Mobile genetic elements 1 & 2 Flashcards
What’s been previously referred to as junk DNA is nowadays acknowledged to be _________ elements.
transposable
What’s the evolutionary origin of transposons?
Retroviruses
Which protein amplification method in baculoviruses utilize transposition?
Bac-To-Bac
Which three classes of transposable elements exist?
- DNA transposons
- Virus-like retrotransposons
- polyA-like retrotransposons
How do DNA transposons move throughout the genome?
DNA transposons encode a single gene, transposase. There are two ways for DNA transposons to traverse the genome, either by excising themselves or duplicating themselves.
Mechanism of excision and duplication.
1. Transposase multimer aggregates at the transposon’s terminal end repeat in a U-shape.
2. Transposon is cleaved out of its genomic context, two transposases will accompany it. Transposon will host overhangs.
3. Transposases recognize target duplication sites and cleave them so that they have overhangs.
4. Transposon ligates, repair machinery, and repair the nicks in DNA.
5. The transposon’s excision leads to a double-strand break which can either be repaired by NHEJ or homologous recombination. If it’s repaired by homologous recombination, the newly ligated genetic context of the transposon will be used as a template for repair, leading to a duplication of the transposon.
What phenomena can transposons induce when moving around the genome?
- Excise other genetic material.
- Invert genetic material.
- Trap genetic material.
How can the excision of genetic material be a consequence of transposition?
If two transposons are located in close proximity, they may spontaneously homologously recombine. It’s possible that they find themselves lined up with a loop connecting them to each other. When they homologously recombine, strand invasion occurs, forming holiday junctions. When the holiday junctions are resolved, the loop needs to be excised.
How can the inversion of genetic material be a consequence of transposition?
If two transposons are in close proximity and they homologously recombine while their genetic context is U-shaped, the DNA within the U-loop will get inverted. The consequence is due to the solving of Holliday junctions.
How can trapping of genes be a consequence of DNA transposition?
It’s possible if two transposons are very close to each other. There’s a chance that the transposase binds the 3’ LTR of 1 transposon and the 5’ LTR of the 2nd transposon and forms its bridge. The entire genetic segment in between the transposons will be co-excised.
This is the underlying mechanism of horizontal gene transfer in bacteria.
Why can’t the P-strain mate with the M-strain of drosophila?
The P-element encodes a p-transposase in drosophila males. The females hosting the p-element produces a p-element inhibitor from the same sequence, allowing genomic stability.
If a P-element male mates with a female w/o the p-element, the progeny will die.
Which are the three families of virus-like retrotransposons (VRTEs)?
- Ty1/copia-like (yeast/drosophila)
- Ty3/gypsy-like (yeast/drosophila)
- Pao-like (animals)
How does virus-like retrotransposons traverse the genome?
Virus-like retrotransposons often contain the gag and pol genes.
The LTRs of the virus-like retrotransposons can act as promoters. The transposon itself must at a minimum contain Integrase and RT. virus-like retrotransposons do not excise themselves, they just multiply.
Integrase cleaves the transposable element so that it has 3’ overhangs, and RT integrates the TE using the host’s tRNA and RNAse H.
What are ty-elements?
Ty = Transposition in yeast.
What do the acronyms SINEs and LINEs stand for?
LINE = Long interspered nucleotide elements.
SINE = Short —-
Fill in the gap:
LINEs and SINEs are the constituents of _______-transposons.
polyA
What defines LINE sequences? How are they generated efficiently?
Integrase, RT, and endonuclease (the enzymes are transcribed in two ORFs)
There are 3’/5’ UTRs, the 3’ UTR hosts a polyA tail.
How do LINEs transpose?
- Both of the LINE ORFs are transcribed and translated (endonuclease, RNA-binding proteins, RT).
- The proteins are imported to the nucleus.
- Endonuclease nicks the genomic DNA, 3’ UTR (polyA) anneals and RT incorporates the transcribed TE.
- RNAse H degrades the RNA in the hybrid, repair machinery repairs the second DNA strand, and fixes the ssDNA break.
How can LINEs generate pseudo genes?
- After the LINE proteins (endonuclease, RT, RBP) are translated, they are re-imported to the nucleus. As they are re-imported, they may co-import some transcript(s). These transcripts can get reverse transcribed and integrated as the LINE TE.
- When LINEs are transcribed, no stop codons are in place. This may lead to elongated transcripts hosting parts of genes or entire genes. These extra fragments can be inserted and thus duplicated.
Do SINEs and LINEs have LTRs?
No. They have UTRs.
How do SINEs transpose?
Since SINEs don’t have any genes, they rely on the LINE transposition machinery.
What does “SVA” abbreviate and what does it consist of?
SVA = SINE-VENTR-Au element
VNTR = Variable number of tandem repeats
What TE out of the following is still active?
DNA tranposons
Virus-like retrotranposons
PolyA-like retrotransposons
PolyA-like retrotransposons, specifically LINE elements.
Is it true that TEs are to blame for loss-of-synteny and exon shuffling?
Yes.
Interesting fact
During embryogenesis and neurogenesis, the fetus and brain are mosaics resulting from differential TE activity.
During aseptic brain inflammation, one theory is that TEs activate themselves, just like in Koalas in Australia.
