Transposable elements

Question 1

How big are TEs usually?

Answer 1

1-3kb

Question 2

They can have a) moderate and b) high levels of repeats. How long are these?

Answer 2

a) 1-100 repeats

b) 1 million

Question 3

Are TEs dispersed across the genome?

Answer 3

Yes

Question 4

Are TEs mobile?

Answer 4

Yes

Question 5

TEs cannot replicate. True or false?

Answer 5

False

Question 6

There are 2 types of TE. What is a retrotransposon?

Answer 6

TEs that use reverse transcriptase to generate cDNA (behave like retroviruses)

Question 7

Describe how retrotransposons replicate.

Answer 7

Transcription of DNA to RNA.
Reverse transcription of RNA to cDNA.
Incorporation of cDNA by integrase.

Question 8

There are 2 types of TE. What is a DNA element?

Answer 8

TEs that transpose as DNA with no RNA intermediate

Question 9

Describe how DNA elements replicate.

Answer 9

‘Cut and paste’ approach:
Transposase enzyme cuts TE free, producing a sticky end.
TE ligates to new target site.
DNA polymerase fills in the gaps.
Ligase closes the sugar-phosphate backbone.

Question 10

Transposition is good for the element. Why is it beneficial before meiosis?

Answer 10

TE copies itself onto both sister chromatids of a chromosome before they segregate, means it ends up in 50% of the gametes.

Question 11

Transposition is good for the element. Why is it beneficial during meiosis?

Answer 11

TE transposes from one chromosome onto another that is NOT its homologue (presumably bc they are all lined up in close proximity). If it has already copied itself onto sister chromatids of the original, will end up in 75% of the gametes.

Question 12

Give 3 major costs of TEs for the host.

Answer 12

1. Expensive to produce extra DNA/RNA/proteins for transposition
2. Major risk of spontaneous mutation, most of which deleterious
3. Ectopic recombination as it causes non-homologous pairings at meiosis, causes unbalanced chromsomes

Question 13

In terms of TEs, what is individual selection?

Answer 13

Competition on each TE individually, causes competition between TEs

Question 14

In terms of TEs, what is group selection?

Answer 14

Competition between hosts

Question 15

Individual selection favours TEs with what?

Answer 15

Higher transposition rates

Question 16

Group selection favours what?

Answer 16

Hosts with fewer TEs

Question 17

Individual and group selection are antagonistic. True or false?

Answer 17

True.

Question 18

Are ‘groups’ permanent?

Answer 18

No bc host genomes are constantly broken up by recombination

Question 19

The Drosophila view of TEs:

What happens to TEs that insert into exons?

Answer 19

They are removed by selection as disrupt gene function

Question 20

The Drosophila view of TEs:

So where do TEs accumulate and why?

Answer 20

In introns, so areas of low gene density and low recombination, bc selection is weaker in these regions.

Question 21

The Drosophila view of TEs:

Give examples of areas of low recombination.

Answer 21

Y chromosome, inversions etc.

Question 22

Harm that results from TEs increases exponentially with copy number. Why?

Answer 22

Because TEs increase the likelihood of ectopic recombination.

Question 23

The Drosophila view of TEs:

What did Petrov (2011) investigate in D. melanogaster?
What did they find?
What did they conclude?

Answer 23

Looked at whether the most damage from TEs came from insertion of the TE or ectopic recombination.

Look at 70+ strains.
Found over 755 different TEs.
None were found in exons, implies strong purifying selection.
All TEs found in introns.
TEs v. rare in areas of high recombination.

Ectopic recombination causes more damage

Question 24

The Drosophila view of TEs:

What evidence did Petrov (2011) find for the theory that TEs cause ectopic recombination?

What

Answer 24

1. Long TEs are rare as increases chance of ectopic recombination.
2. High copy number of TEs v. rare per site, as increases likelihood of ectopic recombination
3. No association of TE with distance from coding region, as if was close to coding region then would disrupt regulatory sequences

Question 25

Hosts can develop repression mechanisms against TEs. Who described P elements in D. melanogaster?

Answer 25

Khurana et al. (2011)

Question 26

Khurana et al., 2011: Piwi proteins associate with different piRNAs. Each piRNA associates with a different transposon. In D. melanogaster which transposons do Piwi proteins associate with? WT females repress P elements. How? How did the authors discover this? What is hybrid dysgenesis? If you mate WT females with lab males, what can be said of the offspring? Why do WT drosophila have p elements and lab strains do not?

Answer 26

P elements They have piRNA and Piwi proteins in their cytoplasm. They mated WT males (p elements with no repression) and lab females (no p elements), F1 displayed hybrid dysgenesis. High mutation rates and sterility due to an explosion of P elements F1 are fine bc have inherited repression along with p elements from mother Lab strains were isolated before the invasion of the p element.

Question 27

Khurana et al. (2011): Why is the P element self-limiting?

Answer 27

P is self limiting as it causes male infertility in hybrids (between P male and lab female) and hybrid dysgenesis

Question 28

Khurana et al. (2011): | What happens to male infertility as males age? Why?

Answer 28

They become fertile as they age as the piRNA machinery assembles and they acquire 'immunity' to the P elements

Question 29

Khurana et al. (2011): | What is piRNA?

Answer 29

Small, anti-sense TE fragments

Question 30

Khurana et al. (2011): | Where is piRNA stored?

Answer 30

In centromeric heterochromatin

Question 31

Khurana et al. (2011): | What does piRNA do?

Answer 31

Binds to TEs

Question 32

Who described one mechanism of the Piwi system?

Answer 32

Brennicke et al., 2007

Question 33

Brennicke et al., 2007: Outline how the Ping Pong cycle works as outlined by the authors.

Answer 33

Aubergine protein is associated w/ antisense piRNA Antisense piRNA binds TE, flags it for destruction Aubergine releases piRNA Argonaute associated w/ sense strand of piRNA Argonaute synthesises antisense piRNA This piRNA used to replenish Aubergine Cycle called Ping Pong as it constantly goes back and forth

Question 34

The Piwi system is a set of proteins associated with piRNAs. What can it be described as?

Answer 34

'Genetic memory' of TEs, like an immune system within the genome.

Question 35

Does selection always favour TEs with high transposition rates?

Answer 35

No

Question 36

Why doesn't selection always favour TEs with high transposition rates?

Answer 36

High transposition rate damages the host. In bacteria hosts are asexual and produce clones. This produces a conflict between individual and group selection (as all hosts are identical), thus TE wants to lower transposition rates

Question 37

Hosts can evolve self-repression mechanisms. Who looked at the TE tn10 in E. coli? How often does it transpose? What is the IS10 element of the tn10 TE?

Answer 37

Kleckner, 1990: Only transposes every 1000th cell division IS10 = encodes functional transposase

Question 38

Kleckner (1990): | What are the two mechanisms behind low transposition of the tn10 element in E. coli?

Answer 38

1. TE is methylated. | 2. Anti-sense RNA inhibitor binds transposase transcripts of IS10 element to prevent translation of an active enzyme.

Question 39

Kleckner (1990): | What evidence is there that a) methylation and b) anti-sense inhibition of transposase are the repression mechanisms?

Answer 39

a) remove methylation and transposition increases 100x b) inhibition increases exponentially with copy number; more inhibitor produced = more IS10 transcripts prevented from translating

Question 40

TEs can contain LTRs. What are they?

Answer 40

Long terminal repeats (basically repeats at the end of DNA sequences)

Question 41

The accumulation of TEs is common. Give a referenced example. Why is it thought TEs were allowed to accumulate by selection?

Answer 41

San Miguel et al. (1998) Looked specifically at TEs near the adh1 gene in maize Maize genome found to have doubled over last 3mya from 1200Mb to 2400Mb due to LTRs. This has been allowed to accumulate by selection as LTRs insert into other LTRs, neutral effect.

Question 42

In the 1960s Barbara McClintock proposed a hypothesis for the retention of TEs. What was it?

Answer 42

They are co-opted for gene regulation

Question 43

What evidence is there for co-option of TEs by the host? Give a referenced example (review paper).

Answer 43

Gifford et al. (2013), REVIEW env protein from retroTE in several mammalian lineages mediates cell-cell fusion of the placenta, co-opted to make syncytin

Question 44

Who described co-option of the TE evr1 in regulation of oct4, a major developmental gene? Oct4 has many names. What is another name for oct4 in humans?

Answer 44

Kunarso et al., 2010 POU5F1 in humans

Question 45

Khurana et al., 2011: After the P elements invade D. melanogaster and produce male infertility, in a few generations male fertility is restored. Why?

Answer 45

Males gain fertility back as they age as Piwi machinery assembles. Resident TEs insert into piRNA clusters, leading to the formation of novel piRNAs. These are transmitted to progeny, and associated with reduced transposition. 'P elements triggers genomic change that induces TE silencing'