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P Nucleotides in V(D)J Recombination: A Fine-Structure Analysis

Meier, Joseph T. and Lewis, Susanna M. (1993) P Nucleotides in V(D)J Recombination: A Fine-Structure Analysis. Molecular and Cellular Biology, 13 (2). pp. 1078-1092. ISSN 0270-7306. http://resolver.caltech.edu/CaltechAUTHORS:20120307-122926596

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Abstract

Antigen receptor genes acquire junctional inserts upon assembly from their component, germ line-encoded V, D, and J segments. Inserts are generally of random sequence, but a small number of V-D, D-J, or V-J junctions are exceptional. In such junctions, one or two added base pairs inversely repeat the sequence of the abutting germ line DNA. (For example, a gene segment ending AG might acquire an insert beginning with the residues CT upon joining). It has been proposed that the nonrandom residues, termed "P nucleotides," are a consequence of an obligatory end-modification step in V(D)J recombination. P insertion in normal, unselected V(D)J joining products, however, has not been rigorously established. Here, we use an experimentally manipulable system, isolated from immune selection of any kind, to examine the fine structure of V(D)J junctions formed in wild-type lymphoid cells. Our results, according to statistical tests, show the following, (i) The frequency of P insertion is influenced by the DNA sequence of the joined ends. (ii) P inserts may be longer than two residues in length. (iii) P inserts are associated with coding ends only. Additionally, a systematic survey of published P nucleotide data shows no evidence for variation in P insertion as a function of genetic locus and ontogeny. Together, these analyses establish the generality of the P nucleotide pattern within inserts but do not fully support previous conjectures as to their origin and centrality in the joining reaction.


Item Type:Article
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URLURL TypeDescription
http://dx.doi.org/10.1128/​MCB.13.2.1078 DOIUNSPECIFIED
http://mcb.asm.org/content/13/2/1078PublisherUNSPECIFIED
Additional Information:© 1993 American Society for Microbiology. Received 26 August 1992; Returned for modification 15 October 1992; Accepted 2 November 1992. We thank L. Czyzyk for superlative technical assistance; E. B. Lewis, D. Mathog, and H. Lipshitz for advice on the statistical analysis; and B. Wold, J. Kobori, L. Hood, P. Fahnestock, H. Lipshitz, and P. Bjorkman for comments on the manuscript. We thank M. Gellert for comments and for communicating his results prior to publication. We thank J. Teale for providing unpublished sequence data. J.T.M. gratefully acknowledges the support of L. Hood and NIH grant GM40867 to L. Hood. This work was funded by research grant IM-599 from the American Cancer Society to S.M.L.
Funders:
Funding AgencyGrant Number
NIHGM40867
American Cancer SocietyIM-599
Record Number:CaltechAUTHORS:20120307-122926596
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20120307-122926596
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ID Code:29622
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:13 Mar 2012 15:27
Last Modified:13 Mar 2012 15:27

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