1. ‘mobile’ DNA: transposable elements

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 by using a self-encoded recombinase called transposase 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 by using a self-encoded recombinase called transposase

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

4. TEs can generate mutations in adjacent genes TEs in Maize Fig 15.19 Genes VII by B. Lewin

5. Common mechanism of transposition Transposons encode transposases that catalyse transposition events Transposons encode transposases that catalyse transposition events Regulation of transposase expression essential Regulation of transposase expression essential Fig13.24a: Hartwell

6. Common mechanism of transposition

7. 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 transpososome

8. Common mechanism of transposition transposase (blue) binds and assembles a paired end complex (PEC) by dimerization, a process that might involve divalent metal ions (Me 2+ ). transposase (blue) binds and assembles a paired end complex (PEC) by dimerization, a process that might involve divalent metal ions (Me 2+ ). PEC is then active for the cleavage reactions that remove flanking donor DNA (thin black lines) and transfer of the transposon ends into target DNA (black dotted line). PEC is then active for the cleavage reactions that remove flanking donor DNA (thin black lines) and transfer of the transposon ends into target DNA (black dotted line). Trends in Microbiology 2005 Vol13(11) pp 543-549

9. Catalytic domain of transposase involved in a transphosphorylation reaction that initiates DNA cleavage & strand transfer Fig 15.14 Fig 15.10 GenesVII Lewin

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

11. How transposons move

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

13. Interspersed repeats (transposon-derived) classfamilysize Copy number % genome* LINE L1 (Kpn family) L2~6.4kb 0.5x10 6 0.3 x 10 6 16.93.2 SINEAlu~0.3kb 1.1x10 6 10.6 LTRe.g.HERV~1.3kb 0.3x10 6 8.3 DNAtransposonmariner~0.25kb 1-2x10 4 2.8 major types * Updated from HGP publications HMG3 by Strachan & Read pp268-272

14. LINEs LINEs (long interspersed elements) Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632

15. 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 LINEs

16. LINEs (long interspersed elements) HMG3 by Strachan & Read pp268-272

17. SINEs SINEs (short interspersed elements) Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632

18.  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. SINEs 100-300bp1,500,00013%

19. 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. 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.

20. 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 http://www.geneticorigins.org/geneticorigins/p v92/intro.html

21. Long Terminal Repeats (LTR) Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632

22. Repeats on the same orientation on both sides of element e.g. ATATATnnnnnnnnnnnnnnATATAT contain sequences that serve as transcription promoters as well as terminators. contain sequences that serve as transcription promoters as well as terminators. These sequences allow the element to code for an mRNA molecule that is processed and polyadenylated. These sequences allow the element to code for an mRNA molecule that is processed and polyadenylated. At least two genes coded within the element to supply essential activities for retrotransposition. At least two genes coded within the element to supply essential activities for retrotransposition. RNA contains a specific primer binding site (PBS) for initiating reverse transcription. RNA contains a specific primer binding site (PBS) for initiating reverse transcription. small direct repeats formed at the site of integration. small direct repeats formed at the site of integration. Long Terminal Repeats (LTR)

23.  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 Long Terminal Repeats (LTR)

24. Ancestral repeats (AR) ‘transpositional fossils’ Comprise ~ 25% of the genome ~780 classes Largely nonfunctional Sporadic cases where AR have acquired anew function after insertion MER121 is highly conserved among mammals!!

25. Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632 DNA transposons

26. DNA intermediate Class II TEs IS elements and transposons bounded by inverted terminal repeats (ITR) e.g. ATGCNNNNNNNNNNNCGTA

27. DNA intermediate Class II TEs Prokaryotic IS elements (e.g. IS10, Ac/Ds, mariner) encode only transposase sequences eukaryotic transposons encode additional genes such as antibiotic resistance genes

28. Some types of rearrangements mediated by DNA transposons Gene (2005)345 pp91-100

29. Transposons move in different ways Classified into 5 families on the basis of their transposition pathways 1) DDE-transposases 2) RT/En transposases (reverse transcriptase/endonuclease) (reverse transcriptase/endonuclease) 3) Tyrosine (Y) transposases 4) Serine (S) transposases 5) Rolling circle (RC) or Y2 transposases Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77)

30. Transposons can be used to transfer DNA between bacterial cells Transposons (pink) integrate into new sites on the chromosome or plasmids by non-homologous recombination. Integrons (dark green) use similar mechanisms to exchange single gene cassettes (brown). Nature Reviews Microbiology 3, 722-732 (2005)

31. Some transposons can encode integrons Integrons are assembly platforms — DNA elements that acquire open reading frames embedded in exogenous gene cassettes and convert them to functional genes by ensuring their correct expression. Integrons are assembly platforms — DNA elements that acquire open reading frames embedded in exogenous gene cassettes and convert them to functional genes by ensuring their correct expression. e.g. bacterial Tn7 also encodes an integron — a DNA segment containing several cassettes of antibiotic-resistance genes. These cassettes can undergo rearrangements in hosts that express a related recombinase, leading to alternative combinations of antibiotic-resistance genes.

32. Mazel Nature Reviews Microbiology 4, 608–620 (August 2006) Integrons Mobile Integrons Superintegrons

33. Reading 1) Chapter 9 pp 265-268 HMG 3 by Strachan and Read 2) Chapter 10: pp 339-348 Genetics from genes to genomes by Hartwell et al (2/e)