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
