the dynamic genome transposons. what are transposons? transposable element (transposon): a sequence...
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The Dynamic Genome
Transposons
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What are Transposons?Transposable element (transposon): a sequence of DNA that is competent to movefrom place to place within a genome
Some definitions and figures from Lisch 2009: Annu. Rev. Plant Biol. 2009.60:43-66.
Transposition of DNA on chromosome 9 of maize explains mottled kernels
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What are Transposons?Transposable element (transposon): a sequence of DNA that is competent to movefrom place to place within a genome
Learn more at: weedtowonder.org/jumpingGenes.html
(1) At the beginning of kernel development, the Ds transposon is inserted 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.
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What are Transposons?Transposable element (transposon): a sequence of DNA that is competent to movefrom place to place within a genome
“Cut & Paste”
“Copy & Paste”
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Autonomous element
Nonautonomous elements
Gene(s)
•Plant genomes contain multiple transposon families.
•Each contains autonomous and non-autonomous elements.•Class I transposons do not move, but are being copied.
•Class II transposons move, but can undergo copying, too (if transposing during DNA replication)
What are Transposons?
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What are Transposons?Transposons make up the major content of eukaryotic genomes
•~50% of the genomes of human, chimp, mouse, ape
•~75% of the maize genome
•~85% of the barley genome
•~98% of the iris genome
Iris brevicaulis Iris fulva
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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
Variation in cereal genomes - transposons & genome duplications
What are Transposons?
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Transposons in Action
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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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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?
Genomic distribution of mPing insertions
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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
Genic distribution of mPing insertions
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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