Transposon and Mechanisms of Transposition

1. Transposon and Mechanisms of Transposition

2. Transposon • DNA sequence that can move in the genome • Also called mobile DNA element or transposable element • “selfish DNA”--exist only to maintain themselves ? • Transposition: The process by which these sequences are copied and inserted into a new site in the genome • Probably had a significant influence on evolution

3. How transposon was found • 1940s, Barbara McClintock discovered the first transposable element in maize, earned a Nobel prize in 1983. • Late 1960s, transposition was also found in Bacteria. Barbara McClintock http://en.wikipedia.org/wiki/Barbara_McClintock

4. Two Categories • DNA transposons • Retrotransposons “cut-and-paste” “copy-and-paste” • Most mobile elements in bacteria is DNA transposons • In contrast, most mobile elements in eukaryotes are retrotransposons, but eukaryotic DNA transposons also occur. Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-8

5. DNA transposons • Bacterial Insertion Sequences (IS element) • P element inDrosophila General structure of bacterial IS elements Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-9

6. General process of transposition for DNA transposons Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-10

7. Retrotransposons • LTR retrotransposons: • Non-LTR retrotransposons: the most common type of transposons in mammals General structure of eukaryotic LTR retrotransposons Lodishet al., Molecular Cell Biology, 7th ed. Fig 10-11 What is the difference from retrovirus?

8. Generation of RNAfrom LTR transposon Lodishet al., Molecular Cell Biology, 7th ed. Fig 10-12

9. Model for reverse transcription Lodishet al., Molecular Cell Biology, 7th ed. Fig 10-13

10. Retrotransposons • Non-LTR retrotransposons • long interspersed elements (LINEs) ≈6 kb in human account for 21% of the genome • short interspersed elements (SINEs) ≈300 bp in human account for 13% of the genome Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-15

11. General Principles of LINE transposition Lodishet al., Molecular Cell Biology, 7th ed. Fig 10-16

12. SINEs (Short Interspersed Elements) Weiner (2000) Fig 1

13. Most are tRNA derived; Alu is 7SL-RNA • Nonautonomous • Dependent on other machinery- genome “parasite” • RNA Pol III • Needs LINE Endonuclease and Reverse Transcriptase for activity

14. Average size 150-200 base pairs • Composed of 3 parts • 5’ head • Body • 3’ tail Vassetzky (2013)

15. http://biol.lf1.cuni.cz/ucebnice/images/rep1.gif

16. Kramerov & Vassetzky (2005)

17. Transport Kramerov & Vassetzky (2005)

18. Batzer & Deininger, Nature Reviews Genetics (2002) Box 1

19. Kramerov & Vassetzky (2005)

20. “Transposons: Mobile DNA” (2012)

21. Where there is a SINE, there is a LINE • Specificity of EN/RT of LINE dictates location • Expressed during early embryogenesis and decreases in development • Active in tumor cells • Integrates into germ lines

22. References • Batzer, M.A. & Deininger, P.L. Alu repeats and Human genomic diversity. Nature Reviews Genetics 3, 370-379 (2002). Doi:10.1038/nrg798 http://www.nature.com/nrg/journal/v3/n5/box/nrg798_BX1.html • Kramerov, D.A. & Vassetzky, N.S. Short Retroposons in Eukaryotic Genomes. International Review of Cytology, vol 247 (2005) doi: 10.1016/S0074-7696/05 • Lodish et al., Molecular Cell Biology, 7th ed. • “Transposons: Mobile DNA”. (2012) http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transposons.html • Vassetzky. SINEBase (2013) http://sines.eimb.ru • Weiner, A. Do all SINEs lead to LINEs? Nature Genetics 24, 332-333 (2000) doi:10.1038/74135http://www.nature.com/ng/journal/v24/n4/full/ng0400_332.html