1. Transposable Elements And Transposition
integration of small DNA segments into chromosomes
Can occur at many locations within genome
transposable elements (TEs)
“jumping genes”
DNA segments that move
1st identified by Barbara McClintock in corn

2. McClintock Discovers Moving Loci in Corn
Babara McClintock identified many unusual features of corn chromosomes
in one strain of corn, chromosome 9 tended to break at a high rate at the same site
termed this a mutable locus
Mutable sites are locations where transposable elements have been inserted into the chromosomes
She received Nobel Prize in 1983

3. Transposition Pathways
3 general types of transposition
Simple transposition
Replicative transposition
Retrotransposition
Class I
Retrotransposons
Class II
DNA transposons

4. Simple Transposition Prokaryotic eukaryotic
Insertion Sequences (IS# ) - only contains transposase gene
Transposons (Tn#) - contain additional genes between 2 IS
eukaryotic
Ac/Ds

5. Regulatory Sequences of Transposable Elements Simple Transposons
Direct repeats – Identical DNA sequences that are and run in the same direction (5’3’)
Originate from bacterial chromosome at insertion site
Inverted repeats - DNA sequences that are identical (or very similar) but run in opposite directions
5’ ATGACTGAC 3’
3’ TACTGACTG 5’
5’ ATGACTGAC 3’
3’ TACTGACTG 5’
and
5’ CTGACTCTT 3’
3’ GACTGAGAA 5’
5’ AAGAGTCAG 3’
3’ TTCTCAGTC 5’
and

6. Bacterial Insertion Sequence
9bp direct repeat
9bp direct repeat
N1N2N3N4N5N6N7N8N9
N1N2N3N4N5N6N7N8N9
Figure 13.23 6

7. Bacterial Transposon
Figure 13.25B 7

8. Simple & Replicative Transposons
Both contain a gene encoding a transposase enzyme
Transposase function
recognizes direct and indirect repeats
cuts DNA for both excision and insertion

9. Replicative Transposition
Involves replication of the TE and insertion of the copy into another chromosomal location
Only found in bacteria

10. Retrotranposons & Retrotransposition
Very common but only occur in eukaryotes
also known as retroelements
Similar organization to retroviruses

11. Composite Transposons
Contain additional genes that are not necessary for transposition per se
Only the inverted repeats at the ends of the transposon are involved in the transposition event
Only these are adjacent to direct repeats

12. Elements of Replicative Transposons
Organization is similar to insertion sequences
Resolvase gene is found between the inverted repeats
Both enzymes are needed to catalyze the transposition of these types of elements

13. Transposase Catalyzes Excision & Insertion
The enzyme transposase catalyzes the removal of a TE and the its reinsertion at another location
Transposase recognize the inverted repeats at the ends of a TE and bring them closer together

14. Cut & Paste Transposition by Transposase

15. Retrotransposons – Retroviral-Like Elements
Evolutionarily related to known retroviruses
Retroviruses - RNA viruses that make a DNA copy that integrates into the host’s genome
LTR – long terminal repeat
act as promoters to transcribe viral genes
RT – reverse transcriptase (pol)
uses RNA as a template to synthesize a cDNA (complementary DNA)
Int – integrase
recognizes DR sequences, cuts host DNA and inserts retroelement sequences
There is no excision of retroelements or retroviruses
There are ~850,000 copies of LINE retroelements in humans
Virtually all have lost function of RT and/or Int genes

16. 16

17. Non-viral Retroelements
Share little sequence similarity with retroviruses
derived from normal eukaryotic genes
some have RT or RT-like gene, many such genes are not functional
Alu family of non-viral retroelements
derived from a single ancestral gene known as the 7SL RNA gene
has been copied by retroposition to > 500,000 copies
~ 6% of the human genome
An example of a SINE – short interspersed element

18. Describing Function of Transposable Elements
Autonomous
contain all the information necessary for transposition to occur
functional transposase, RT, Int etc…
DNA elements – DRs, IRs, LTR, etc…
Nonautonomous
lack a gene or sequence element necessary for transposition
If element is missing – transposon will not transpose
if Transposase is mutated, element can still transpose if enzyme from another transposon “helps” it
McClintock’s Ds element is nonautonomous
lacks transposase gene
McClintock’s Ac locus (Activator) is autonomous
has functional transposase enzyme
If Ds and Ac are both present in genome, transposition of Ds can occur

19. Transposable Elements Influence Mutation & Evolution
Over the past few decades, researchers have found that transposable elements occur in the genomes of all species
17-74
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20. Repetitive Sequences on Chrom 22

21. Telomere probe
Centromere probe
Alu repeat probe
rDNA probe

22. In some cases, repetitive sequences in eukaryotic genomes are due to the proliferation of TEs
In mammals, for example
LINEs
Long interspersed elements
Usually 1,000 to 5,000 bp long
Found in 20,000 to 100,000 copies per genome
SINEs
Short interspersed elements
Less than 500 bp in length
Example: Alu sequence
Present in 500,000 to 1,000,000 copies in the human genome

23. There are two schools of thought
biological significance of transposons in evolution remains a matter of debate
There are two schools of thought
1. TEs exist because they simply can
In other words they are like parasites
They can proliferate within the host as long as they do not harm the host to the extent that they significantly disrupt survival
This has been termed the selfish DNA theory
2. TEs exist because they offer some advantage
Bacterial TEs carry antibiotic-resistance genes
TEs may cause greater genetic variability through recombination
TEs may cause the insertion of exons into the coding sequences of structural genes
This phenomenon, called exon shuffling, may lead to the evolution of genes with more diverse functions

24. Transposable elements can rapidly enter the genome of an organism and proliferate quickly
Drosophila melanogaster
A TE known as the P element was introduced into the species in the 1950s
Remarkably, in the last 50 years, the P element has expanded throughout D. melanogaster populations worldwide
The only strains without the P element are lab stocks collected prior to 1950
Transposable elements have a variety of effects on chromosome structure and gene expression

26. Transposons Have Become Important Tools in Biology
The features of transposons have made them an important experimental tool in molecular biology
1. The introduction of transposons into a cell is a convenient way to abolish the expression of a gene
2. It can be used to clone a particular gene in an approach known as transposon tagging

27. An early example of transposon tagging involved an X-linked gene in Drosophila that affects eye color
Wild-type = red ; Mutant = white
In 1981, Paul Bingham, Robert Levis and Gerald Rubin use transposon tagging to clone this gene
They started with a wild-type population of Drosophila that carried a transposon called copia
From this red-eyed strain, a white-eyed strain was obtained
The copia element transposed into the X-linked eye color gene, thereby inactivating it