BIOB11H3 Lecture Notes - Lecture 3: Transposase, Genomics, Restriction Fragment Length Polymorphism
Genome Evolution & Polymorphisms
▪ It generates a staggered cut to generate a partial single stranded characters at both ends
1. after the transposon inserts
2. host cell enzymes repair the damaged DNA in the middle
3. it uses one strand to create the template to create the other one and there is the
generation of the direct repeat AATC on both ends of the transposon
▪ How do you get a direct repeat?
▪ If the transposon gets cut there, its cut by an
enzyme called transposase which is usually
encoded by a gene on that transposon
▪ One of the genes that an active transposon has is
one that catalyzes the cleavage of the end
structures so that the transposon can jump out of
one place and be put into another place
▪ Transponsons can make the cuts in the targets
side and that generates the end structures that you
see here
▪ Cut/paste method of bacterial transposition
▪ Transponsons can move in two distinct mechanisms, bacteria
cells tend to move by “cut and paste” method
▪ what you see is that here is the transponson and donor
DNA
o transposase is generated
o it binds to the inverted repeats at the end
o it makes a cleavage to take it out of the donor
DNA
o it then captures a target DNA as you see in step 3
o it nicks these two strands and integration occurs to
put it in
o repair synthesis occurs to generate those direct
repeats at the end
o so transposase recognizes those inverted repeats as
“oh these are the boundaries of myself” and
cleaves such that it is transferred as an intact unit
▪ It may also select a target site, usually non specific
o it recognizes the specific inverted repeats at the
end (to know where to cut) but where it cuts the
donor DNA is usually non specific
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Genome Evolution & Polymorphisms
▪ In eukaryotes this can occur in a couple of different ways:
1. cut and paste mechanism
a. it is coming out of the donor DNA and selecting a recipient DNA
i. your moving from one place to another
ii. what is left behind may be thought of as a footprint of where that
transposable element use to because there is a direct repeat
If your examining a sequence and you see a short direct
repeat side by side that might be the footprint of where a
transposon use to lie
▪ A more complicated way involves transcription, replication and reverse transcription
used by retro transposons
o The host RNA polymerase transcribes the RNA (region of the transposable
element)
o Another transposon located gene encodes an enzyme called reverse transcriptase
(takes an RNA and turns it back into a copy of DNA)
o That DNA can be converted to a double stranded form now you have a
replicated transposable element sequence
o it can now find a recipient DNA, catalyze its integration
▪ now you can move a new copy to a another location but you have also
stayed in the same location (ask someone about this)
o Consequence moved to a new place (may create a mutation) but you also
stayed in the same location (genome size has increased)
1. Cut and
paste
method
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