Transcript Transposons - iPlant Pods

The Dynamic Genome
Transposons
What are Transposons?
Transposable element (transposon, TE):
DNA sequence competent to insert into new places
Transposition of DNA explains mottled kernels in maize
Some definitions and figures from Lisch 2009: Annu. Rev. Plant Biol. 2009.60:43-66.
What are Transposons?
Transposable element (transposon, TE): DNA sequence competent to insert into new places
(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.
Learn more at: weedtowonder.org/jumpingGenes.html
What are Transposons?
Transposable element (transposon, TE): DNA sequence competent to insert into new places
(Ac/Ds)
“Cut & Paste”
(Alu)
“Copy & Paste”
What are Transposons?
•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.
Autonomous element
Gene(s)
Nonautonomous elements
Class I transposons are being copied  multiplicative. Class II transposons can
undergo copying, too, if transposing during DNA replication
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
What are Transposons?
Effect of transposons & genome duplications on genomes
Sorghum 700 Mb
Rice 450 Mb
Barley 5,000 Mb
Wheat 20,000 Mb
Maize 2,500 Mb
Oats ~20,000 Mb
Transposons in Action
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.
Ping/mPing
mPing:
MITE (Multi-insertional TE)
Deletion-derivative of Ping
Requires Ping transposase to jump
MITEs are being amplified to
high copy numbers
mPing copy number in O. 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)
mPing insertions in genome
• predominantly in genic regions in euchromatin
• even inserts in heterochromatin are in genes
• where does mPing insert in and around genes?
mPing insertions in genes
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
TEs can alter gene expression
Can this have phenotypic consequences?
Nipponbare
EG4
EG4 is salt tolerant
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 for student research projects
• (relatively) simple
• incredibly abundant
• evolve rapidly
• promote rapid genome evolution
• largely ignored (discovery)
Suppl.: DNA transposons can be copied, too
Gap repair from sister chromatid
Jump into site that is then replicated
Yellow Line Walk-through
(Advanced Yellow Line Example)
• 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