We are having here a discussion over a scientific topic and I thought I can get here the help to settle it. The diversity of the immunoglobulins is generated by stochastic rearrangement of genetic segments encoding the immunoglobulins variable domains. The rearrangement occurs by somatic recombination and it is guided by complementary recombination signal sequences (RSS) flanking the gene segments. Moreover, it is mediated by the RAG complex which binds to RSS (more information here http://mcb.asm.org/content/22/20/7217.full). The question is whether this recombination requires some kind of pairing between RSS or not. Thanks in advance for sharing your expertise.
V(D)J recombination is initiated by the synapsis and cleavage of a complementary (12/23) pair of recombination signal sequences (RSSs) by the RAG1 and RAG2 proteins. As stated in the review by Swanson PC, Kumar S, Raval P.
Adv Exp Med Biol. 2009;650:1-15.
Early steps of V(D)J rearrangement: insights from biochemical studies of RAG-RSS complexes.
While the statements above may be true, I'm not sure they answer the stated question directly. Of course, this could be because the question was not stated precisely - but this distinction underscores the importance of using words precisely in science.
As stated above, the question is whether RSS pair during V(D)J recombination, and I would answer "no". The RAG dimer DOES bind a pair of RSSs, at separate binding sites, and sets up cleavage and other downstream events - but the RSS don't bind each other, as far as I know. Ultimately, they are joined end-to-end to effectively discard (or invert) the excised segment. If I'm wrong about this, I'd be interested to learn more.
Here is a public-access article from the same author as the review above, with a 2002 cartoon of the process:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC134746/
And here's a really nice review from Alt's group with a nice diagram (fig 4):
http://dx.doi.org/10.1016/S0092-8674(04)00039-X
Hope this helps.
-- Stuart
Just to be clear, are you asking if the conserved heptamer and nonamer sequences of different RSS actually form watson-crick base pairs that mediate recognition/recombination? I'm not an expert on this but I don't think it is known. It would probably take crystallographic evidence to be sure, right? Anyway, your reference suggests that there is dynamics of the RSS that depends on complex formation. In addition, I think bacterial recombinases like Rec A do require basepairing between homologous ends. So...I would guess that there is some base-pairing requirement. Please post if you find a reference that definitively answers your question.
Cheers
To Stuart Ray. I believe my question was very clear, Do RSS pair during V(D)J segment rearrangement ?
Pedro: I did not mean to criticize your question - but the range of answers illustrates that your readers had various interpretations. Given your question as stated, then I think my response ("no") is correct. My understanding is that RAG binds each RSS, and RAG dimerizes (without bringing the RSS into direct contact).
I'll amend that if someone can provide strong evidence that RSS bind directly to each other during V(D)J recombination.
Thanks for the responses. RSS will NOT need to pair with each others but I have seen text books and presentations, may all wrong, depicting some kind of pairing (not always the same). RAG actually binds to the nonamer portion of each RSS and I still wonder if there will be some pairing between RSS; between the heptamers?. If so it may help to stabilize the RAG complex and/or define the recombination site.
One more thing. V(D)J recombination is contingent on DNA transcription.
The N terminus of RAG1 binds the nonamer directly. The central domain of RAG1 binds the heptamer. RAG1 also binds the midportion (12/23) of the RSS. While this does not exclude pairing of RSS, my sense is that the cartoons showing pairing of RSS are simplifications, and it's RAG dimerization that brings them close together (but not touching).
I think your question is already answered. You can find additional information as follow
Recombination centres and the orchestration of V(D)J recombination.
Link to the article: http://www.nature.com/nri/journal/v11/n4/full/nri2941.html
Hi,
Good question. DNA segment rearrangement does not seem to be completely random and might be control by the position of the segment in the chromosomes. See the following article:
Williams GS, Martinez A, Montalbano A, Tang A, Mauhar A, Ogwaro KM, Merz D, Chevillard C, Riblet R, Feeney AJ. Unequal VH gene rearrangement frequency within the large VH7183 gene family is not due to recombination signal sequence variation, and mapping of the genes shows a bias of rearrangement based on chromosomal location.J Immunol. 2001 Jul 1;167(1):257-63.
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