Transposons & Mechanisms of

Transposition
Krystine Garcia, Tao Jing, Alexander Meyers
Genomic Distribution
 98.5% of human genome non-coding
 25% non-repeat spacer DNA
 Repetitious DNA
-Tandemly repeated genes
-Sattelite DNA (6%)
 Interspaced repeats
Transposable Elements
Interspaced repeats have the capability to
“move around” in the genome, and are thus
referred to as transposable elements.

Transposition in germ cells are passed

down to progeny resulting in an
accumulation in the genome.
Transposable Elements
 Began as symbiont DNA
 Transposons provide a mechanism for
bringing about DNA rearrangements
throughout evolution
 Adjacent DNA sequences sometimes
mobilized
 Transposons, retrotransposons
Transposons and Retrotransposons
 Transposons excise themselves and move
to another location
 Retrotransposons duplicate and
reintegrate themselves
IS: Insertion Sequence
IS: Insertion Sequence
Transposase
 Cis-acting enzyme
 Is coded for in
transposon
 Cuts the IS at inverted
repeats
 Transmits it to another
part of the DNA at a
target sequence
 Multiple types of
transposase

http://www.rcsb.org/pdb/101/motm.do?momID=84
Transposase Regulation

 Frequency of
transposition is
regulated by
transposase regulation
 Not all transposase
genes are transcribed

http://www.rcsb.org/pdb/101/motm.do?momID=84
Autonomous &
Nonautonomous
 Autonomous (activator elements) are
very similar to bacterial IS elements in
structure and function
 Nonautonomous (dissociation elements)
lack transposase gene
◦ Cannot move by themselves
◦ Must have a cis transposable element with
transposase gene to move
 3 principle classes of transposons:
1. DNA transposons:
move using cut and paste or
replicative mechanism

2. Virus-like retrotransposons
(aka long terminal repeat
[LTR] retrotransposons): RNA
intermediate, includes
retroviruses

3. Poly-A retrotransposons
(aka nonviral retrotransposons):
RNA intermediate
 Cut and paste mechanism of transposition:
 Nonreplicative
1. Transposase (usually 2 or 4 subunits)
binds terminal inverted repeats
2. Brings 2 ends together  stable protein
complex called synaptic complex or
transpososome
3. Transposase cleaves one DNA strand at
each end at junction between
transposon DNA and host DNA 
transposon sequence terminates with
free 3’-OH groups at each end
4. Other DNA strands cut by various
mechanisms  transposon excised
 Cut and paste mechanism of transposition:
5. 3’-OH ends of transposon DNA attack
DNA phosphodiester bonds at site of
new insertion (target DNA)
6. Nicks introduced in other target DNA
strands few nucleotides apart 
transposon joined via reaction called
DNA strand transfer
7. Few nucleotides between nicks leaves
small ss gaps  filled in by host DNA
repair polymerase  small target site
duplications on either side transposon
8. DNA ligase seals final nicks
9. Ds break where transposon left
repaired by homologous recombination
 Nontransferred strand cleavage:
 Nontransferred strands = 5’ ends of transposon (ends not
covalently linked to target DNA during strand transfer)

 Cleavage can use enzyme other than transposase:

◦ Tn7 encodes specific protein called TnsA with structure similar
to restriction enzyme – works with transposase to cleave
nontransferred strands

 Cleavage can be performed by transposase:

◦ Tn5 and Tn10 form DNA hairpin (3’-OH attacks its
complementing strand) to cause nicks  hairpin opened by
transposase  3’-OH’s join to target DNA via strand
transfer
◦ Hermes forms DNA hairpins in target DNA
Nontransferred strand cleavage:
 Replicative transposition:
 Transposon DNA replicated during
each round of transposition
1. Transposase assembles on each end of
transposon to form transpososome
2. Transposase introduces nicks at
junctions between transposon and
flanking host DNA  generates 3’-OH
ends on transposon (but transposon
NOT excised from flanking DNA)
3. 3’-OH joined to target DNA by strand
transfer reaction (same mechanism as
cut-and-paste)  intermediate is
double branched DNA molecule
 Replicative transposition:
4. 3’ ends transposon covalenty linked
to target DNA, but 5’ ends still linked
to old flanking DNA
5. 2 branches like replication forks, DNA
replication proteins assemble at these
forks, 3’-OH serves as primer
6. Replication proceeds through
transposon and stops at 2nd fork  2
copies of transposon flanked by short
target site duplications
 Frequently causes chromosomal
inversions and deletions detrimental
to host
Virus-like retrotransposons and retroviruses:

 Carry inverted terminal repeats (recombination

sequences) embedded within longer direct repeat
sequences (aka long terminal repeats [LTR])

 Encode 2 proteins needed for mobility: integrase

(transposase) and reverse transcriptase
Virus-like retrotransposons and retroviruses:
 Reverse transcriptase: Enzyme that uses RNA
template to synthesize DNA

 Retrovirus: genome packaged into viral particle,

leaves host cell, infects new cell

 Retrotransposon: can only move to new DNA sites

within cell
 Virus-like retrotransposons and retroviruses:
1. Retrotransposon DNA transcribed into
RNA by host RNAP (transcription
starts at promoter within LTR)
2. RNA reverse-transcribed (by RT) 
RNA:DNA  dsDNA (cDNA)
3. Integrase (transposase) recognizes
and binds ends of cDNA then cleaves
few nucleotides off 3’ end of each
strand (just like cleavage step of DNA
transposons)
4. Integrase performs strand transfer
reaction to insert 3’ ends into target
DNA
5. Gap fill and ligation by host proteins
Transposon Excision
Plant genomes are rich in transposons:

 Barbara McClintock
discovered transposons
in the late 1940’s
 Maize color varigation
due to chromosome
breakage by
transposition
 Snapdragons: size of
white patches related to
frequency of
transposition