Transcript Slide - iPlant Pods

The Dynamic Genome:
Why are some of kernels striped or spotted?
McClintock: sole recipient of 1983
Nobel Prize in Physiology or Medicine
Why awarding such a
“trivial” discovery?
Why 40 years from discovery
to prize?
TEs rule
~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
Varying genome sizes among cereal grasses
Sorghum 700 Mb
Maize 2,500 Mb
Rice 450 Mb
Barley 5,000 Mb
Wheat 20,000 Mb
Oats ~20,000 Mb
Due to transposons & genome duplications
TEs are (relatively) simple genetic systems:
“Cut & Paste”
RNA (class 1) elements:
“Copy & Paste”
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DNA (class 2) elements:
Transposon Families
• 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)
Autonomous element
Gene(s)
Nonautonomous elements
Ping/mPing
mPing:
MITE (Multi-insertional TE)
MITEs are being amplified to
high copy numbers
Deletion-derivative of Ping
Requires Ping transposase to jump
How do organisms live with TEs?
Most TEs are broken (cannot tranpose; “fossils”).
Active TEs evolved to insert into “safe-havens.”
Host regulates TE movement.
TEs can provide advantages.
mPing copy number in Oryza japonica
OVER 1000 mPing copies
mPing
Japonica strains
Over 1000 copies of mPing in 4 related strains….
Naito et al PNAS (2006))
Takatoshi Tanisaka lab (Kyoto University)
Genomic distribution of mPing insertions
- predominantly in genic regions in euchromatin
- even inserts in heterochromatin are in genes
- where does mPing insert in and around genes?
Genic distribution of mPing insertions
12
shared
(n=926)
10
unshared
(n=736)
(%)
8
expect.
6
4
2
0
5'UTR
UTR
exon
Exon
intron
3'UTR
UTR
mPing insertions rare in coding-exons
TEs can alter gene expression
Os02g0135500 (-41)
2.5
NB
EG4 (mPing+)
A123 (mPing+)
A157
2
1.5
1
0.5
0
control
cold
salt
dry
mPing found to confer cold and salt inducibility
Can this have phenotypic
consequences?
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Nipponbare
EG4
EG4 is salt tolerant
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Rapid mPing amplification (burst)
• Massive amplification largely benign
• Subtle impact on the expression of many genes
• Produces stress-inducible networks (cold, salt, others?)
• Generates dominant alleles
Naito et al, Nature, 2009
TEs as Tools of Evolutionary Change
• 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 in Student Research
-they are (relatively) simple
-they are incredibly abundant
-they evolve rapidly
-they promote rapid genome evolution
-they are largely ignored (discovery)
Genomic analysis of TEs using DNA Subway
-Find out whether an element is actively transposing
-Find out where to find a particular element in the genome
-Find out about relationships among elements (TE family,
autonomous vs. nonautonomous elements)
Suppl.: DNA transposons can be copied, too
Gap repair from sister chromatid
Jump into site that is then replicated