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‘mobile’ DNA or ‘jumping’ DNA Transposable elements as drivers of evolution

‘mobile’ DNA or ‘jumping’ DNA Transposable elements as drivers of evolution

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‘mobile’ DNA or ‘jumping’ DNA Transposable elements as drivers of evolution

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  1. ‘mobile’ DNA or ‘jumping’ DNA Transposable elements as drivers of evolution

  2. Transposable elements • Discrete sequences in the genome that have the ability to translocate or copy itself across to other parts of the genome without any requirement for sequence homology byusing a self-encoded recombinase called transposase

  3. Transposable elements move from place to place in the genome • 1930s Marcus Rhoades • 1950s Barbara McClintock – transposable elements in corn • 1983 McClintock gets Nobel Prize • Found in all organisms • Most 50 – 10,000 bp • May be present hundreds of times in a genome

  4. TEs can generate mutations in adjacent genes TEs in Maize

  5. Transposition can occur via • DNA intermediates • Class II TEs • Use a ‘cut and paste’ mechanism • Generally short sequences • RNA intermediates • Class I TEs – Use a ‘copy & paste’ mechanism See interspersed repeats from the repetitive elements lecture

  6. Classes of transposable elements Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632

  7. Interspersed repeats (transposon-derived) major types * Updated from HGP publications HMG3 by Strachan & Read pp268-272

  8. LINEs Most ancient of eukaryotic genomes • Autonomous transposition (reverse trancriptase) • ~6-8kb long, located mainly in euchromatin • Internal polymerase II promoter and 2 ORFs • 3 related LINE families in humans – LINE-1, LINE-2, LINE-3. LINE-1 still active (~17% of human genme) • Believed to be responsible for retrotransposition of SINEs and creation of processed pseudogenes

  9. SINEs • Non-autonomous (successful freeloaders! ‘borrow’ RT from other sources such as LINEs) • ~100-300bp long • Internal polymerase III promoter • No proteins • Share 3’ ends with LINEs • 3 related SINE families in humans – active Alu, inactive MIR and Ther2/MIR3. 100-300bp 1,500,000 13%

  10. LINES and SINEs have preferred insertion sites • In this example, yellow represents the distribution of mys (a type of LINE) over a mouse genome where chromosomes are orange. There are more mys inserted in the sex (X) chromosomes.

  11. Try the link below to do an online experiment which shows how an Alu insertion polymorphism has been used as a tool to reconstruct the human lineage

  12. Long Terminal Repeats (LTR) Repeats on the same orientation on both sides of element e.g. ATATATnnnnnnnnnnnnnnATATAT • encodes transcription promoters as well as terminators. • Encodes mRNA molecule that is processed and polyadenylated. • Encodes ORFs essential for retrotransposition. • RNA contains a specific primer binding site (PBS) for initiating reverse transcription. • small direct repeats formed at the site of integration.

  13. Long Terminal Repeats (LTR) • Autonomous or non-autonomous • Autonomous LTR encode retroviral genes gag, pol genes e.g HERV • Non-autonomous elements lack the pol and sometimes the gag genes e.g. MaLR

  14. Class II TEs IS elements and transposons bounded by invertedterminal repeats (ITR) e.g. ATGCNNNNNNNNNNNCGTA DNA transposons • Prokaryotic IS elements (e.g. IS10, Ac/Ds, mariner) encode only transposase sequences • eukaryotic transposons encode additional genes such as antibiotic resistance genes

  15. Mechanism of DNA transposition • DNA transposons encode transposases that catalyse transposition events • Regulation of transposase expression essential

  16. Mechanism of DNA transposition

  17. Catalytic domain of transposase involved in a transphosphorylation reaction that initiates DNA cleavage & strand transfer

  18. Mechanism of DNA transposition 2 sequential steps Site specific cleavage of DNA at the end of TE Complex of transposase-element ends (transpososome) brought to DNA target where strand transfer is carried out by covalent joining of 3’end of TE to target DNA Mediated by divalent Me2+ Transpososome (paired end complex) Trends in Microbiology 2005 Vol13(11) pp 543-549

  19. Effects of TEs on the genome • Depends on the insertion/splice site • Benign (affects genome size) • Detrimental • insertion into regulatory / coding regions • Beneficial? • Contribute to genetic diversity • create new genes • some TEs show high tissue-specific expression during development!! • some SINEs show imprinting patterns! • Some LINE-1s preferentially jump within regulatory regions of neurons in mice NATURE 443 (7111): 521-524 OCT 5 2006

  20. TEs can be activated by the epigenetic status • Insertion of TEs can affect epigenetic regulation • Epigentic control may be sensitive to environmental conditions e.g. early nutrition NATURE 443 (7111): 521-524 OCT 5 2006

  21. TEs as drivers of evolution

  22. Xenotransplantation Activation of Porcine Endogenous RetroViral elements (PERVs) TEs in biotechnology – blessing or curse? Engineered delivery vectors e.g. Sleeping Beauty (SB) Tc1/Mariner family

  23. Reading Chapter 9 HMG 3 by Strachan and Read OR Chapter 10: Genetics by Hartwell et al (3/e) Kazazian HH in Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632 Transposons by P Capy and Jean-Marc Deragon NATURE 443 (7111): 521-524 OCT 5 2006