The Dynamic Genome Transposons. What are Transposons? Some definitions and figures from Lisch 2009:...
Transcript of The Dynamic Genome Transposons. What are Transposons? Some definitions and figures from Lisch 2009:...
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The Dynamic Genome
Transposons
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What are Transposons?
Some definitions and figures from Lisch 2009: Annu. Rev. Plant Biol. 2009.60:43-66.
Transposition of DNA explains mottled kernels in maize
Transposable element (transposon, TE):DNA sequence competent to insert into new places
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What are Transposons?
Learn more at: weedtowonder.org/jumpingGenes.html
(1) At the beginning of kernel development, the Ds transposon inserts into the colored (C) gene, resulting in colorless tissue. (2) Ds transposition early in kernel development restores the C gene, giving rise to a large colored sector. (3) Transposition later in kernel development results in smaller sectors.
Transposable element (transposon, TE): DNA sequence competent to insert into new places
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What are Transposons?
Transposable element (transposon, TE): DNA sequence competent to insert into new places
“Cut & Paste”
“Copy & Paste”
(Alu)
(Ac/Ds)
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Autonomous element
Nonautonomous elements
Gene(s)
•Most genomes contain multiple transposon families.
•Each family contains autonomous and non-autonomous elements.
•Autonomous elements encode their own moving competency.
•Non-autonomous elements are moved by other elements.
What are Transposons?
Class I transposons are being copied multiplicative. Class II transposons can undergo copying, too, if transposing during DNA replication
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What are Transposons?
Transposons make up most of (most) eukaryotic genomes•~50% of the genomes of human, chimp, mouse, gorilla
•~75% of the maize genome
•~85% of the barley genome
•~98% of the iris genome
Iris brevicaulis Iris fulva
Hs 11: http://dnalc.org/resources/3d/chr11.html
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Sorghum 700 Mb
Barley 5,000 Mb
Maize 2,500 Mb
Oats ~20,000 MbWheat 20,000 Mb
Rice 450 Mb
Effect of transposons & genome duplications on genomes
What are Transposons?
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• Most TEs are broken (cannot tranpose; “fossils”).
• Active TEs evolved to insert into “safe-havens.”
• Host regulates TE movement.
• TEs can provide advantages.
How do organisms live with TEs?
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mPing:
MITE (Multi-insertional TE)
Deletion-derivative of Ping
Requires Ping transposase to jump
MITEs are being amplified to high copy numbers
Ping/mPing
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Transposons in Action
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OVER 1000 mPing copies
Japonica strains
mP
ing
cop
y n
um
ber
Naito et al PNAS (2006))
mPing
Over 1000 copies of mPing in 4 related strains….
Takatoshi Tanisaka lab (Kyoto University)
mPing copy number in O. japonica
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• predominantly in genic regions in euchromatin
• even inserts in heterochromatin are in genes
• where does mPing insert in and around genes?
mPing insertions in genome
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0
2
4
6
8
10
12
5'UTR exon intron 3'UTR
(%)
shared(n=926)
unshared(n=736)
expect.
mPing insertions rare in coding-exons
UTR Exon UTR
mPing insertions in genes
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Os02g0135500 (-41)
0
0.5
1
1.5
2
2.5
control cold salt dry
NBEG4 (mPing+)A123 (mPing+)A157
mPing found to confer cold and salt inducibility
TEs can alter gene expression
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Nipponbare EG4
EG4 is salt tolerant
TEs can alter gene expressionCan this have phenotypic consequences?
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Naito et al, Nature, 2009
• Massive amplification largely benign• Subtle impact on the expression of many genes• Produces stress-inducible networks (cold, salt, others?)• Generates dominant alleles
Rapid mPing amplification (burst)
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• TEs usually inactive.
• “Stress” conditions may activate TEs.
• Active TEs increase mutation frequency.
• Most mutations caused by TEs neutral or harmful.
• A rare TE-induced mutation (or rearrangement) may be adaptive.
Transposable elements can shake up otherwise conservative genomes and generate new genetic diversity.
TEs as tools of evolutionary change
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• (relatively) simple
• incredibly abundant
• evolve rapidly
• promote rapid genome evolution
• largely ignored (discovery)
TEs for student research projects
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Suppl.: DNA transposons can be copied, tooGap repair from sister chromatid
Jump into site that is then replicated
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• Find homologs using DNA
• Find homologs using protein
• Locate transposons
• Examine surroundings of transposon insertions
• Identify active transposons and “molecular fossils”
• Show recent transposon activity
Yellow Line Walk-through(Advanced Yellow Line Example)