1. Transposon and Mechanisms of Transposition

2. Transposon Probably had a significant influence on evolution
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
Late 1960s, transposition was also found in Bacteria.
Barbara McClintock

4. Two Categories DNA transposons Retrotransposons “cut-and-paste”
Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-8
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.

5. DNA transposons Bacterial Insertion Sequences (IS element)
P element in Drosophila
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. General structure of eukaryotic LTR retrotransposons
Non-LTR retrotransposons: the most common type of transposons in mammals
General structure of eukaryotic LTR retrotransposons
Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-11
LTR retrotransposons encode all the proteins of the most common type of retroviruses, except for the envelope proteins. Lacking these envelope proteins, LTR retrotransposons cannot bud from their host cell and infect other cells; however, they can transpose to new sites in the DNA of their host cell.
What is the difference from retrovirus?

8. Generation of RNA from LTR transposon
Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-12

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

10. Lodish et al., Molecular Cell Biology, 7th ed. Fig 10-15
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
Lodish et 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
Non protein encoded regions, related to tRNA (except Alu-7SL RNA)
Nonautonomous- does not encode own machinery, instead relies on cell machinery (Pol III) and LINES RT/EN complex
Found in CpG regions

14. Average size 150-200 base pairs Composed of 3 parts
5’ head
Body
3’ tail
5’head region is related to tRNA, has type 2 promoter, specfic for tRNA, is internal and has 2 short sequences A and B (promoter regions)
Its function is for initiation, regulation and aid in transport to cytoplasm
Body-tRNA unrelated. 3’ end of the body is similar to 3’ end of LINE- needed for RT
3’Tail-AT rich or repeats; poly T tail- termination signal for Pol III
Function-termination and delievery to LineRT
Vassetzky (2013)

15. Alu example Left and right connected by A rich regions

16. Dependent on upstream cis factors-could inhibit transcription
Pol III binds to TRIIIB to DNA and recruits Pol III complex, terminated by U’s
Dependent on upstream cis factors-could inhibit transcription
Kramerov & Vassetzky (2005)

17. Transport
Not much is known about the mechanism of transport to cytoplasm
Theory is that it uses RanGTP-independent mRNA pathway
Needs an “A” rich tail
No introns
Caps not required
Nuclear Import
Importins, are proteins that bind NLS
Kramerov & Vassetzky (2005)

18. RT-Uses LINE Machinery Alu gene for example
RNA binds by 2 SRP proteins (SRP9 and SRP14)
Binds ribosome translating L1 RNA and presents A tail to RT where it is recognized and transcribed
Batzer & Deininger, Nature Reviews Genetics (2002) Box 1

19. Jumps forward-deleted
Due to repeats seen in SINEs (conserved), RT can jump from 1 template to another. Jumps backwards-duplicated
Jumps forward-deleted
Kramerov & Vassetzky (2005)

20. “Transposons: Mobile DNA” (2012)
What happens when inserted? Usually inserts in Introns, ends, other non coding regions. But if spicesome recognizes SINE as exon, spliced out and create a new gene-can be harmful or beneficial. Genetic disorders (such as hemophila ) or cancer (breast) results in SINE disrupting
“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
Found in GC rich areas-highly methylated so turned off
Be enhancers/silencers, encoded into genome, splice out, etc

22. References
Batzer, M.A. & Deininger, P.L. Alu repeats and Human genomic diversity. Nature Reviews Genetics 3, (2002). Doi: /nrg
Kramerov, D.A. & Vassetzky, N.S. Short Retroposons in Eukaryotic Genomes. International Review of Cytology, vol 247 (2005) doi: /S /05
Lodish et al., Molecular Cell Biology, 7th ed.
“Transposons: Mobile DNA”. (2012)
Vassetzky. SINEBase (2013)
Weiner, A. Do all SINEs lead to LINEs? Nature Genetics 24, (2000) doi: /