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Evolutionary and Population Genetics (GEU33075) > Lecture 24 - Transposition > Flashcards

Lecture 24 - Transposition Flashcards

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1
Q

What is a transposable element (TE)?

A

A type of mobile genetic element that is able to move or propagate intragenomically (i.e., within a genome). Some can also move intergenomically (i.e., between genomes).

NOTE! Mobile elements that can only move intergenomically (and not intragenomically) are not transposable!

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2
Q

What is transposition?

A

Movement of genetic material from one genomic location (donor site) to another (target site) within the same genome.

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3
Q

How can transposition be categorised?

A
  1. Conservative - cut and paste transposition.
  2. Replicative - copy and paste transposition.
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4
Q

What is conservative transposition?

A

Where the transposable element (TE) is CUT out of a donor site and inserted into the target site.

The donor site is therefore left without the TE.

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5
Q

What is replicative transposition?

A

Where the transposable element (TE) is COPIED from a donor site and the copy inserts itself into the target site.

The TE remains in the donor site, but we now also have a copy in the target site.
- This is an example of how transposition can be a duplicative mechanism

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6
Q

How are TEs classified?

A
  1. Class I or retrotransposable elements
    - Must move via an RNA intermediate and reverse transcriptase (retrotransposition or retroposition)
    - Retrotransposition is ALWAYS REPLICATIVE
  2. Class II elements
    - DNA mediated transposition
    - Don’t move via an RNA intermediate
    - Can be conservative OR replicative (with a few class II elements using both)
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7
Q

What is the main enzyme needed for class II transposition?

A

Transposase - responsible for the movement of DNA segments from one region to another.

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8
Q

What enzymes are required for class I transposition (retrotransposition)?

A
  • Always require a reverse transcriptase (RT)
  • Also often require a transposase (usually integrase or an endonuclease)
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9
Q

What is another way of classifying TEs?

A

Based on whether the sequence of the TE contains all the genes necessary for transposition.

  1. Active
    - Autonomous
    - Non-autonomous
  2. Fossil
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10
Q

What is an autonomous TE?

A

Encodes all parts of the transposition machinery itself.
- E.g., transposase in class II elements
- E.g., reverse transcriptase and integrase in class I elements

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11
Q

What is a non-autonomous TE?

A

Does not encode all the parts of transposition machinery.
- Thus, has to recruit machinery (transposase and RT etc.) from elsewhere
- Often recruit them from the host genome or from an autonomous TE

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12
Q

What is a fossil element?

A

Can no longer be transposed!
- Roughly 200,000 fossil non-autonomous and 50,000 fossil autonomous TEs in the human genome!
- However, no active class II TEs are known in humans!

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13
Q

What happens at the target sites when a TE is being inserted?

A
  • Transposition almost always causes duplication of a small stretch of DNA (4-12 bp) at the target site
  • This is due to a staggered cut made by transposase before inserting the TE
  • The fill-in repair of these gaps results in direct repeats flanking the TE, a hallmark of transposition
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14
Q

What are direct repeats?

A

A small duplicated stretch of DNA created by the fill-in repair of the gaps flanking the TE.
- Presence of direct repeats can be used as evidence of a transposition event

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15
Q

What are terminally inverted elements (TIRs)?

A

Repeats that duplicate the target site (i.e., they are inverted repeats of the flanking direct repeats).
- TIRs are part of the element
- Possessed by virtually all class II TEs
- Different TIRs are recognised by different transposases (which initiate cleavage and insertion)

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16
Q

What are the 3 main types of “cut and paste” class II TEs?

A
  1. Insertion sequences (IS)
  2. Transposons
    (Both of which are autonomous, encoding for their own transposase)
  3. Non-autonomous elements
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17
Q

How are DNA transposons a really powerful force for evolution?

A

Allow for a intragenomic cross transfer of genes (e.g., transposons in bacterial resistance).

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18
Q

Transposons can be either…

A
  1. Composite transposons
  2. Simple transposons
19
Q

What class of TEs are DNA-mediated?

A

Class II TEs.

20
Q

What class of TEs are RNA-mediated?

A

Class I TEs (defined by the use of reverse transcriptase, RT).

21
Q

What are retroelements?

A

Any sequence that encodes reverse transcriptase (RT).

22
Q

What are the prokaryotic retroelements?

A
  • Retrons
  • Retroplasmids
  • Retrointrons

They are relatively rare and only retrointrons have the capacity to transpose!

23
Q

What are the eukaryotic retroelements?

A
  • Retrointrons
  • Retroviruses
  • Retrotransposons

They are abundant, particularly the transposable retrotransposons.

24
Q

What are retroviruses?

A

Single-stranded RNA viruses that infect vertebrates exclusively!

25
Q

How do retroviruses insert their DNA into the host?

A
  • Viral genomic RNA is reverse transcribed into cDNA after invasion
  • Integrase then pastes cDNA into the host genome (now called a provirus)
26
Q

What are long terminal repeats (LTRs)?

A

They are duplicated regions that flank the viral coding region (within in the host genome) which contain promoters for transcription and reverse transcription.

These promoters allow high expression levels of the viral proteins and new viral RNA synthesis.

27
Q

Give some examples of different ways which retroviruses can cause disease.

A
  1. Induced lysis and immune destruction of infected cells (HIV).
  2. Introduction of oncogenes mistakenly incorporated into provirus (Rous sarcoma virus).
  3. Provirus promoter can cause over-expression of oncogenes nearby.
28
Q

What can result from retroviruses infecting the germline of the host?

A

They can potentially be transmitted vertically through the generations of the host. These vertically transmitted retroviruses are called Endogenous Retroviruses (ERVs).

29
Q

What are endogenous retroviruses (ERVs)?

A

Retroviruses that are transmitted vertically through the generations of the host (after infecting the host germline).

30
Q

What are retrotransposons?

A

RT-mediated transposable elements that do not construct virion particles, defined by their lack of the env (envelope) gene.

31
Q

How are retrotransposons often classified?

A

Often classified by presence or absence of long terminal repeats (LTRs).

  1. LTR-retrotransposons
    - Retrovirus-like
    - Uses similar mechanisms as retroviruses
  2. Non-LTR-retrotransposons
    - Seemingly monophyletic with their own mechanisms of transposition
    - They don’t transfer horizontally, ONLY vertically (through the host germline)
32
Q

What are the non-LTR-retrotransposons also known as?

A

LINEs and SINEs

33
Q

What are LINEs (long interspersed nuclear elements)?

A

Autonomous non-LTR-retrotransposons.
- Found across eukaryotes, but are mostly fossils (roughly 20% of human genome)

34
Q

What are SINEs (short interspersed nuclear elements)?

A

Non-autonomous non-LTR-retrotransposons (basically non-autonomous LINEs).
- Do not encode their own RT
- SINE propagates itself by using the machinery of a corresponding LINE

NOTE! If the LINE fossilises, then so does the SINE!

35
Q

Give an example of a famous example of SINEs in humans.

A

Alu sequences (found in humans and other supraprimates).

36
Q

What is a retrosequence? How do they come about?

A

Any mRNA or RNA transcript in the cell may be reverse transcribed back into the genome.

Retrosequences are the result of such an event!
- But they show no special adaptions for retrotransposition (they are usually once off accidents)!

37
Q

What do retrosequences indicate?

A

Bears the hallmarks of RNA processing, thus they are so-called processed sequences!

38
Q

What are the diagnostic features of retrosequences?

A
  • No introns
  • Has a poly(A) tail
  • Has terminal direct repeats (TDRs) on either side, a hallmark of transposition
39
Q

What is the evolutionary fate of retrosequences?

A

Usually are “dead on arrival”.

  1. Reverse transcription is very inaccurate.
    - Can introduce loss-of-function mutations which can knock out the function of the retrogene before it is even expressed!
  2. They are inserted in regions without the necessary regulatory regions, thus never get expressed.
40
Q

What are retropseudogenes (A.K.A., processed pseudogenes)?

A

These are retrogenes that never go on to achieve anything (i.e., the “dead on arrival” retrogenes).

41
Q

What can happen to retrogenes on rare occasion?

A

They may be inserted near a promoter and get expressed!

If there are no loss-of-function mutations, a functional protein will be expressed!
- When this happens, there is the opportunity for big phenotypic effects/evolution
(See lecture 24 @ 38 mins for example!)

42
Q

What are the evolutionary effects of TEs?

A
  • Can act as mutagens
  • Can carry regulatory elements
  • Can carry exogenous genes
  • Can encourage genomic rearrangements
  • RT can allow for gene duplication
  • TE genes can be domesticated (e.g., syncytins)
43
Q

What is a dramatic evolutionary effect that replicative TEs can have?

A

Can cause huge differences in genome size!
(See lecture 24 @ 39 mins)

Evolutionary and Population Genetics (GEU33075) (10 decks)

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