Next we'll cover retro-transposons.
FischerMG and SuttleCA (2011) A virophage at the origin of large DNA transposons. Science332 (6026): 231–234.
Larger transposons are often compositetransposons.
NeuvegliseC, FeldmannH, BonE, GaillardinC and CasaregolaS (2002) Genomic evolution of the long terminal repeat retrotransposons in hemiascomycetous yeasts. Genome Research14 (6): 930–943. DOI: 10.1101/gr.219202.
In addition to the Echinoderms (sea urchins and starfish), a damaged coding core of a TransibSU transposon was identified also in the genome of the mollusk Crassostrea gigas (Pacific oyster) (Additional file ).
Genetic properties of transposons.
In considering such a cycle, a major question is the source of the antisense transposon information. Because heterochromatic transposon fragments had been previously linked to active transposon silencing (; ), this seemed to be a logical starting point from which to investigate the origin of antisense transcripts. In fact, many fragments do not exist as isolated truncated transposons, but instead sit within what appear as transposon “graveyards,” containing countless nested transposon fragments, most of which have accumulated significant mutations, leaving them otherwise inert (). On the basis of sequence divergence, these loci were demonstrated to produce abundant piRNAs and were therefore termed “piRNA clusters.” These are typically, although not exclusively, transcribed in both orientations as long RNA transcripts () that are parsed into small RNAs. In the case of ping-pong, cluster-derived transcripts are proposed to serve as the source of antisense transposon content, after slicing by Piwi proteins harboring sense piRNAs (; ). Although the transcriptional regulation of piRNA clusters is not well understood, it appears that at least double-strand cluster transcription may be triggered by a specialized HP1 homolog, Rhino (). Regardless, many interesting questions remain about the selection of RNA transcripts to feed the transposon silencing program.
These observations led to a model of piRNA biogenesis that, like dicer-based pathways, requires sense and anti-sense RNA transcripts. However, these appear to be required in trans as single-stranded RNA, and not double-stranded RNA precursors, as seen in canonical RNAi pathways. Here, active transposon RNAs are recognized by a Piwi protein (mainly Aubergine in Drosophila), bound with a near-perfect, reverse-complementing antisense piRNA. This Piwi protein then cleaves the transposon RNA 10 nucleotides distal to the 5′ end of its bound piRNA (). The sliced transcript is then further processed by an as yet defined machinery to generate the 3′ end of a new piRNA. This sense-piRNA is then loaded into the Argonaute3 (AGO3) protein (in Drosophila), which then targets antisense transposon transcripts in the cell for cleavage (). After slicing and again further processing, a new antisense piRNA is produced and loaded back into Aubergine to further target active transposon transcripts. This feed forward amplification cycle, called piRNA “ping-pong,” shapes the population of piRNAs, optimizing control of expressed elements (; ).
Replicative mechanism of transposition.
Based on these and similar observations, Petrov laid out a new model of genome size. Transposons, he argued, would always accumulate, sometimes very quickly. (Maize, for example, has doubled its genome in only 3 million years.) But over eons, small excisions would slowly chip away at a genome’s bulk. Eventually, the pace of expunction would match the pace of creation, and the genome would settle into equilibrium. Any number of forces in the chaotic nucleus might set—or reset—this balance.
In this article, Kapitonov and Koonin report on the discovery of a new subgroup of Transib transposons (denoted TransibSU) that encode both RAG1- and RAG2-like proteins. The authors present compelling evidence for the mobility of these transposons and narrow down on the organization of the transposon that gave rise to the V(D)J recombination machinery of jawed vertebrates. This is an important discovery which allows putting to rest the hypothesis that RAG2 gene was not part of the ‘RAG transposon’ (1) and instead supports the alternative possibility that the ‘RAG transposon’ contained genes for both RAG1 and RAG2 (2,3). The article is very well written and I have only a few minor comments:
What keeps transposition frequencies down.
Only high frequency transposon is Mu, which does kill cell.
KW - Transposable element
One and only one transposon perreplicon allowed.
Transposons in bacteria.
How geneticists use transposons
HuangCR, BurnsKH and BoekeJD (2012) Active transposition in genomes. Annual Review of Genetics46: 651–675.
Transposable element - Wikipedia
There was only one likely explanation: Bats must have jettisoned a lot of DNA. When Kapusta joined Feschotte’s lab in 2011, her first project was to find out how much. By comparing transposons in bats and nine other mammals, she could see which pieces many lineages shared. These, she determined, must have come from a common ancestor. “It’s really like looking at fossils,” she said. Researchers had previously assembled a rough reconstruction of the ancient mammalian genome as it might have existed 100 million years ago. At 2.8 billion base pairs, it was nearly human-size.
A transposable element (TE or transposon) ..
MorganteM, BrunnerS, PeaG, et al. (2005) Gene duplication and exon shuffling by helitron‐like transposons generate intraspecies diversity in maize. Nature Genetics37 (9): 997–1002.
Transposons in Eukaryotes (Part B): Genomic Consequences of ..
Authors’ response: The tree topology in Figure E follows the commonly accepted species phylogeny of sea urchins and other deuterostomes that is maintained by the sea urchin genome database  and EchinoBase (). We added the definition of the magenta ellipse in FigureE: it corresponds to the uncharacterized RAG1-RAG2-transposon identified recently as a polymorphic insertion in a lancelet genome .
(Part B): Genomic Consequences of Transposition ..
The threat posed by transposons comes on many fronts. Specifically, transposons are incredibly diverse in number, composition, and pattern of expression. This allows individual transposon types to fill specific niches, being expressed at different developmental stages and in particular cell types. As an extreme example, in Drosophila, the gypsy family of LTR (long terminal repeat) retrotransposon limits its expression to ovarian somatic cells that surround the germline compartment. This initially seems at odds with the imperative to expand copy number in the germline genome. However, gypsy family elements, unlike others in Drosophila, have regained features of their viral past, reconciling somatic expression and germline transmission.
This “epi-transposon hypothesis ..
For Feschotte, the tip-off came from a bat. By the early 2000s, following advances in DNA sequencing, labs had begun decoding whole genomes and sharing the data online. At the time, Feschotte’s group was not particularly interested in the evolutionary dynamics of genome size, but they were extremely curious about what transposons could reveal about the history of life. So when the genome of the common little brown bat (Myotis lucifugus), the first genome sequence from a bat, appeared in 2006, Feschotte was thrilled. Bats have strikingly small genomes for a mammal—they’re more like those of birds—and it seemed likely they would hold surprises.
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