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Molecular & structural basis of disease > Epigenetics and disease > Flashcards

Epigenetics and disease Flashcards

1
Q

what is fetal growth restriction (FGR)?

A

Fetal growth restriction (FGR) is most often defined as an estimated fetal weight less than the 10th percentile for gestational age by prenatal ultrasound evaluation. The condition is associated with a number of short-term and long-term complications that can severely impact the quality of life.

A baby’s growth slows or stops in utero - the embryo and the fetus do not grow to their full potential, effecting birth and lifecourse

can be caused by altered placental gene expression

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2
Q

give three things that can cause fetal growth restriction

A
  • Chromosomal defects
  • Placental insufficiency
  • Environment ~ multiple gestation (twins, triplets), smoking, alcohol, or abusing drugs, maternal illness or infections, nutrition or stress
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3
Q

fetal growth restriction leads to what potential consequences

A
  • Babies can be stillborn
  • At risk of developing lifelong disabilities (e.g. cerebral palsy)
  • At risk of developing non-communicable diseases in adulthood
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4
Q

how do we know a pregnancy has fetal growth restriction?

A

we can monitor the fetus through ultrasound and compare to growth charts

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5
Q

why is a healthy placenta/baby the foundation of life long health?

A

because it underlies the furture development of the baby, from epigenetic mark to laying down/detting up cell numbers and tissue structures

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6
Q

what things in the meternal environment can effect the placenta and so the fetal development?

A

body composition
diet/nutrients
toxins/drugs

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7
Q

what factors contributes to a healthy placenta?
(4)

A

Size and structure
Transport capacity – nutrients, toxins, igG
Blood flow – maternal and fetal
Metabolism – nutrients, drugs

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8
Q

what is the functional unit of the placenta?

A

placental cotyledon

fetal vessels are bathed with maternal blood in the placenta surrounded by epithelial cell layer

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9
Q

how are amino acids transported from mother to fetus

A

Amino acids are transported from mother to fetus though exchangers – controlled by gene expression within the simple cell layer of the placenta

Syncytiotrophoblasts of the placenta contain exchanges, transporting amino acids from one side where the mohters blood is to the other where fetal blood is

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10
Q

what happens to the fetus if they dont receive the proteins?

what can this lack in supply be caused by

A

It can impact upon development of organs and set it up for diseases later in life
caused by changes in gene expression

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11
Q

describe the evidence that shows smaller babies have a higher risk of non communicable diseases

A

Dr Barker in Southampton looked at people with a range of illnesses then went back to look at their birth weight - they saw a correlation with low birth weight and different conditions
Low birth weight saw a change in: hypertension, raised serun cholesterol, impaired glucose tolerance, type 2 diabetes, obesity
potentially due to fewer cells being layed down in various organs making them weaker and more suseptible with greater risk of failing

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12
Q

what was the dutch hunger winter and how did it help us discover the consequences of lack of nutrients?

A

In 1944/45 a town was cut off by bombing of the railways being they could not
People consumed an average of only 500kcal a day
The women expoed to famin during pregnancy had smaller babies
These babies developed cardiovascular disease, disbetes etc.
Lack of nutrients altered their gene expression that affected their pathological status later in their lifecourse

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13
Q

what things in the maternal body can have physiological impacts by changing gene expression?
(4)

A

environment, nutrition, changes to hormones and stress levels

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14
Q

at what stage does the zygote begin to differentiate

A

at the blastocyst stage

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15
Q

what regulates the embryo early on

A

mRNAs inherited from the oocyte

maternally inherited

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16
Q

when is the embryonic genome gradually turned on?

A

during early cleavage

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17
Q

describe how body composition can affect the fetus

A

it was shown that mothers with a higher pre-pregnant arm muscle mass had a higher TAT mRNA level (increased neonatal lean mass)

Stem cells from donated umbilical cords are examined and the cells from babies who had mothers of normal weight during their first prenatal visit and mothers who were obese at the time.
They then grew the cells into fat and muscle cells in a lab. Boyle noted that none of the women gained excessive weight during their pregnancies.
The researchers noticed a 30 percent higher fat content in both types of cells in the children whose mothers were obese.

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18
Q

what is epigenetics?

A

The study of heritable changes in gene regulation activity that occur without a change in the DNA sequence

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19
Q

what are epigenetic mechanisms?
give four examples

A

the factors that determine which genes are switched on and off at certain times
DNA methylation, histone modification, histone variants and non coding RNAs

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20
Q

how much of the genome is made out of coding sequences?

A

5%

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21
Q

what things determine whether a gene is transcribed

A

RNA pols ability to attach to control element/DNA
determined by the packaging of the nucleosomes
packaging caused by the modification s on the histone proteins

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22
Q

what is the epigenome?

A

the genome wide epigenetics - all of the epigenetic modification in the cells genome

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23
Q

what are epigenetics tags and what are epigenetic modifiers?

A

Epigenetic tags: Epigenetic marks or modifications
Epigenetic modifiers: Enzymes that catalyse the addition or removal of epigenetic tags

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24
Q

what is the most commonly methylated base?

A

Cytosine next to guanine
Cytosine (CpG) is methylated to 5-methyl cytosine (5mC)

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25
Q

how does DNA methylation affect transcription?

A

Provides a physical block for transcription factors binding, can also attract methyl binding proteins to block or change the DNA transcription

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26
Q

what is a CpG dinucleotide?

A

Palindromic Motif – C then G from 5’ to 3’ on both strands

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27
Q

what enzymes catalyse DNA methylation?

A

DNA methyltransferase

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28
Q

what is the function of Dnmt3a & Dnmt3b?

A

de novo methylation of the DNA

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29
Q

what is the function of Dnmt1?

A

maintenance of DNA methylation
- adds on the methylation to the sister strand based on the mark on the template strand

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30
Q

what enzyme removes the methylation marks on DNA?
how?

A

Tet enzymes convert 5-methyl cytosine (5mC) to 5-hydroxymethylcytosine (5-hmc)
Deaminated to thymine
Both repaired as part of the normal DNA mechanism

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31
Q

what reasons could there be for a methylated CpG island on a control element

A

imprinted genes
x-inactivation
cancer
environmental influences

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32
Q

give a common example of how dna methylation at CpG islands represses gene expression

A

Hypermethylation of 1 X chromosome in females
As females have 2 X chromosomes (males only 1) – random switch-off

switching off of one of the x-chromosomes can lead to mosaic patterns in the cells

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33
Q

X inactivation represses of gene expression is involved in what three major things

A

– Cell-Specific Differences in Transcription
– Developmental Differences in Transcription
– Genomic imprinting

cell differentiation and tissue specific expression

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34
Q

in what two processes is DNA methylation critical?

A
  • variable in different tissues and involved in
    regulating tissue-specific gene expression patterns
  • permanently ‘imprinted‘, therefore maintained and memorised in (nearly) all tissues
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35
Q

in what two processes in DNA methylation critical?

A
  • variable in different tissues and involved in
    regulating tissue-specific gene expression patterns
  • permanently ‘imprinted‘, therefore maintained and memorised in (nearly) all tissues
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36
Q

disturbed methylation patterns are involved with what human diseases

A

cancer
growth defects
behavioural disorders

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37
Q

methylation marks are erased in what specific cell types

A

primordial germ cells

oocytes and sperm continue to re-acquire methylation marks unti/during maturation yet in different time frames and to different extents

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38
Q

when and how does the fertilised egg remove the methylation marks of the parental DNA

A

Following fertilisation

The cell can recognise which genome comes form the sperm and which from the egg
The fertilised egg removes all of the methylation marks using TET, the maternal and paternal marks occurs along different timelines, with the paternal removes faster

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39
Q

when does remethylation occurs in the fertilised egg?

A

Re-methylation begins at the blastocyst stage in a cell- type specific manner (ICM vs TE) by DNMT3a and DNMT3b
TE has a much lower methylation pattern than the ICM – the ICM has more functions to carry out so needs more genes turned on
DNMT1 maintains these marks – adds on the methylation to the sister strand based on the mark on the template strand

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40
Q

what genes withstand the fluctuation during global demethylation in the preimplantation embryo?

A

imprinted genes

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41
Q

what occurs during global demethylation in the preimplantation embryo

A

→ Somatic & placental methylation established
→ Imprinted genes withstand this fluctuation

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42
Q

what is responsible for normal epigenetic drift?

A

intrinsic and environmental factors affecting remethylation every time the cell divides
leading to altered chromatin functions and an altered phenotypes

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43
Q

describe the principle of the battle of the sexes in an embryo

A

Genes that promote fetal and placental growth are maternally imprinted (to secure the survival of the mother).
Genes that inhibit fetal and placental growth are paternally imprinted (to secure passing on of the father‘s genes at cost of the mother).

The paternal genome wants to pass on the genes that promote growth
But the maternal wants to restrict it so that there is enough nutrients for future pregnancies – maternal copy will switch off the growth promoting genes
For these particular genes the marks remain
These signals will be balanced so you get an appropriately growing fetus

44
Q

what does maternal imprinting do?

A

limits use of maternal resources by baby in utero

45
Q

what does paternal imprinting do?

A

maximises use of maternal resources by baby in utero

46
Q

what is imprinting?

A

a process that leads to the heritable silencing of a gene on one of the parental chromosomes

Imprinting refers to the Gene that is Silenced NOT the Gene expressed
∴ Where the precise DNA methylation occurs

47
Q

what happens if the balance of maternal and paternal imprinting fails?

A

it can be severly detrimental to fetal growth

48
Q

how is imprinting regulated?

A

methylation of regulatory regions on one of the parent chromosomes - differentiationally methylated regions (DMR) and imprinting control regions (ICRS)

49
Q

in a gene that restricts growth, which parently gene will be methylated?

A

the paternal gene

50
Q

if the maternal imprinting marks are removed what will the baby be like

A

big baby
because growth genes are now able to be expressed

51
Q

paternal imprinting occurs on what genes

A

Genes that inhibit fetal and placental growth are paternally imprinted (methylated)
= switch off inhibition of growth to increase growth

52
Q

what effect does IVF have on methylation?

A

In ivf changes to the culture media can effect the methylation marks of imprinted genes, only minor but sees bovine overgrowth of the embryos
the effects of IVF are predictive/ risks

53
Q

hypomethylation on imprinted genes causes what effect on fetal growth

in either parental genome

A

reduced growth

removal of methylation marks

54
Q

hypermethylation of imprinted genes causes what effect on fetal growth?

on either parental genome

A

increase growth

55
Q

what is IGF2?

A

insulin –like growth factor 2 (IGF2) gene
on chromosome 11
it is a major fetal growth factor involved in differentiation, organogenesis and metabolic regulation
matches placental nutrient supply to fetal demand - when the gene is on it leads to increased nutrient supply and increased growth
altered IGF2 expression is related to FGR

56
Q

describe the molecular events that block IGF2 expression

A

CTCF insulator binds to maternal unmethylated ICR1 (imprinting control region 1)- Provides a physical structure that blocks the gene from the enhancer
Allowing the H19 gene to be expressed (which controls the switch)
blocking IGF2 expression

57
Q

Describe the molecular events that allow IGF2 to be expressed

A

Paternal methylation at ICR1
Prevents CTCF binding
So the enhancer can now bind
IGF2 is expressed

58
Q

describe what occurs at the imprinted gene cluster on chr11p15
IGF2/ICR1/H19

A

The maternal copy of H19 (ICR1) is unmethylated
CTCF insulator binds to the unmethylated ICR1 - H19 gene expressed
Blocks IGF2 expression

the paternal copy of H19 is methylated so no proteins can bind, so the enhancer can attach to IGF2 gene and transcription can occur

59
Q

give an example of how methylation effects a process that leads to disease

A

Loss of imprinting at the IGF2/ICR1/H19 domain leads to Silver-Russell syndrome - prenatal growth failure

Loss of methylation leads to less IGF2 reduction leading to fetal growth restriction
Methylation mean higher IGFR2 expression and fetal overgrowth – issues with birth and the development of the individual

60
Q

how can maternal nutrition affect the baby?

A

Maternal nutrition can affect the epigenetic regulation of genes leading to long term changes metabolism and altered disease susceptibility

maternal diet effects the methylation marks in the baby

61
Q

what was the association of % RXRA in the umbilical cord between early pregnancy carb intake and childhood adiposity?

A

association with low maternal early pregnancy carbohydrate intake and with greater childhood adiposity age 9 year

higher methylation in this gene tend to have higher fat mass as a baby and a child which can increase the risk of obesity later in life

this gene is a transcirption factor so it has wide effects

62
Q

what is Beckwith-Weidemann syndrome?

A

prenatal overgrowth (macrosomica) caused by a loss of imprinting in the IC2 of IGF2 - resulting in inappropriate expression of IGF2

most common features include macrosomia (large body size), macroglossia (large tongue), abdominal wall defects, an increased risk for childhood tumors, kidney abnormalities, hypoglycemia (low blood sugar) in the newborn period
these become more pronounced as the child grows older

63
Q

what was found when studying the mouse model of pregnancy and alterations mothers diet has?

A

shown that change in mother diet can change phenotype of blastocyst embryo and post natal pups relating to cardiovascular disease and adiposity. Even prior to implantation.
certain imprinted genes were also studied, and showed reduction in methylation levels
Other imprinted genes also high methylation levels

64
Q

what happened to the methylation pattern in mouse blastocysts when cultured in certain situations?

A

during preimplantation stages they see effects on methylation patterns in certain imprinted genes
reduction in methylation of paternal H19 and maternal Snrpn and Peq3
this effects the balance of the paternal and maternal genes and so the growth of the offspring

  • effects on methylation and on cell number (in the outer layer of the blastocyst that forms the placenta) causiing a reduction in fetal growth
65
Q

what two ways did the culture media affect methylation

A
  • Reduced methylation in in vitro cultured blastocysts.
  • Altered gene expression in Trophoblast cells = H19 > IGF2
66
Q

how much does the risk of imprinting disorders increase when babies are made in vitro?

A

Risk of imprinting disorders increased 3.5 fold

67
Q

Placental-specific IGF-II is a major modulator of….

A

placental and fetal growth

68
Q

what happens when the IGF2 gene is deleted?

A
  • Mouse fetuses in which the Igf2 gene has been completely deleted weigh ≈60% of wild-type fetuses.
  • Deletion of the Igf2 gene transcript (P0) specifically expressed in the placenta leads to fetal growth restriction. (Leads to reduced growth of the placenta, Followed several days later by fetal growth restriction = Greater fetal/placental ratio)
  • Placental amino acid transport is initially upregulated.
    Later the compensation fails = fetal growth restriction.
    Experimental evidence: imprinted gene action in the placenta directly controls supply of maternal nutrients to the fetus and fetal growth (a decrease in the transfer capacity of the placenta)
69
Q

relaxed chromatin structure means…

A

access for transcription factors and activation of transcription

70
Q

condensed structure of chromatin means…

A

no access for transcription factors and inhibition of transcription

71
Q

what is the degree of compaction of linear DNA in nucleosomes?

A

1:6

72
Q

what is the degree of compaction of linear DNA in 30nm fibre

A

1:36

73
Q

what is the degree of compaction of linear DNA for metaphase chromsomes?

A

> 1:10000

74
Q

what is chromatin?

A
  • Complex of DNA & Histone Protein in Chromosomes
  • Basic Structural Unit = Nucleosome
75
Q

how much DNA is in a nucleosome?

A

around 147 base pairs wraps 1.67 lefthanded super helical turns

76
Q

what are the histone components of a nucleosome?

A

= 2 copies of each core histone: H2A, H2B, H3, H4
= 2 H2A-H2B dimers & 1 H3-H4 tetramer
Histone 1 linker molecule

77
Q

what are the three histone modifiers?

A

Writers: add groups e.g. HATs, HMTs (histone methyl transferases)
Erasers: remove groups e.g. HDATs KDM (lysine demethylase)
Readers: molecules that read and recognise the mark, and bind

78
Q

what are the functions of histone modifications?

3

A
  • Create or Prevent binding of Chromatin Remodelling Factors
  • Influence Nucleosome mobility & function
  • Scaffold for the recruitment of regulatory proteins
79
Q

what methylation marks on histone tails result in activation?

A

H3K4me3
methylation at lysine 4

80
Q

what methylation marks on histone tails result in repression?

A

H3K9me3
H3K27me3
methylation at lysine 9 and 27

81
Q

what acetylation marks on histone tails result in activation?

A

Acetylation at lysine 27 = activation

82
Q

CxxC domain proteins bind…

A

unmethylated CpGs

83
Q

what are MBPs?

A

methyl binding proteins
can attach to methylated marks on the genome

84
Q

what are CxxC domain proteins?

A

CxxC domain proteins read where CG islands are in the genome and bind
CxxC domain proteins Xfamily with 11 – enzymatic activity to change the structure arround it to help it be more transcriptionally active
Enzymes that modify epigenetic structure – add or remove marks
Do not bind when CpG islands are methylated

84
Q

what are CxxC domain proteins?

A

CxxC domain proteins read where CG islands are in the genome and bind
CxxC domain proteins Xfamily with 11 – enzymatic activity to change the structure arround it to help it be more transcriptionally active
Enzymes that modify epigenetic structure – add or remove marks
Do not bind when CpG islands are methylated

85
Q

how does CFP1 switch on genes?

A

CFP1 (not enzyme) physically associates with the enzyme complex SET1
CxxC domain protein, CFP1 recognises unmethylated CpG islands bringing in SET1 which alters marks on adjacent histone, methylating H3K4 to open up the DNA
Opens up a landing site for the enzymes
Can also remove repressive marks

86
Q

how does KDM2A switch on genes?

A

KDM2A = lysine specific demethylase 2A
 Removes mono/di methylation on histone H3 at lysine 33
 these marks block the transcriptional machinery from binding
 This CxxC cuts these marks off to open up the structure

87
Q

Describe the association of KDM2B and PRC1?

A

CxxC domain protein KDM2B binds at CG islands
 KDM2B associates with the polycomb protein repressive complex = PRC1
 KDM2B guides PRC1 to the CG island creating the restrictive chromatin state

88
Q

what are polycomb group proteins PcG?

A

PcGs form two main complexes: polycomb repressive complex 1 and 2 (PRC1 & PRC2)
they work independently or together and mediate gene silencing and x inactivation

they come in and bind to CxxC domain protein that recognise particular unmethylated sites - remove marks on histones to shut it down
also involve other gene silencing proteins as part of the complex
PCR2 catalyses tri-methylation at H3K27 via EZH2
Functional link with HDAC and DNMT

89
Q

what is meCP2?

A

 A basic housekeeping protein that reads DNA methylation – expressed all of the time in all of the cells
a methyl binding protein (reader of DNA)

90
Q

what is Rett syndrome?

A

Rett syndrome is a neurodevelopmenal disorder that affects girls.
 Characterized by normal early growth and development followed by a slowing of development, loss of purposeful use of the hands, distinctive hand movements, slowed brain and head growth, problems with walking, seizures, and intellectual disability.
 Life expectancy ~ 40 years
 No effective treatment

91
Q

why are there no males with Rett syndrome?

A

 Males die = no male rett syndrome - meCP2 gene is on the X chromosome (x inactivation)

92
Q

what mutated gene causes rett syndrome?

A

meCP2

93
Q

mutations in meCP2 methylated binding domain means that..

A

it cannot bind DNA

94
Q

what are DMRs?

A

A differentially methylated region (DMR) is a genomic region that has different DNA methylation patterns among multiple samples

95
Q

mutations in meCP2 TRD mean that…

A

cannot recruit the proteins HDAC so cant shut down the histone complex, inappropriately on so ra pol can switch on genes that are not normally switched on

96
Q

what are the most common hotspots for mutations in the meCP2 gene?

A

MBD
TRD

97
Q

give an example of a reader of histone acetylation

A

SWI/SNF
Preferentially binds to acetylated histone, on binding it clears the nucleosomes away from the promoters of the gene making it easier for RNA pol to bind to the gene – make a region easy for it to bind and transcribe

98
Q

give an example of a reader of histone methylation (at K9 & K27)

A

HPI1 heterochromatin protein 1 - Binds preferentially to methylation at K9 or K27 coats dna inducing permanent silencing of that gene

99
Q

give an example of an epigenetic writer

A

Polycomb repressive complex (PRC) PRC1/2 work together. PRC2 thought to be most important because it has catylitic activity. Comprises 4 subunit, (EZH2 of PRC2 has catalytic ability – a HMT).
Transfers 3 methyl groups to K27 (mediates trimethylation of H3K27).
Key role in making sure the right genes are on it the right cell types.

100
Q

give two examples of CxxC domain proteins

A

CFP1
KDM2A

101
Q

how does PCR2 silence genes?

A

PCR2 catalyses tri-methylation at H3K27 via EZH2
Functional link with HDAC and DNMT

102
Q

what are PcGs responsible for?

A

genes silencing and x inactivation

103
Q

what type of placenta do humans have ?

A

Discoid, hemochorial

104
Q

what is premature birth defined as?

A

gestation length less than 37 weeks

105
Q

what is low birth weight defined as

A

birth weight less than 2500 grams,

106
Q

assisted reproductive technologies can lead to an increased risk of what?

A

births involving assisted reproductive technology (ART) may have an increased risk of imprinting disorders such as Beckwith–Wiedemann syndrome and Angelman syndrome

Human ART epigenetic risks - Risk of rare diseases such as Beckwith-Wiedemann and Angelmans syndrome increased 3.5 fold as a result of in vitro fertilisation

Molecular & structural basis of disease (6 decks)

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