1. Evolution of eukaryote genomes
Lecture 8 – Transposable elements I

2. Introduction - Transposons
Piece of DNA that can move from place to place in an organisms genome
Structurally and functionally distinct
Excised from one site and inserted at another site
Alternate names
“jumping genes”
Mobile genetic elements
Transposable elements
Exist in all organisms
More prevalent in eukaryotic than bacterial genomes e.g % mammalian chromosomes consist of transposable elements

3. Mechanisms of transposition
Conservative transposition
Element is moved and not replicated
“cut and paste” transposition
Non-conservative (replicative) transposition
Element is replicated during transposition
Retrotransposition
Transposition mediated by an RNA intermediate

4. Conservative transposition

5. Non-conservative transposition

6. Retrotransposition

7. Classification of transposons
Classified based on mechanism of transposition
Class I elements (Retroelements)
Transpose via RT of RNA intermediate
Class II elements (DNA elements)
Transpose directly as DNA using cut and paste mechanism

8. Classification of transposons
Non-viral
Retroelements
Copia elements (Drosophila)
Ty elements (Yeast)
Viral
DNA elements

9. Classification of transposons

10. Transposons in humans

11. Retroviruses Single stranded RNA animal viruses
Use ds DNA as an intermediate for replication

12. Class I - SINEs (Retrotransposons)
Not similar to retroviruses
Short (<500bp) interspersed elements
E.g.. Alu sequence
+10% of human DNA
300 bp sequence
Modified from processed retrogene (7SL RNA)
Found between genes in introns
Do not encode their own transposition machinery
Retrotransposed by enzymes coded for elsewhere

13. Class I - LINEs (Non-LTR elements)
Long (>5kb) interspersed elements
E.g.. L1 and L2 elements in humans
21% of human genome
Usually encode enzymes necessary for the transposition
Consist of two ORFs + promoter
RT often prematurely terminated

14. Class I - LTR retrotransposon
Virtually identical to structure of retrovirus
Flanked by two identical LTR
1-3 ORFs encoding structural proteins and enzymes needed for transposition
Completely autonomous
Only found in eukaryotes

15. Class II – DNA transposons
Terminal inverted repeat sequences flank ORF for transposase
DNA sequence recognised by transposase
Cut out and inserted at new position
Conservative transposition
No replication of transposon

16. Ty elements in yeast LTR - retrotransposon
TyB = pol
 340 np
≈ 5900 np
TyA = gag
LTR - retrotransposon
Ty1 35 copies in Saccharomyces cerevisiae
330 bp delta (d) sequences are found in about 100 copies
d sequences show significant sequence divergence
Direct repeat sequences - not Inverted repeats (IRs) like bacteria

17. Ty elements in yeast 
Generate a repeated sequence of target DNA (5bp) during transposition
Caused mutation by insertion

18. Mechanism of transposition –Ty element

19. Ty elements in yeast Boeke and Fink (1985)
Ty element altered by adding galactose promoter
Galactose increased frequency of transposition
An intron was added
Newly transposed elements lacked intron