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

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

evolutionevolution

Transposable elementsTransposable elements

Discrete sequences in the genome that have Discrete sequences in the genome that have

the ability to translocate or copy itself the ability to translocate or copy itself

across to other parts of the genome across to other parts of the genome without without

any requirement for sequence homology any requirement for sequence homology byby

using a self-encoded recombinase called using a self-encoded recombinase called

transposase transposase

Transposable elements move from Transposable elements move from place to place in the genomeplace to place in the genome

1930s Marcus Rhoades 1930s Marcus Rhoades 1950s 1950s Barbara McClintock Barbara McClintock – –

transposable elements in corn transposable elements in corn 1983 McClintock gets Nobel Prize1983 McClintock gets Nobel Prize

Found in all organismsFound in all organisms Most 50 – 10,000 bpMost 50 – 10,000 bp May be present hundreds May be present hundreds

of times in a genomeof times in a genome

TEs can generate mutations in adjacent genesTEs can generate mutations in adjacent genes

TEs in MaizeTEs in Maize

RNA intermediatesRNA intermediates Class I TEsClass I TEs – –

Use a ‘copy & paste’ Use a ‘copy & paste’ mechanismmechanism

DNA intermediatesDNA intermediates Class II TEsClass II TEs Use a ‘cut and paste’ mechanism Use a ‘cut and paste’ mechanism Generally short sequencesGenerally short sequences

Transposition can occur viaTransposition can occur via

See interspersed repeats from the repetitive elements lecture

Classes of transposable elementsClasses of transposable elements

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Interspersed repeats (transposon-derived)Interspersed repeats (transposon-derived)

classclass familyfamily sizesize Copy Copy numbnumb

erer

% % genomgenom

e*e*LINELINE L1 (Kpn family)L1 (Kpn family)

L2 L2

~6.4kb~6.4kb 0.5x100.5x1066

0.3 x 100.3 x 1066

16.916.9

3.23.2

SINESINE AluAlu ~0.3kb~0.3kb 1.1x101.1x1066 10.610.6

LTRLTR e.g.HERVe.g.HERV ~1.3kb~1.3kb 0.3x100.3x1066 8.38.3

DNA DNA

transposontransposon

Tc1/marinerTc1/mariner ~0.25kb~0.25kb 1-2x101-2x1044 2.82.8

major types

* Updated from HGP publications HMG3 by Strachan & Read pp268-272

Most ancient of eukaryotic genomesMost ancient of eukaryotic genomes Autonomous transposition (reverse trancriptase)Autonomous transposition (reverse trancriptase) ~6-8kb long, located mainly in euchromatin~6-8kb long, located mainly in euchromatin Internal polymerase II promoter and 2 ORFsInternal polymerase II promoter and 2 ORFs 3 related LINE families in humans 3 related LINE families in humans

– – LINE-1, LINE-2, LINE-3.LINE-1, LINE-2, LINE-3.

LINE-1 still active (~17% of human genme)LINE-1 still active (~17% of human genme) Believed to be responsible for retrotransposition Believed to be responsible for retrotransposition

of SINEs and creation of processed pseudogenesof SINEs and creation of processed pseudogenes

LINEs

Non-autonomousNon-autonomous (successful freeloaders! ‘borrow’ RT (successful freeloaders! ‘borrow’ RT from other sources such as LINEs)from other sources such as LINEs)

~100-300bp long~100-300bp long Internal polymerase III promoter Internal polymerase III promoter No proteinsNo proteins Share 3’ ends with LINEsShare 3’ ends with LINEs 3 related SINE families in humans 3 related SINE families in humans

– – active Alu, inactive MIR and Ther2/MIR3.active Alu, inactive MIR and Ther2/MIR3.

SINEs

100-300bp 1,500,000 13%

LINES and SINEs have preferred insertion sitesLINES and SINEs have preferred insertion sites

In this example, In this example, yellow represents the yellow represents the distribution of distribution of mysmys (a (a type of LINE) over a type of LINE) over a mouse genome where mouse genome where chromosomes are chromosomes are orange. There are orange. There are more more mysmys inserted in inserted in the sex (X) the sex (X) chromosomes. chromosomes.

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

http://www.geneticorigins.org/http://www.geneticorigins.org/geneticorigins/pv92/intro.htmlgeneticorigins/pv92/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-autonomousAutonomous or non-autonomous Autonomous LTR encode retroviral genes Autonomous LTR encode retroviral genes gag, polgag, pol

genes e.g HERVgenes e.g HERV Non-autonomous elements lack the Non-autonomous elements lack the polpol and and

sometimes the sometimes the gag gag genes e.g. MaLRgenes e.g. MaLR

Long Terminal Repeats (LTR)

DNA transposonsDNA transposonsClass II TEsClass II TEs

IS elements and transposonsIS elements and transposons

bounded by bounded by invertedinverted terminal repeats (ITR)terminal repeats (ITR)

e.g. ATGCNNNNNNNNNNNCGTAe.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 transpositionMechanism of DNA transposition DNA transposons encode transposases that DNA transposons encode transposases that

catalyse transposition eventscatalyse transposition events Regulation of transposase expression Regulation of transposase expression

essentialessential

Mechanism of DNA transpositionMechanism of DNA transposition

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

Mechanism of DNA transpositionMechanism of DNA transposition

2 sequential steps2 sequential steps

Site specific cleavage of Site specific cleavage of DNA at the end of TEDNA at the end of TE

Complex of transposase-Complex of transposase-element ends element ends (transpososome)(transpososome) brought to DNA target brought to DNA target where strand transfer is where strand transfer is carried out by covalent carried out by covalent joining of 3’end of TE to joining of 3’end of TE to target DNA target DNA

Transpososome(paired end complex)

Trends in Microbiology 2005 Vol13(11) pp 543-549

Mediated by divalent Me2+

Effects of TEs on the genomeEffects of TEs on the genome

NATURE 443 (7111): 521-524 OCT 5 2006

Depends on the insertion/splice siteDepends on the insertion/splice site Benign (affects genome size)Benign (affects genome size) Detrimental Detrimental

insertion into regulatory / coding regionsinsertion into regulatory / coding regions Beneficial?Beneficial?

Contribute to genetic diversityContribute to genetic diversity create new genescreate new genes some TEs show high tissue-specific expression some TEs show high tissue-specific expression

during development!!during development!! some SINEs show imprinting patterns! some SINEs show imprinting patterns! Some LINE-1s preferentially jump within Some LINE-1s preferentially jump within

regulatory regions of neurons in miceregulatory regions of neurons in mice

NATURE 443 (7111): 521-524 OCT 5 2006

Insertion of TEs can affect epigenetic Insertion of TEs can affect epigenetic regulationregulation

Epigentic control may be sensitive to Epigentic control may be sensitive to environmental conditions e.g. early environmental conditions e.g. early nutritionnutrition

TEs can be activated by the TEs can be activated by the epigenetic statusepigenetic status

TEs as drivers of evolutionTEs as drivers of evolution

TEs in biotechnology – blessing or curse?TEs in biotechnology – blessing or curse?XenotransplantationXenotransplantation

Activation ofActivation of P Porcine orcine EEndogenous ndogenous RRetroetroVViral iral elements (PERVs)elements (PERVs)

Engineered delivery vectorsEngineered delivery vectors e.g. e.g. Sleeping BeautySleeping Beauty (SB) (SB)

Tc1/Mariner familyTc1/Mariner family

ReadingReading

Chapter 9Chapter 9 HMG 3 by HMG 3 by Strachan and Strachan and ReadRead

OROR

Chapter 10: Chapter 10: Genetics by Genetics by Hartwell et alHartwell et al (3/e)(3/e)Kazazian HH in Science 12 March

2004: Vol. 303. no. 5664, pp. 1626 - 1632

NATURE 443 (7111): 521-524 OCT 5 2006

Transposons by P Capy and Jean-Marc Deragonwww.els.net