1. The Dynamic Genome
Transposons

2. Transposable element (transposon, TE):
What are Transposons?
Transposable element (transposon, TE):
DNA sequence competent to insert into new places
Left image are sketches of McClintock’s observation of chromosomes in Maize.
Transposition of DNA explains mottled kernels in maize
Some definitions and figures from Lisch 2009: Annu. Rev. Plant Biol :43-66.

3. 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

4. What are Transposons? “Cut & Paste” “Copy & Paste” (Ac/Ds) (Alu)
Transposable element (transposon, TE): DNA sequence competent to insert into new places
(Ac/Ds)
“Cut & Paste”
(Alu)
“Copy & Paste”

5. Nonautonomous elements
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
Nonautonomous elements
Gene(s)
Class I transposons are being copied  multiplicative. Class II transposons can undergo copying, too, if transposing during DNA replication

6. Transposons make up most of (most) eukaryotic genomes
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:

7. Effect of transposons & genome duplications on genomes
What are Transposons?
Effect of transposons & genome duplications on genomes
Rice 450 Mb
Sorghum 700 Mb
Maize 2,500 Mb
Barley 5,000 Mb
Wheat 20,000 Mb
Oats ~20,000 Mb

8. 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.

9. MITEs are being amplified to high copy numbers
Ping/mPing
mPing:
MITE (Multi-insertional TE)
Deletion-derivative of Ping
Requires Ping transposase to jump
MITEs are being amplified to high copy numbers

10. Transposons in Action
The majority of transposition events are ancient, but in Sue Wessler’s story, we se tranpsons in action.

11. mPing copy number in O. japonica
OVER 1000 mPing copies
mPing
mPing copy number
Japonica strains
Over 1000 copies of mPing in 4 related strains….
Naito et al PNAS (2006))
Takatoshi Tanisaka lab (Kyoto University)

12. 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?

13. mPing insertions in genes
UTR
Exon
mPing insertions rare in coding-exons

14. TEs can alter gene expression
mPing found to confer cold and salt inducibility

15. TEs can alter gene expression
Can this have phenotypic consequences?
Nipponbare
EG4
EG4 is salt tolerant

16. 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

17. 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.

18. TEs for student research projects
(relatively) simple
incredibly abundant
evolve rapidly
promote rapid genome evolution
largely ignored (discovery)

19. Suppl.: DNA transposons can be copied, too
Gap repair from sister chromatid
Jump into site that is then replicated

20. 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