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

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

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

TEs can generate mutations in adjacent genes TEs in Maize

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

Classes of transposable elements Science 12 March 2004: Vol no. 5664, pp

Interspersed repeats (transposon-derived) classfamilysize Copy number % genome* LINE L1 (Kpn family) L2~6.4kb 0.5x x SINEAlu~0.3kb 1.1x LTRe.g.HERV~1.3kb 0.3x DNAtransposonTc1/mariner~0.25kb 1-2x major types * Updated from HGP publications HMG3 by Strachan & Read pp

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

 Non-autonomous (successful freeloaders! ‘borrow’ RT from other sources such as LINEs)  ~ bp 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 bp1,500,00013%

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.

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 v92/intro.html

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. 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 Long Terminal Repeats (LTR)

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

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

Mechanism of DNA transposition

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

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 Transpososome (paired end complex) Trends in Microbiology 2005 Vol13(11) pp Mediated by divalent Me2+

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

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

TEs as drivers of evolution

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

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 no. 5664, pp NATURE 443 (7111): OCT Transposons by P Capy and Jean-Marc Deragon