Uneven Distribution of Repetitive Trinucleotide Motifs in Human Immunoglobulin Heavy Variable Genes Johan Lantto, Mats Ohlin Department of Immunotechnology, Lund University, P.O. Box 7031, Lund, Sweden Received: 10 April 2001 / Accepted: 27 August 2001 Abstract. Insertions and deletions of entire codons have recently been discovered as a mechanism by which B cells, in addition to conventional base substitution, evolve the antibodies produced by their immunoglobulin genes. These events frequently seem to involve repetitive sequence motifs in the antibody-encoding genes, and it has been suggested that they occur through polymerase slippage. In order to better understand the process of codon deletion, we have analyzed the human immuno- globulin heavy variable (IGHV) germline gene repertoire for the presence of trinucleotide repeats. Such repeats would ensure that the reading frame is maintained in the case of a deletional event, as slippage over multiples of three bases would be favored. We demonstrate here that IGHV genes specifically carry repetitive trinucleotide motifs in the complementarity-determining regions (CDR) 1 and 2, thus making these parts of the genes that encode highly flexible structures particularly prone to functional deletions. We propose that the human IGHV repertoire carries inherent motifs that allow an antibody response to develop efficiently by targeting codon dele- tion events to the parts of the molecule that are likely to be able to harbor such modifications. Key words: Antibody — Deletion — IGHV — Muta- tion — Repetitive sequences — Variable genes Introduction During the course of an immune response, B cells popu- lating germinal centers of secondary lymphoid organs have the capacity to evolve the antibodies they produce by a combination of mutational and subsequent clonal selection steps. The hypermutation events usually in- volve substitution of single nucleotides, sometimes re- sulting in a modification of the properties of the pro- duced antibody. Recently, however, it has become apparent that the mutational machinery also has the ca- pacity to introduce larger modifications, involving inser- tions and deletions, and not only substitutions of nucleo- tides, in the genes encoding the antibody variable (V) regions (De Wildt et al. 1999; Goossens et al. 1998; Ohlin and Borrebaeck 1998; Wilson et al. 1998a). A large part of these modifications results in an inability of the antibody gene to encode a functional protein, either because the deletions and insertions produce an out-of- frame gene downstream of the modification, or because the modification alters the protein so dramatically that it cannot fold properly. Even if a properly folded protein is produced, it may have lost its antigen-binding properties and, as a result, the B cell producing it will be deleted. Nevertheless, a fraction of the B cells introducing such insertions and deletions in the antibody coding sequence continue to produce an antigen-specific antibody that survives the selection process and will contribute to the peripheral population of antibodies. By making use of this mechanism of introducing insertions and deletions into immunoglobulin genes, the B cell is able to expand antibody structure space even further beyond what is possible to create by the combinatorial recombination of the few germline genes found in the immunoglobulin loci and through base substitution alone. In fact, about 1.5–6.5% of normal B cells have been reported to carry insertions or deletions in their hypermutated antibody- Correspondence to: M. Ohlin; email: mats.ohlin@immun.lth.se J Mol Evol (2002) 54:346–353 DOI: 10.1007/s00239-001-0049-2 © Springer-Verlag New York Inc. 2002