meiotic nondisjunction
82
what happens if there is mitotic nondisjunction
tetrasomic and disomic daughter cells
83
if there is mitotic nondisjunction, what will happen to tetrasomic cells
they will die- only the disomic cells will develop into baby
84
what is the danger in mitotic nondisjunction
if there is unequal passing of maternal/paternal alleles via the mitotic nondisjunction
85
what is the chance a child will have uniparental disomy if there is mitotic nondisjunction
1/3
86
what is chance a child will be normal if there is mitotic nondisjunction
2/3
87
what is idiosomy
resulting cell will have both alleles from same parent
88
when does idiosomy occur
through disomic amete from non-disjunction in meiosis II
89
what is a danger phenotypically with idiosomy
if the allele inherited carried recessive allele, the child could have AR disease
90
What is heterodisomy
two different alleles but both from same parent - baby only has contribution from one parent
91
how do you diagnose PWS or AS
southern blot
92
what is the probe for PWS or AS when doing southern blot
SNRPN probe
93
Why is NotI used to detect PWS
to detect the allele being expressed
94
How does NotI work?
will not cut methylated DNA (imprinted) but will cut non-methylated DNA - so it only cuts what is expressed
95
Are genes inherently paternal or maternal?
no
96
what do imprinting patterns refer to when we say they are paternal or maternal
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
How does Xbal work?
restriction enzyme that cuts either allele, it isn't sensitive to methylation
98
Where is mutation in Albinism Type 2
OCA2
99
What is MOI of Albinism Type 2
AR
100
OCA2 gene for albinism is in same region as what
SNRPM - (in same region that both angelman and PWS is)

MCB1 Block 4 (17 decks)

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