1. Why are some of kernels striped or spotted? The Dynamic Genome:

2. McClintock: sole recipient of 1983 Nobel Prize in Physiology or Medicine Why awarding such a “trivial” discovery? Why 40 years from discovery to prize?

3. ~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 brevicaulisIris fulva TEs rule

4. Sorghum 700 Mb Barley 5,000 Mb Maize 2,500 Mb Oats ~20,000 Mb Wheat 20,000 Mb Rice 450 Mb Varying genome sizes among cereal grasses Due to transposons & genome duplications

5. DNA (class 2) elements: RNA (class 1) elements: TEs are (relatively) simple genetic systems: “Cut & Paste” “Copy & Paste” II

6. Transposon Families 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)

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

8. 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?

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

10. - 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

11. mPing insertions rare in coding-exons Genic distribution of mPing insertions UTRExonUTR

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

13. Can this have phenotypic consequences? NipponbareEG4 EG4 is salt tolerant IIIIII

14. Rapid mPing amplification (burst) 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

15. 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

16. -they are (relatively) simple -they are incredibly abundant -they evolve rapidly -they promote rapid genome evolution -they are largely ignored (discovery) TEs in Student Research

17. -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) Genomic analysis of TEs using DNA Subway

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