The Dynamic Genome
Transposons
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
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
What are Transposons?
Transposable element (transposon, TE): DNA sequence competent to insert into new places
“Cut & Paste”
“Copy & Paste”
(Alu)
(Ac/Ds)
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
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
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?
• 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?
mPing:
MITE (Multi-insertional TE)
Deletion-derivative of Ping
Requires Ping transposase to jump
MITEs are being amplified to high copy numbers
Ping/mPing
Transposons in Action
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
• 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
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
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
Nipponbare EG4
EG4 is salt tolerant
TEs can alter gene expressionCan this have phenotypic consequences?
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)
• 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
• (relatively) simple
• incredibly abundant
• evolve rapidly
• promote rapid genome evolution
• largely ignored (discovery)
TEs for student research projects
Suppl.: DNA transposons can be copied, tooGap repair from sister chromatid
Jump into site that is then replicated
• 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)