- Retrotransposition is one of the two basic types of transposition we find in biology. It's sort of fun to survey where transposons are in the tree of life: in the case of more eukaryotes, most of the genome is transposons; little of microbial genomes are retrotransposons.
LINEs (L1) transposon sequences comprise ~ 21% of the human genome, and generally dominate mammalian genomes.
- The RNA is oth mRNA and "genome" (template) RNA
- Most of the ~500,000 L1 copies are severely 5' truncated and live 1) in introns or 2) between genes
- normally inserts only in the germ line - not somatically.
- The promoter is entirely embedded in the mRNA and hence is taken along with the transposon.
make synthetic ORF2 and ORF1. Properties:
- 25% of the nucleotides altered - new species of retrotransposons
- adenosine content reduced 40%.
Besides mutagenesis, another application might be cancer gene discovery: they've developed a method of activating retrotransposition in any tissue of interest.
Anyhow, they've built 7+ new transposons (thanks DNA 2.0). And now for something completely different: the systems biology of yeast is the best of any, os if we know so much, can we use that knowledge to refactor it and make a "synthetic" strain?
Boeke's lab is designing and synthesizing yeast chromosome 3. They're doing so in an iterative fashion, refactoring the chromosome in chunks of 30Kb at a time, so they can check their work as they go. It's a straightforward procedure; get thousands of colonies from ~ug of refactored DNA.
Changes to make; want to make a super-stable genome:
- remove all transposons
- remove all introns
- downsize telomeres
- relocate all tRNA genes
P.S. - Joel Bader is writing a Genome Revision control System!