Lecture 30 Flashcards
What is the consequence of Ac transposing into a coding region of a gene vs a non coding region
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
What is the difference between Ac and Ds?
Ac=Activator element and can act autonomously while Ds= Dissociator element and must have Ac present to transpose so is therefore non-autonomous
What is the relation ship between Ac and Ds?
Most Ds are simply deletion mutants of Ac
What are the characteristics of Ac transpositon?
follows 50-70% of excisions
Often hops to linked sites
Occurs after DNA replication
Occurs in both somatic and germ line cells
What is the P element in drosophila?
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
How many genes are in the human genome?
21,000
What percentage of the human genome is made of transposable elements?
45%
What percentage of the human genome are made up of retroviral transposable elements and how many copies are present?
8% with an average size of 5-10 kb and 450000 copies
What percentage of the human genome are made up of SINE transposable elements and how many copies are present?
13%, average size of 100-300 bp and 1.5 million copies
What percentage of the human genome are made up of LINE transposable elements and how many copies are present?
21%, average size of 6-8 kb and 850,000 copies
What transposable elements transpose via RNA?
LINES, SINES and retroviral
What is the number of transposable elements correleated with?
Genome size for example drosophila has a small compact 120 Mb genome but only 10% transposable elements
How do integrated RNA viruses transpose? and what are there features?
Through use of an RNA intermediate
Have long terminal direct repeats and also generate short repeats at insertion site
What is ty1?
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
What are LINES?
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
What are SINEs
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
How frequently do transposable elements move?
Very infrequently in eukaryotes with the exception being drosophila and maize
Only appears to have happened with humans through two evolutionary bursts of activity
What are the function of transposable elements?
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
What are the 17 properties of eukaryotic TEs?
- Short DNA elements (0.2-10kb) able to transpose
- Found in different locations in different genomes
- Encode transposase and sometimes additional genes
- Flanked by inverse repeats (sometimes direct repeats or sometimes no repeats) which is the binding site for transposase
- Generate short direct repeats of characteristic length at insertion site
- Replicative or conservative transpostion
- Insertion site can be random or have sequence specificity
- Excision of conservative elements can be precise, imprecise or lethal
- Frequently cause deletions, inversions and rearrangements
- Transposition frequency is tightly controlled
- Many Eukaryotic TEs are non-autonomous
- Eukaryotes do have bacterial like DNA transposable elements but most will move via a RNA intermediate
- Some are closely related to retroviruses with terminal direct repeats and some similar genes but are not packages of transmitted from cell-cell
- Other classes of retrotransposons exist
- TEs are more abundant in eukaryotes than prokaryotes
- Most Eukaryotes are inactivated, dead copies
- Their function is unclear so they may simply be tolerated parasites