The links below indicate "clear" connections between immunology and mobile genomics, especially when we look at the case of Paleo-immunology cerca and V(D)J recombination.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005778
http://en.wikipedia.org/wiki/Transposable_element
http://en.wikipedia.org/wiki/V(D)J_recombination
http://www.mobilednajournal.com/
It is believed that V(D)J recombinase is closely related to the transposase of mobile elements. Thus, the connection between mobile elements and immunology.
thank you, on the other hand, I always thought this is the work of the 1.5% of the active genes of the genome not the inactive line, sine and other segments of the DNA. ?
Actually, recombinase, which is involved in V(D)J recombination, is an active gene and strictly speaking evolutionary related to transposase of DNA transposons, but recombinase is not transposase, it is not a part of current mobile element (mobilome) in the genome, it is very important protein in its own right.
So I do not see what is conundrum about.
The opposite-transcriptional-direction, back-to-back RAG1/2 proteins required and involved in V(D)J recombination are thought to have viral origins as a transposable element, among other theories.
(see the link at bottom of post)
In general, all these responses above stem from the semantics that what we call a transposable element usually is defined as some j nucleotides in length from an exogenous source with a flanking repeated sequence that has been inserted (relatively) stably into the genome, usually has no direct effect (but obviously this may change over time and with chance), and may replicate, copy, or shift (cut + paste) predictably based on nucleotide content at the excision and insertion sites.
RAG1/2 have been shown to have transposase activity in vitro as cited in the attached paper, the Rag locus is highly compact and conserved since its appearance in jawed bony fish, and Rag1 has been shown to be similar to transposases and integrases.
http://www.pnas.org/content/103/10/3728.full.pdf+html
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