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  December 5, 2017

GENOME EVOLUTION (cond.)





Learning checklist:
A. Transposons are a Major Component of Plant Genomes
B. Transposons mobilize in short evolutionary time frames
C.Transposons are activated by stress
D. Know the different possible roles for repetitive elements in eukaryotic genomes


The Role of Transposons in Genome Evolution

A.Transposons are a Major Component of Plant Genomes

Raja Ragupathy, Frank M. You, Sylvie Cloutier, Arguments for standardizing transposable element annotation in plant genomes, In Trends in Plant Science, Volume 18, Issue 7, 2013, Pages 367-376, ISSN 1360-1385, https://doi.org/10.1016/j.tplants.2013.03.005.
(http://www.sciencedirect.com/science/article/pii/S1360138513000587)

The data in Table 1 bring out a number of important points:

B. Transposons mobilize in short evolutionary time frames

Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt SC, et al. 2006 Global Mapping of Transposon Location. PLoS Genet 2(12): e212. doi:10.1371/journal.pgen.0020212

As a proof of concept experiment, the authors developed an approach to use microarrays to detect the locations of transposons in yeast. This method was tested on two yeast strains whose genomes have been fully sequenced, and the locations of transposons identified from the sequence. Microarrays were designed with oligonucleotide probes from unique sequences, spaced roughly every 300 bp throughout the genome. The results verify that the the locations of almost all annotated transposons were correctly identified.

1. Isolation of regions flanking transposable element insertions

1. Digest yeast genomic DNA with a restriction enzyme known to cut within transposons Ty1 and Ty2.
2. DNA samples from 2 strains RM11 and S288c.
3. Many fragments have a partial transposon at one end and regions flanking the insertion at the other end.
4. Denature DNA and use transposon-specific primer to synthesize DNA containing biotinylated nucleotides. To purify biotinylated fragments, are purified by mixing with streptavidin-coated magnetic beads. Biotinylated DNA is bound by streptavidin, and magnetic beads are washed to remove unbound DNA. After washing, biotinylated DNA is released from the beads by washing in a buffer.
5. Purified sequences are enriched for unique sequences which flank transposon insertions.
6. Sequences are labeled with fluorescently labeled nucleotides: RM11 - Cy3 (green); S288c - Cy5 (red)
7. Mix labeled DNAs and hybridize with a yeast microarray containing unique yeast probes. Probes have been designed so that they do not contain Ty1 and Ty2 sequences. Consequently, probes will hybridize based on the unique flanking regions from the labeled DNA.
8. Results are superimposed on chromosome maps.

Red Peaks: Ty1 or Ty2 unique to S288c
Green Peaks: Ty1 or Ty2 unique to RM11
Black circles: full length Ty1 or Ty2 elements identified from S288c genomic sequence
Triangles: full length Ty2 elements identified from RM11 genomic sequence
1,2,3,4 - false negatives
5,6 - false positives


2. Differences in transposon location between yeast strains




These data show that even between strains, tremendous rapid changes in the locations of transposons can occur. The differences in the locations of transposons between the two strains provide evidence that locations and numbers of transposons in yeast can change, genome wide, over very short evolutionary time scales.

C. Transposons are activated by stress

In most species, transposition is suppressed by epigenetic imprinting. Methylation of C residues prevents mobilization of transposons, which results in genome stability across generations. Methylation patterns are known to be inherited from one generation to the next in most higher  eukaryotic species.

Barbara McClintock first observed that what we now know to be the suppression of transposition is relaxed during stress, resulting an a de-repression of transposition.

Table 2 shows that there are many stress conditions which can mobilize transposons,  including:

As well, mutations in methyltransferases and even the genetic background of plants in a cross can induce mobilize transposons.



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