Junctional diversity in the absence of N regions. Neonatal T cell receptor beta chain junctional sequences are more heterogeneous than neonatal T cell receptor gamma delta or IgH junctions.
Early in ontogeny, Ig, TCR-alpha beta, and TCR-gamma delta lack N regions. In addition, Ig and TCR-gamma delta junctions preferentially occur at regions of short sequence homology, thus limiting junctional diversity for these neonatal lymphocyte populations. Here, we analyze the extent of heterogeneity in TCR-beta chain junctions made early in ontogeny. DNA and cDNA from fetal/neonatal thymocytes were amplified by polymerase chain reaction, and the V-D and D-J junctions from these randomly generated sequences were analyzed. The D-J junctions were very heterogeneous, and displayed little evidence of homology-directed recombination. The V beta 8-D and V beta 5-D junctions that we analyzed each had a particular junctional sequence that was created at the site of a two-nucleotide homology, but in each case that sequence only comprised 10 to 17% of the total sequences. This junctional heterogeneity of N region lacking TCR-beta chains can be partially explained by a relative paucity of homologies at the appropriate locations near the coding ends, particularly at the D-J junction, but other factors such as the sequence surrounding the homology may also contribute. Thus, TCR-beta chains have extensive junctional heterogeneity early in ontogeny before N regions begin to be added. Since TCR-alpha beta CDR3 plays a major role in binding antigenic peptides, this junctional heterogeneity is likely to be advantageous for establishing a diverse TCR repertoire. We suggest that the sequences of the coding ends of the TCR-alpha beta have been selected through evolution to avoid the restricted junctional diversity resulting from homology-directed recombination.
Scripps Research Institute, Department of Immunology IMM-22, La Jolla, CA 92037.
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Feeney
D000818:Animals; D000831:Animals, Newborn; D001483:Base Sequence; D015333:Gene Rearrangement, beta-Chain T-Cell Antigen Receptor; D016694:Gene Rearrangement, delta-Chain T-Cell Antigen Receptor; D015334:Gene Rearrangement, gamma-Chain T-Cell Antigen Receptor; D007143:Immunoglobulin Heavy Chains / Q000235:genetics; D051379:Mice; D008807:Mice, Inbred BALB C; D008810:Mice, Inbred C57BL; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics*; D016692:Receptors, Antigen, T-Cell, gamma-delta / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
D007143:Immunoglobulin Heavy Chains; D009838:Oligodeoxyribonucleotides; D016693:Receptors, Antigen, T-Cell, alpha-beta; D016692:Receptors, Antigen, T-Cell, gamma-delta