Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Y3 (2) Epigenetics in Development and Disease > Lecture 5 - Genomic imprinting in mammals, epigenetic mechanisms in plants > Flashcards

Lecture 5 - Genomic imprinting in mammals, epigenetic mechanisms in plants Flashcards

1
Q

Describe genomic imprinting in mammals

A
  • A form of epigenetic regulation that results in mono-allelic expression in a parent-of-origin dependent manner
  • essential for normal development
  • over 90 imprinted genes have been identified
  • often occur in large clusters regulated by an imprinting control region (ICR), non-coding RNAs and differential DNA methylation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is the pattern of imprinted genes in mammalian development?

A
  • imprint established in the germ cells
  • And is not removed in the global erasure
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Describe mouse germ cell development

A

Mouse germ cell development is similar to human development but different timings

  • E3.5: Blastocyst
    • differentiation to epiblast stage
    • extra embryonic tissue and primordial germ cell precursors
    • form a founder population
    • migrate through the embryo before settling in a final position
    • Erasure takes place during migration
  • Depending on whether sperm or eggs are going to be produced the timing of imprinting differs
    • male: quite early before birth, in the development of pre-sperm cells. This is maintained throughout divisions
    • female: occurs post birth during maturation of the oocyte
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the experimental evidence for needing a male and female parent when mammals reproduce?

A
  • nuclear transfer
  • took pronuclei from a fertilised egg
  • generated male/male, female/female and male/female pronuclei in the manipulated fertilised egg
  • only got successful development when have male and female pronuclei
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the experimental evidence that there are some required factors from the male pronuclei and some required factors from the female pronuclei?

A
  • Looked at whole embro, yolk sack and tropoblast development of male/female pronuclei (PN) control, female/female PN and male/male PN.
  • In F/F: trophoblast fails to develop substantially and the embryo does not develop well
  • In M/M: Placenta gets an overgrowth, the embryo does not develop well
  • only in the control do you get a good balance.
  • Transgenic observations showed that genes were differentially methylated whether mother or father
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Outline the H19-insulin growth factor 2 (Igf2) as an example of genomic imprinting

A
  • H19 encodes a 2.3kb non-coding RNA
    • active on maternal allele
  • Igf2 encodes a protein that plays a role in promoting embryonic and placental growth and development
    • active on paternal allele
  • Explain placental effects
  • regulated by intra-chromosomal interaction
    • Igf2 and H19 separaed by an imprinting control region (ICR) and this is differentially regulated in the maternal and paternal chromosomes
    • In females - ICr is not methylated, CTCF (a DNA binding protein that acts as an insulator) binds to the ICR and blocks effect of enhancers which then act on H19
    • In males ICr is methylated, CTCF cannot bind and enhancers act on Igf2
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How were the identities of the imprinted genes identified?

A

Myagenesis studies

  • Female Igf2 mutant crossed to normal male
    • offspring all normal sized
  • Normal female crossed to Igf2 mutant male
    • off spring small
  • Paternal allele promotes growth, maternal allele supresses growth
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Outline two imprinting disorders

A

Beckwith-Wiedemann (BWS)

  • gain of methylation on the maternal ICR
  • Igf2 is expressed from both alleles
  • overgrowth disease

Silver-Russell syndrome (SRS)

  • Loss of DNA methylation from the paternal ICR
  • No Igf2 expression
  • growth retardation disease

Imprinting disorders occur in a pairwise manner

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Outline Insulin growth factor 2 receptor (Igf2R) and Air (ncRNA) as an example of genomic imprinting

A
  • controlled by antisense transcription and differential DNA methylation
  • Air overlaps Igf2R (growth suppressor) and is transcribed in the antisense direction
  • Set up by methylation in the maternal region, more likely to ocur in the maternal region
  • In the maternal chromosome Igf2R is active (when maternal ICR is methylated).
  • In the paternal chromosome Air (ncRNA) is active (ICR not methylated). IGF2R becomes methylated as a consequence.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What organisms imprint, how and why ?

A
  • placental mammals and flowing plants use imprinting
  • genes expressed from the paternally derived genome are often enhancers of pre- and post-natal growth (Igf2)
  • those expressed from the materally derived genome are often growth supressors (Igf2R)
  • this is the parental conflict theory
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are the implications for assisted reproductive strategies for epigenetic reprogramming?

A

In vitro fertilisation

  • children have statistically significanly increased occurance of imprinting disorders
  • in non IVF, epigenetic changes take place within the mother
  • This doesn’t happen in IVF leading to errors of maintaing the imprint, or being removed incorrectly
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Outline the similarities and differences of epigenetics in plant

A

Similarities

  • Use DNA methylation, histone modification and non-coding RNAs
    • histone codes are broadly conserved
  • Undergo dynamic changes in epigenetic modifications during development
  • perform genetic imrinting (in edosperm tissue)

Differences

  • Cytosine methylation in all sequence contexts in all tissues, predominantly in CG dinucleotides in vertebrates
  • changes in DNA methylation can be transmitted though multiple generations (but not 100% stable)
  • plant cells can switch fate - they retain potency
  • Do not do a complete erasure and reestablishment as seen in vertebrates
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How do epigenetic patterns differ in egg laying mammals?

A
  • short lived placenta before egg development
  • don’t imprint
  • can’t directly influence growth of embryo

placental mammals

  • imprinting common in placental mammals
  • lots of imprinting in brain
  • evidence that paternally expressed genes affect subtlty of behaviour post birth
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Describe the parental conflict theory with reference to cats

A
  • In a litter of kittens they may not all have the same father as mother has multiple ovulations
  • same mother, different father
  • Mother wants to even out nutrient allocation as equally related to all
  • Father wants preference for his offspring
  • balance of nutrient allocation due to the parental conflict theory
  • other theories due to sexual selection
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Outline DNA methylation in plants

A
  • Mosaic pattern over the genome
    • ​Arabidopsis thaliana
    • ‘gene body’ DNA methylation (occasional)
      • mainly CG configurations
      • significance unknown
    • Repetitive sequences (ALWAYS methylated)
      • CG, CHG, CHH contexts
      • maintaining heterochromatin and supressing TEs
  • Global DNA methylation
    • ​Zea mays
    • packed full of transposable elements
    • more extreme version of arabisopsis
    • cereals and grasses
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the similarities in methyltransferases between plants and animals?

A
  • plants have different methyltransferases with different substrates like mammals
  • De novo methylation
    • Mammals: Dnmt3a, Dnmt3b
    • Plants: Drm2 (CG, CHG, CHH)
  • Mainenance methylation
    • Mammals: Dnmt1
    • Plants: Met1 (CG), Cmt3 (CHG)
  • Have the same enzymology as the mammal enzymes
17
Q

How essential is DNA methylation for normal development in plants?

A
  • DNA methylation is essential for normal development in plants as it is in mammals
  • lowered levels of DNA methylation across genome (ddm1 required to maintain methylation)
  • phenotypesof ddm1/ddm1 lines propagated by self cross
  • seriusly impacts development, very dwarfed
  • the phenotypes of these plants are not the same
    • stochastic effect - action of the transposable elements
18
Q

What is the status of the global erasure in plants?

A
  • Plants DON’T do a global erasure and resetting of information as mammals do
  • affects the heritability of the epigenetic marks
  • if methylation pattern changes, this is likely to be maintained in the next generation
19
Q

Gernerally - how might stress memories in plant progeny be generated?

A
  1. Plants take in environmental information
  2. Change epigenome accordingly
  3. Stress memory
20
Q

How do the generation of germ cells differ in plants and mammals?

A
  • In mammals, germ cells arise very early
  • can still be influenced by the environment of their mother
  • In plants, have a vegetative stage, then flower - can pass epigenetic changes influenced by the environment onto progeny
  • these progeny may have advantages
    • prepared for stressful conditions
    • useful as plants can’t move
21
Q

What is the experimental evidence that plants that undergo stress affect epigenetic changes that are passed onto their progeny, giving them a survival advantage?

A
  • the progeny of arabidopsis plants exposed to salt may have a higher tolerance to salt stress than control plants
  • Looked at DNA methylation differences reported between control and stress progeny plants
    • higher in progeny of plants exposed to 25mM or 75mM NaCl
  • Looked at the germination rates of progeny
    • at higher concentration of NaCl, progeny of parents that had already been exposed had a higher germination level
  • Yes. Methlyation does change as a result of environmental differences in the progeny of stress affected plants
  • Contraversial: respond to the environment and pass this onto progeny. Led to major plant breeding experiement, does exposing plants to stress make them more tolerant
22
Q

What is the experimental evidence that ddm1 mutants partially regain DNA methylation levels when WT levels of DDM1 are restored?

A
  • Molecular analysis of ddm1 mutant and developmental phenotypes
  • Decreased levels of methylation by reducing levels of the ddn1 mutant
  • If ddn1 is put back does this re-establish methylation?
    • wouldn’t expect it to as plants don’t do erasure and re-establishment
    • area where it fails to respond to WT levels are regions that correspond to gene bodies (GC methylation)
    • when gene body methylation gone, it is not re-established
    • however do restore methylation levels on transposable elements
    • therefore they must have an ability to recognise and methylate transposable elements
23
Q

What is the experimental evidence that there is a strong correlation between TE methylation and sRNA accumulation?

A
  • genome wide analysis of DNA methylation patterns (epigenome single base analysis - where is m, where are the small RNAs that direct m?)
  • sRNA accumulation analysis
  • strong correlation between TE and sRNA accumulation
  • compared to gene body methylation, which does not correlated with sRNA accumulation
  • are sRNAs on TE used to re-establish methylation?
24
Q

What is the process of RNA-directed DNA methylation (RdDM) in plants?

A
  1. sRNAs come from regions of dsRNA
  2. Dicer like (RNAseIII enzyme) cuts into small interfering (si) RNAs
  3. siRNA and effctor (Argonaute AGO) proteins form a complex with DRM2 (de novo DNA methyltransferase)
  4. siRNA-effector complex directs sequence specific DNA methylation with the aid of PolV
  5. PolIV then transcribes the region
  6. RNA-dependent RNA polymerase 2 (RDR2) copies the PolIV transcript and produces more double stranded RNA and siRNAs via DCL3 cleavage
  7. cycle
25
Q

How is the process of RNA-directed DNA methylation (RdDM) affected in ddm1 mutant plants?

A
  • affects the efficiency of the process
  • once ddm1 restored, cycle will again methylate TE regions and genome repeats
  • RdDM cycle present to keep methyation on in TE and genome repeats
26
Q

What is the primary role of DNA methylation in plants and how does this relate to animal methylation?

A
  • the primary role of DNA methylation in plants may be to control transposable elements
  • Animals also use small RNAs to epigenetically silence transposons
27
Q

How do plants control gene expression at key developmental stages and what are these stages?

A

Plants use Polycomb (PcG) and trithorax (trxG) group proteins to control gene expression at key developmental stages

  • fertilisation
  • seed development
  • transition to flowering
  • flower organogenesis

Different to mammals: get post embryonic development and clear developmental transitions

28
Q

Why are many plant genomes packed full of transposable elements and how are these recognised and distinguished from host genes?

A
  • Over evolutionary time can compare different types of transposable elements/genome rearrangement
  • hybridisation of different species results in genomic shocks
  • lots of methylation changes can occur if bring together two different genomes
  • results in a burst of transposable element activity
  • Also may be a selective pressure: transposable elements may confer advantages
  • Germ cells TE most highly methylated in all organisms
29
Q

What are the PCR complexes of plants?

A
  • mammals have two major PCR complexes
  • plants only have PCR2 but have multiple versions
    • FIS
    • EMF
    • VRN
  • Act at different stages of the arabisopsis life cycle
30
Q

How is epigenetics involved in flowering?

A
  • plants need to flower in favourable conditions
  • many only flower after an extended period of cold (e.g. arabidopsis)
  • acceleration of flowering by prolonged cold is known as vernalisation
  • epigenetics is involved
    • FLC is a TF that blocks the floral transition
      • acts by repressing SOC1 and FT
      • FT is the main flowering promoting gene
    • Arabidopsis must turn off FLC in order to flower
      • mutant that cannot turn of FLC doesn’t leave vegetative stage, produces lots of vegetation
31
Q

What is vernalisation and how is epigenetics involved?

A
  • Vernalisation is flowering after a long period of cold
    • FLC expression is downregulated by cold
    • FLC repression is maintained after plants resume growth in the warm (epigenetic?)
    • VRN2 polycomb reperssive complex is involved (H3K27 methylation)
      FLC expression is reactivated in the developing embryo
  • Vernalisation fits the definition of a true epigenetic process
    • FLC expression high at 20degrees, FLC decreases in prolonged cold exposure (trigger), FLC reduction is maintained in the absence of the trigger (20degrees)
32
Q

What is the model for epigenetic silencing of FLC during vernalisation?

A
  • Looking at FLC locus
  • Before cold (high FLC) VRN is present on the gene but not adding repressive marks
  • Vin3 is upregulated by prolonged cold, brings together VEL1 and VRN5 to the VRN complex (PHD-PRC2 complex)
  • This complex contains VRN complex to add a methylating mark
  • Vin2 leaves and repression spread out and is maintained
33
Q

What is the model of the regulation at VIN3 chromatin by vernalisation?

A
  • Vin3 is normally repressed with known repressive marks
    • CLF/SWN (polycomb repressive complex)
    • lys37 and lys9 methylation
    • very repressed state
  • Cold trigger
    • get slight opening of Vin3
    • recruitment of trithorax activity, puts down active marks
      • lys4
    • allows Vin3 to be activated and transscribed
    • even during transcription keeps active and repressive marks (like bivalent domains seen in stem cells - all quick removal of Vin3 when gets hot again)
34
Q

Outline epigenetics in seed development

A
  • imprinting occurs primarily in the endosperm of flowering plants
    • endosperm is triploid and formed from fusion between sperm cell (haploid) and the central cell (diploid)
    • imprinting due to differences in epigenetic marks on the alleles of the central and sperm cells
35
Q

What is the process of seed development~?

A
  1. producton of maternal and paternal gamete (gametogenesis)
    1. maternal gametophyte undergoes multiple divisions - some meiotic, some mitiotic. Have a haploid egg cell (contributes to the embryo) and a diploid central cell (contributes to the endosperm)
    2. In paternal gametophyte (pollen), have 2 sperm cells and a vegetative cell.
  2. Sperm cells takes place in double fertilisation
    1. one fertilises the egg cell to generate a diploid embryo which will form the seed
    2. the diploid central cell gets fertilised by the other sperm cell to generate a triploid endosperm (2 X maternal, 1 X paternal): this balance is essential for normal endosperm development
  3. Only the embryo contributes to the next generation, endosperm is purely nutritive
36
Q

How is the plant endosperm prevented from proliferating before fertilisation?

A
  • The 4 PRC2 FIS complex components
    • MEA
    • FIS2
    • FIE
    • MSI1
  • are normally expressed in the central cell and repress central cell proliferation until fertilisation
  • mutants in these complex components produce endosperm in the absence of fertilisation
  • Imprinting: self regulatory system to keep level of endosperm balanced
37
Q

What gene are imprinted in the endosperm?

A
  • MEA, FIS, FWA (maternal expression) are imprinted in the endosperm by MET1
    • specific de-methylation occurs in the central cell by the demeter (DME) DNA glycosylase
    • doesn’t happen in the sperm - proteins stay methylated
    • upon fertilisation in the endosperm get balance of the correct level of PcG complex
    • genes from the maternal side repress the paternal side and proliferation, and other targets (PHE1 - represses maternal allele but not paternal allele)
    • balance ensures optimal growth of the endosperm
  • If balance is affected
    • e.g. different ploidy
    • normally crossing 2 diploid plants
    • if cross female 4n with male 2n get a doubling of the female chromosome and too little endosperm
38
Q

Why is studying the epigenetics of the endosperm important?

A
  • 70% of worldwide calories come from endosperm
    • cereals
    • plant breeding efforts to manipulate endosperm
    • but this affects the developmetn of the seed
39
Q

What ar teh features of epigenetics in plants?

A
  • plants use many of the same epigenetic mechanisms as animals
  • DNA methylation is linked to genome defense
  • polycomb and trithorax group proteins are involved in kep developmental transitions
  • imprinting in closely linked with seed development and is consistent with the parental conflict theory

Y3 (2) Epigenetics in Development and Disease (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions