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‘mobile’ DNA: transposable elements. 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. - PowerPoint PPT Presentation
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‘‘mobile’ DNA: transposable elementsmobile’ DNA: transposable elements
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 and 1950s 1930s Marcus Rhoades and 1950s Barbara McClintock Barbara McClintock – transposable – transposable elements in corn elements in corn
1983 McClintock received Nobel 1983 McClintock received Nobel PrizePrize
Found in all organismsFound in all organisms Most 50 – 10,000 bpMost 50 – 10,000 bp May be present hundreds of times in May be present hundreds of times in
a genomea genome
TEs can generate mutations in adjacent genesTEs can generate mutations in adjacent genes
TEs in MaizeTEs in Maize
Fig 15.19 Genes VII by Fig 15.19 Genes VII by B. LewinB. Lewin
Common mechanism of transpositionCommon mechanism of transposition Transposons encode transposases that Transposons encode transposases that
catalyse transposition eventscatalyse transposition events Regulation of transposase expression Regulation of transposase expression
essentialessential
Fig13.24a: Hartwell
Common mechanism of transpositionCommon mechanism of transposition
Common mechanism of transpositionCommon mechanism of 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
Common mechanism of transpositionCommon mechanism of transposition transposase (blue) binds and assembles a paired end complex transposase (blue) binds and assembles a paired end complex
(PEC) by dimerization, a process that might involve divalent (PEC) by dimerization, a process that might involve divalent metal ions (Memetal ions (Me2+2+). ).
PEC is then active for the cleavage reactions that remove PEC is then active for the cleavage reactions that remove flanking donor DNA (thin black lines) and transfer of the flanking donor DNA (thin black lines) and transfer of the transposon ends into target DNA (black dotted line).transposon ends into target DNA (black dotted line).
Trends in Microbiology 2005 Vol13(11) pp 543-549
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
Fig 15.14
Fig 15.10GenesVII Lewin
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
How transposons moveHow transposons move
Classes of transposable elementsClasses of transposable elements
Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632
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
marinermariner ~0.25kb~0.25kb 1-2x101-2x1044 2.82.8
major types
* Updated from HGP publications HMG3 by Strachan & Read pp268-272
LINEs LINEs (long interspersed elements)
Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632
Most ancient of eukaryotic genomesMost ancient of eukaryotic genomes Autonomous transposition (reverse Autonomous transposition (reverse
trancriptase)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 Believed to be responsible for
retrotransposition of SINEs and creation of retrotransposition of SINEs and creation of processed pseudogenesprocessed pseudogenes
LINEs
LINEs (long interspersed elements)
HMG3 by Strachan & Read pp268-272
SINEs SINEs (short interspersed elements)
Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632
Non-autonomousNon-autonomous (successful freeloaders! (successful freeloaders! ‘borrow’ RT from other sources such as LINEs)‘borrow’ RT 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
Long Terminal Repeats (LTR)
Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632
Repeats on the Repeats on the same orientationsame orientation on both sides of element on both sides of element e.g. ATATATnnnnnnnnnnnnnnATATATe.g. ATATATnnnnnnnnnnnnnnATATAT• contain sequences that serve as transcription contain sequences that serve as transcription
promoters as well as terminators. promoters as well as terminators. • These sequences allow the element to code for an These sequences allow the element to code for an
mRNA molecule that is processed and mRNA molecule that is processed and polyadenylated. polyadenylated.
• At least two genes coded within the element to At least two genes coded within the element to supply essential activities for retrotransposition. supply essential activities for retrotransposition.
• RNA contains a specific primer binding site (PBS) for RNA contains a specific primer binding site (PBS) for initiating reverse transcription. 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)
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)
Ancestral repeats (AR)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!!
Science 12 March 2004: Vol. 303. no. 5664, pp. 1626 - 1632
DNA transposonsDNA transposons
DNA intermediateDNA intermediateClass 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
DNA intermediateDNA intermediateClass II TEsClass II TEs
Prokaryotic IS elements (e.g. IS10, Prokaryotic IS elements (e.g. IS10, Ac/Ds, mariner) encode only transposase Ac/Ds, mariner) encode only transposase sequences sequences
eukaryotic transposons encode eukaryotic transposons encode additional genes such as antibiotic additional genes such as antibiotic resistance genesresistance genes
Some types of rearrangements mediated by DNA Some types of rearrangements mediated by DNA transposonstransposons
Gene (2005)345 pp91-100
Transposons move in different Transposons move in different waysways
Classified into 5 families on the basis of their Classified into 5 families on the basis of their transposition pathwaystransposition pathways
1) DDE-transposases1) DDE-transposases2) RT/En transposases2) RT/En transposases
(reverse transcriptase/endonuclease) (reverse transcriptase/endonuclease) 3) Tyrosine (Y) transposases 3) Tyrosine (Y) transposases 4) Serine (S) transposases4) Serine (S) transposases5) 5) Rolling circle (RC) or Y2 transposasesRolling circle (RC) or Y2 transposases
Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77Nature Rev Mol. Cell Biol (Nov2003) 4(11):865-77))
Transposons can be used to transfer Transposons can be used to transfer DNA between bacterial cellsDNA 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)
Some transposons can encode Some transposons can encode integronsintegrons
Integrons are assembly platforms — DNA Integrons are assembly platforms — DNA elements that acquire open reading frames elements that acquire open reading frames embedded in exogenous gene cassettes and convert embedded in exogenous gene cassettes and convert them to functional genes by ensuring their correct them to functional genes by ensuring their correct expression. expression.
e.g. bacterial Tn7 also encodes an integron — a e.g. bacterial Tn7 also encodes an integron — a DNA segment containing several cassettes of DNA segment containing several cassettes of antibiotic-resistance genes. These cassettes can antibiotic-resistance genes. These cassettes can undergo rearrangements in hosts that express a undergo rearrangements in hosts that express a related recombinase, leading to alternative related recombinase, leading to alternative combinations of antibiotic-resistance genes.combinations of antibiotic-resistance genes.
Mazel Nature Reviews Microbiology 4, 608–620 (August 2006)
IntegronsIntegrons
Mobile IntegronsMobile Integrons
SuperintegronsSuperintegrons
ReadingReading
1)1) Chapter 9 pp 265-268 Chapter 9 pp 265-268 HMG 3 by HMG 3 by Strachan and Strachan and
ReadRead
2)2) Chapter 10: pp 339-348Chapter 10: pp 339-348Genetics from genes to Genetics from genes to genomes by genomes by Hartwell et alHartwell et al (2/e) (2/e)