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Cell and Developmental > Epigenetics > Flashcards

Epigenetics Flashcards

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1
Q

Eukaryotic DNA packaging

A

DNA double helix
DNA associates and wraps around histones to form chromatin
30-nm chromatin fibre of packed nucleosides
Further packaging

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2
Q

What histones are ‘core histones’ and form nucleosomes?

A

2A, 2B 3 and 4

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3
Q

What is histone 1?

A

Linked histone

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4
Q

What is euchromatin?

How much DNA is euchromatin?

A

Dispersed, transcriptionally active DNA

90%

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5
Q

What is heterochromatin?

How much DNA is heterochromatin?

A

Compact, transcriptionally inactive DNA

10%

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6
Q

What percentage of euchromatin is active at any one time?

A

10%

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7
Q

How does the remainder of the euchromatin which is not transcriptionally active exist?

A

In an intermediate state of condensation between heterochromatin and euchromatin

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8
Q

Methods of regulating gene expression

A
  1. Differential gene transcription: regulates which nuclear genes are transcribed into RNA
  2. Selective nuclear RNA processing: regulates which of the transcribed RNAs are able to enter the cytoplasm and become mRNAs
  3. Selective mRNA translation: regulates which of mRNAs in cytoplasm become translated into proteins
  4. Differential protein modification: regulates which proteins are allowed to remain or function in the cell
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9
Q

Two way epigenetic modifications can modulate transcription

A
  1. Histone modification

2. DNA methylation

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10
Q

What part of a histone can undergo modifications?

A

Histone tail

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11
Q

Range of post-translational modifications that histone tail can undergo

A
  1. Acetylation
  2. Methylation
  3. Phosphorylation
  4. Ubiquitination
  5. ADP ribosylation
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12
Q

What do modifications to the histone tail do (in general)?

A

Alter the electrostatic interaction of the DNA and histones and influence the recruitment of proteins to the chromatin. All mechanisms modify the accessibility of the DNA to transcription factors

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13
Q

What acetylates and deacetylates histone tails?

A

Acetylation: histone acetyltransferases (HATs)
Deaceylation: histone deacetylases (HDACs)

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14
Q

What happens after a histone tail is acetylated?

A

Activation of gene expression

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15
Q

What happens after a histone tail is deacetylated?

A

Repression of gene expression

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16
Q

Where are the main histone acetylation sites?

A

Lysine residues 9, 14, 18 and 23
HDAC leaves a positive charge on the amino group
HAT leaves no charge on the amino group

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17
Q

Why does the histone group having no charge allow gene expression?

A

Removed positive charge means reduced affinity between histones and DNA. This makes it easier for RNA polymerase and transcription factors to access gene promoters

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18
Q

What else does histone acetylation allow (other than loosening affinities between histones and DNA)?

A

Can specifically recruit transcriptional activators to genes

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19
Q

In what animals has histone acetylation been found in low levels in heterochromatin?

A

Drosophila polytene chromosomes

Inactive X chromosome in female mammalian cells

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20
Q

What is a polytene chromosome?

A

Chromosome replicated without cell division

Found in large Drosophila salivary glands - required to provide large amounts of glue proteins for pupation

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21
Q

Why must X chromosome inactivation occur and which X chromosome is inactivated?

A

So only one copy of X chromosome genes is transcribed - example of dosage compensation
In placental mammals, this is random
In marsupials, the paternal X chromosome is inactivated
Irreversible in somatic cells, reversible in germ cells

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22
Q

What does inactivation of the X chromosome involve?

A

Shortening and condensing of one X chromosome to form a structure known as a ‘Barr body’
Process termed ‘Lyonisation’ after Mary Lyon

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23
Q

How many genes are left on during X inactivation and for what reason?

A

10-15% switched on

Gene encoding XIST RNA involved in Barr body production left on

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24
Q

Can females develop X-linked recessive diseases?

A
  • Female mammals contain some cells in which faulty gene is activated and some cells where the working copy of gene is activated
  • Women do not normally display symptoms of these diseases as sufficient protein product is produced by working copy of the gene
  • In rare cases, Lyonisation is skewed towards one X chromosome and women may develop the disease
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25
Dosage compensation in Drosophila
Transcription rate of male X chromosomes is doubled so that the single male X chromosome makes the same amount of transcript as the two female X chromosomes -This is achieved through acetylation of nucleosomes throughout male X chromosomes (thereby giving RNA polymerase more efficient access to promoters)
26
Where on histones does methylation activate genes?
H3 lysine 4
27
Where on histones does methylation inactivate genes?
H3 lysine 4 / lysine 27
28
DNA methylation
- Involves the addition of a methyl group to a cytosine base that is part of a CpG dimer - Involved in the initiation and maintenance if gene silencing - Targeted to certain regions of the genome (eg repetitive DNA and transposable elements) - Promoters of housekeeping genes are hypomethylated and therefore transcriptionally active - DNA methylation is regulated by DNA methyltransferases (DNMTs) - DNA methylation patterns are inherited
29
Inheritance of DNA methylation pattern
DNA methyltransferase only methylates a CG sequence which is paired with a methylated CG dimer. This maintains the original pattern after DNA replication
30
How can DNA methylation lead to histone modifications?
DNA methylation by DNMTs DNMTs recruit HDACs Histone deacetylation by HDAC complex Transcriptional repression
31
What is the name for combinations of epigenetic modifications combining to regulate transcription?
‘The histone code’
32
What do cloned animals share and not share?
Share a genome | Do not share an epigenome
33
Epigenetic basis of coat patterning in calico cats
One X chromosome contains an organ allele for pigmentation and the other contains a black allele. These are randomly inactivated during development. Additional interaction with white spotting gene
34
How can monozygotic twins vary in susceptibility to disease? Examples of issues
Epigenetic differences Cancer Schizophrenia Bipolar disorder
35
The Norrbotten Study
- Remote isolated community in Northern Sweden - During the 1800s, the community went from feast to famine due to crop failure and success - Dr Lars Olov Bygren started a study in the 1980s analysing the health of residents and the diet of their parents and grandparents whilst growing up - He found a correlation between the lifespan of Norrbotten residents and the diet of their grandparents. Children experiencing feast-famine conditions produced grandchildren with a shorter lifespan - Suggests epigenetic changes are heritable and could be diet-mediated
36
How homeotic genes determine Drosophila body plan
- Mutations in homeotic genes cause one structure to be replaced by another - Homeotic genes specify the identity of body segments - Homeotic genes share a conserved DNA sequence (approx 180 bp) termed the homeobox - The homeobox encodes a 60 amino acid homeodomain which recognises specific DNA sequences
37
How are homeotic gene expression patterns ‘locked’ in to place?
By epigenetic modification of chromatin
38
What maintains homeotic gene repression?
The Polycomb family of proteins
39
What activates homeotic gene expression?
The Trithorax family of proteins
40
What specific DNA motifs do Polycomb and Trithorax recognise?
PRE: Polycomb Response Element TRE: Trithorax Response Element
41
What regulates the development of the Halteres?
Ultrabithorax
42
What are halteres?
Organs which help maintain stability during flight | Halteres develop from groups of cells in the embryo termed ‘imaginal discs’
43
How are polycomb proteins involved in haltere development?
Early embryo: embryonic enhancer ensures Ubx expression is posterior to parasegment 6. Repressor proteins prevent expression in anterior region Later embryo: polycomb proteins ‘lock’ patterns of gene expression in place Imaginal disc: imaginal disc enhancer active later in development and ensures expression in imaginal discs. Polycomb proteins repress expression in head and wing discs
44
What are the three elements needed to allow correct expression of Ubx genes in haltere imaginal disc?
Embryonic enhancer PRE (polycomb response element) Imaginal disc enhancer
45
How do trithorax proteins prevent transcriptional silencing by polycomb group proteins?
- Trithorax (Trx) proteins have histone methyltransferase (HMTase) activity - Trithorax proteins are required to prevent polycomb group protein-mediated silencing of homeotic genes - Trx proteins methylate the H3/H4 tail, inhibiting the binding of the polycomb complex - Methylation marks associated with transcriptional repression prevented
46
What external cues regulate flowering in plants?
- Day length - Temperature - Environmental stress
47
What is vernalization?
Winter annual plants require a prolonged cold period (vernalization) to promote flowering Without vernalization, they flower much later, thereby producing many more leaves
48
Molecular mechanism controlling vernalization
Flowering is suppressed by a repressor factor, FLOWERING LOCUS C (FLC). Plants with a vernalization requirement have another gene, FRIGIDA (FRI). FRI promotes the expression of FLC, inhibiting flowering. During winter, low temperatures suppress FLC expression. This means that plants can flower the following spring when the photoperiod is long enough. The suppression of FLC by low temperatures involved two other groups of proteins, the VIN (VERNALIZATION INSENSITIVE) and the VRN (VERNALIZATION)
49
Study on up-regulation of FLC
He and Amasino, 2005 | Up-regulation of FLC results in severe repression of flowering Arabidopsis
50
What protein is involved in repression of FLC?
VIN3: protein containing PHD (plant homeodomain) motif found in chromatin remodelling factors
51
What proteins are involved in maintenance of FLC repression?
VRN1: DNA binding protein VRN2: Homologue of SU(Z)12 polycomb protein
52
Is FLC repression inherited?
yes, through mitosis which suggests an epigenetic basis
53
What is ChIP?
Chromatin immunoprecipitation
54
Process of ChIP:
1. Harvest experimental tissue samples (eg treated and untreated) 2. Crosslink DNA and histones with formaldehyde and digest into smaller pieces 3. Incubate sample with an antibody raised against a histone with specific modification (eg methylated H3K9) 4. Extract DNA attached to histone with specific modification using antibody (enrichment) 5. Remove histones from DNA 6. Use DNA as a template for PCR (primers designed against gene of interest). If the PCR band is bigger in the treated sample, then it can be assumed that the treatment results in greater association of your gene of interest with a particular modification
55
What epigenetic modifications regulate the repression of FLC?
A decrease in H3 acetylation (due to VIN3) and increase in methylation of H3K9 and H3K37 (due to VRN1/2) occurs around the FLC gene
56
When is FLC reactivated?
During gametogenesis - active FLC in seedlings of next generation so they will also require vernalization
57
What is asymmetric cell division?
- Many cells divide asymmetrically to produce two different cell types after cell division - Unicellular organisms can differentiate into different cell types - Multicellular organisms often produce progeny cells with different fates
58
What bacteria species has stalk/swarmer cells?
Caulobacteria crescentus
59
How do Caulobacteria crescentus attach to surfaces?
Stalks attach them | They secrete a glue-like polysaccharide that may be the strongest adhesive in nature
60
Caulobacteria cell cycle
- A motile swarmer cell of Caulobacteria finds a nutrient-rich place to attach and grow - It loses its flagellum, replacing it with a stalk that attaches to detritus in the pond - The stalk cell then divides, forming two daughter cells: a swarmer (flagellated) and a cell with the original stalk - The swarmer cell swims off to find a new location, avoiding competition with the stalk cell left behind
61
What specific proteins symmetrically localise in the dividing Caulobacteria cell?
PleC: localisation at the end of the cell with the flagella DivJ: localisatjon at the end of the cell with the stalk ZapA: cell division protein localised to the FtsZ ring
62
DivJ
- Synthesised in the STALK cell - Accumulates at the stalk pole - Remains polar throughout rest of cell division - Ends up at stalk end of stalk cell after division
63
PleC
- Localised at the flagellated pole in the SWARMER cell - Delocalises during cell elongation - Ends up at what will be the flagellated end of the swarmer cell after cell division

Cell and Developmental (4 decks)

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