Lecture 30

Question 1

What is the consequence of Ac transposing into a coding region of a gene vs a non coding region

Answer 1

Excision of Ac is imprecise so there are 6-8 base pair insertions remaining if this occurs in the coding region there will be a stable mutant as the gene will not function correctly even when Ac is excised
If it is in a non coding region then the gene may be expressed normally after Ac is excised

Question 2

What is the difference between Ac and Ds?

Answer 2

Ac=Activator element and can act autonomously while Ds= Dissociator element and must have Ac present to transpose so is therefore non-autonomous

Question 3

What is the relation ship between Ac and Ds?

Answer 3

Most Ds are simply deletion mutants of Ac

Question 4

What are the characteristics of Ac transpositon?

Answer 4

follows 50-70% of excisions
Often hops to linked sites
Occurs after DNA replication
Occurs in both somatic and germ line cells

Question 5

What is the P element in drosophila?

Answer 5

A standard DNA transposable element with 31 bp terminal inverted repeats
An example of a transposase which is cell specific as it is only expressed in the germ line cells therefore is a drosophila embryo is injected with a DNA plasmid containing P then its offspring not it will experience the effect of that transposable element

Question 6

How many genes are in the human genome?

Answer 6

21,000

Question 7

What percentage of the human genome is made of transposable elements?

Answer 7

45%

Question 8

What percentage of the human genome are made up of retroviral transposable elements and how many copies are present?

Answer 8

8% with an average size of 5-10 kb and 450000 copies

Question 9

What percentage of the human genome are made up of SINE transposable elements and how many copies are present?

Answer 9

13%, average size of 100-300 bp and 1.5 million copies

Question 10

What percentage of the human genome are made up of LINE transposable elements and how many copies are present?

Answer 10

21%, average size of 6-8 kb and 850,000 copies

Question 11

What transposable elements transpose via RNA?

Answer 11

LINES, SINES and retroviral

Question 12

What is the number of transposable elements correleated with?

Answer 12

Genome size for example drosophila has a small compact 120 Mb genome but only 10% transposable elements

Question 13

How do integrated RNA viruses transpose? and what are there features?

Answer 13

Through use of an RNA intermediate

Have long terminal direct repeats and also generate short repeats at insertion site

Question 14

What is ty1?

Answer 14

A yeast transposable element, which can be used to show that some transposons move via an RNA intermediate as insertion of an intron into the ty1 showed the replicated forms of this did not contain an intron

Question 15

What are LINES?

Answer 15

Long Interspersed Elements which are abundant in mammalian genomes, have an Reverse transcriptase and integrase activity
Transpose via RNA
Have no terminal repeats (though do have a poly A at the 3’ end)
Generate short direct repeats when they integrate

Question 16

What are SINEs

Answer 16

Short Interspersed Elements which transpose via RNA are extremely abundant in mammals, do not code for genes and are likely to have come from cellular RNAs derived from splicing
Non-Autonomous, require LINEs to spread
No terminal repeats
Generate short direct repeats when they integrate

Question 17

How frequently do transposable elements move?

Answer 17

Very infrequently in eukaryotes with the exception being drosophila and maize
Only appears to have happened with humans through two evolutionary bursts of activity

Question 18

What are the function of transposable elements?

Answer 18

Have a close relationship with viruses but it is not clear which came first
Probably genomic parasites which will either have no benefit to the host or may confer some benefit in circumstances such as antibiotic resistance, an ability to allow for new proteins to form through exon shuffling
Some species do however have a high selection to clear inactive Transposable elements with RNAi most likely developed as a method of silencing both viruses and TEs

Question 19

What are the 17 properties of eukaryotic TEs?

Answer 19

1. Short DNA elements (0.2-10kb) able to transpose
2. Found in different locations in different genomes
3. Encode transposase and sometimes additional genes
4. Flanked by inverse repeats (sometimes direct repeats or sometimes no repeats) which is the binding site for transposase
5. Generate short direct repeats of characteristic length at insertion site
6. Replicative or conservative transpostion
7. Insertion site can be random or have sequence specificity
8. Excision of conservative elements can be precise, imprecise or lethal
9. Frequently cause deletions, inversions and rearrangements
10. Transposition frequency is tightly controlled
11. Many Eukaryotic TEs are non-autonomous
12. Eukaryotes do have bacterial like DNA transposable elements but most will move via a RNA intermediate
13. Some are closely related to retroviruses with terminal direct repeats and some similar genes but are not packages of transmitted from cell-cell
14. Other classes of retrotransposons exist
15. TEs are more abundant in eukaryotes than prokaryotes
16. Most Eukaryotes are inactivated, dead copies
17. Their function is unclear so they may simply be tolerated parasites