Transposable Elements (Transposons)

1. Transposable Elements (Transposons) • DNA elements capable of moving ("transposing") about the genome • Discovered by Barbara McClintock, largely from cytogenetic studies in maize, but since found in most organisms • She was studying "variegation" or sectoring in leaves and seeds • She liked to call them "controlling elements“ because they affected gene expression in myriad ways

2. 1. Nobelprize.org (1983 Nobel Prize in Physiology and Medicine) 2. profiles.nlm.nih.gov/LL/ Barbara McClintock 1902-1992 Corn (maize) varieties

3. Corn evolution in 7000 yrs of domestication cob of Hopi Blue corn cob of wild teosinte

4. Maize (domesticated corn) kernel structure

5. Mutant Kernel Phenotypes • Pigmentation mutants • affect anthocyanin pathway • elements jump in/out of transcription factor genes (C or R) • sectoring phenotype - somatic mutations • whole kernel effected - germ line mutation Starch synthesis mutants - stain starch with iodine, see sectoring in endosperm

6. Some maize phenotypes caused by transposable elements excising in somatic tissues. Start with lines that produce kernels defective in starch synthesis (endosperm phenotypes) or anthocyanin synthesis (aleurone and pericarp phenotypes) because of an inserted element, and the element excises during development.

7. Somatic Excision of Ds from C Wild type Mutant Sectoring Fig. 23.9

8. Other Characteristics of McClintock's Elements • Unstable mutations that revert frequently but often partially, giving new phenotypes. • Some elements (e.g., Ds) correlated with chromosome breaks. • Elements often move during meiosis and mitosis. • Element movement accelerated by genome damage.

9. Molecular Analysis of Transposons • Transposons isolated by first cloning a gene that they invaded. A number have been cloned this way, via "Transposon trapping“. • Some common molecular features: • Exist as multiple copies in the genome • Insertion site of element does not have extensive homology to the transposon • Termini are an inverted repeat • Encode “transposases” that promote movement • A short, direct repeat of genomic DNA often flanks the transposon : “Footprint”

10. Ac and Ds • Ds is derived from Ac by internal deletions • Ds is not autonomous, requires Ac to move • Element termini are an imperfect IR • Ac encodes a protein that promotes movement - Transposase • Transposase excises element at IR, and also cuts the target

11. Structure of Ac and Ds deletion derivatives Ds is not autonomous, requires Ac to move! Fig. 23.10

12. How duplications in the target site probably occur. Duplication remains when element excises, thus the Footprint. Fig. 23.2

13. Mu/MuDR (Mutator) • Discovered in maize; differs significantly from Ac and En/Spm families • Autonomous and non-autonomous versions; many copies per cell • Contain a long TIR (~200 bp) • Transpose via a gain/loss (somatic cells) or a replicative (germline cells) mechanism.

14. Structure of MuDR (autonomous Mu) and its promoters. • MuDrA and B expressed at high levels in dividing cells and pollen, because of transcriptional enhancers. • MURA is transposase & has NLS. • MURB needed for insertion in somatic cells.

15. Retro- Transposons Can reach high numbers in the genome because of replicative movement. Fig. 7.34 in Buchanan et al.

16. Control of Transposons • Autoregulation: Some transposases are transcriptional repressors of their own promoter(s) • e.g., TpnA of the Spm element • Transcriptional silencing: mechanism not well understood but correlates with methylation of the promoter (also methylation of the IRs)

17. Biological Significance of Transposons • They provide a means for genomic change and variation, particularly in response to stress (McClintock’s "stress" hypothesis) (1983 Nobel lecture, Science 226:792) • or just "selfish DNA"? • No known examples of an element playing a normal role in development.