Expression of K2 isotype mRNA in normal and Basilea rabbits

Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20

We report on the analyses of genes encoding immunoglobulin heavy and light chains in the rabbit 6.51× whole genome assembly. This OryCun2.0 assembly confirms previous mapping of the duplicated IGK1 and IGK2 loci to chromosome 2 and the IGL lambda light chain locus to chromosome 21. The most frequently rearranged and expressed IGHV1 that is closest to IG DH and IGHJ genes encodes rabbit VHa allotypes. The partially inbred Thorbecke strain rabbit used for whole-genome sequencing was homozygous at the IGK but heterozygous with the IGHV1a1 allele in one of 79 IGHV-containing unplaced scaffolds and IGHV1a2, IGHM, IGHG, and IGHE sequences in another. Some IGKV, IGLV, and IGHA genes are also in other unplaced scaffolds. By fluorescence in situ hybridization, we assigned the previously unmapped IGH locus to the q-telomeric region of rabbit chromosome 20. An approximately 3-Mb segment of human chromosome 14 including IGH genes predicted to map to this telomeric region based on synteny analysis could not be located on assembled chromosome 20. Unplaced scaffold chrUn0053 contains some of the genes that comparative mapping predicts to be missing. We identified discrepancies between previous targeted studies and the OryCun2.0 assembly and some new BAC clones with IGH sequences that can guide other studies to further sequence and improve the OryCun2.0 assembly. Complete knowledge of gene sequences encoding variable regions of rabbit heavy, kappa, and lambda chains will lead to better understanding of how and why rabbits produce antibodies of high specificity and affinity through gene conversion and somatic hypermutation.

In utero suppression of kappa 2 isotype in homozygous bas/bas rabbits through embryo transfer

Allotypes of rabbit Ig provide a useful tool for the study of quantitative expression of alternative allelic forms. In the rabbit, maternal Ig is transmitted to the foetus and protects the immunologically immature newborn during several of the first weeks of life. Induced maternal antibodies directed towards a paternally inherited allotype of the offspring can influence the expression of that allotype drastically. Normal Ig level in heterozygous allotype suppressed animals is provided by increased expression of the alternative allele. On the other hand, allotype suppression in homozygous animals leads to increased expression of non-allelic alternative gene products. We quantitatively analysed the expression of bas, a marker on the kappa 2 light chain isotype of the mutant strain Basilea, in homozygous bas/bas rabbits which had been fostered in utero of b4/b6 mothers producing anti-bas. All of the offspring studied expressed the kappa 2 isotype at a very low level at two months of age, and, in some individuals, bas was hardly expressed after 6 to 12 months. A suppressed rabbit, which was immunized to produce auto-antibodies against bas, continued to do so for at least 2.5 years. The long duration of homozygous bas suppression contrasts with homozygous suppression of other allotypes (CL kappa 1 and VHa) which generally lasts for a much shorter period.

Mapping of the duplicated rabbit immunoglobulin kappa light chain locus

The rabbit has two isotypic forms of the immunoglobulin kappa light chain, K1 and K2, which probably arose by duplication. In the normal rabbit, only traces of K2 light chains are produced. However, K2 levels are elevated in allotype-suppressed rabbits and in the Basilea strain which does not produce K1 because of a K1 mRNA splice site mutation. Previous cloning and sequencing showed that each isotype has its own set of J kappa genes but it was not known whether the two isotypes utilize shared or separate sets of V kappa genes. In addition, although genetic linkage of allotypes associated with the K1 and K2 genes has been demonstrated, physical linkage had not been previously demonstrated by overlapping cosmid or phage clones. We used pulsed field and transverse alternating field electrophoresis to obtain megabase maps and to estimate the size of the duplication of the rabbit kappa light chain locus. We found that the two C kappa genes are about 1 megabase apart. One explanation for the poor expression of K2, could be great physical distance from V kappa genes. However, we found that there are V kappa, J kappa and C kappa 2 genes within a approximately 105-kb fragment. Thus, physical distance of V kappa from C kappa 2 may not be the basis for poor K2 expression.

Rearrangement of the immunoglobulin kappa light chain genes in a b4 rabbit and a Basilea rabbit

The immunoglobulin chi light chain gene family of the rabbit is characterized by the presence of two constant region exons, C chi 1 and C chi 2 encoded at the chi 1 and chi 2 loci, and linked to their own cluster of joining pieces (J chi). The gene segments at the two loci are very unequally expressed. Thus, in domestic rabbits, the immunoglobulin light chains are essentially of the chi 1 type, even though the gene segments at the chi 2 locus are structurally functional. We have investigated the origin of the weak expression of the genes at the chi 2 locus by analysing the pattern of rearrangement of the chi 1 and chi 2 J chi segments in rabbit B-cell populations. Southern blot analysis of B cells isolated from a rabbit expressing chi 1 light chains suggests that the genes at the chi 2 locus underwent very few, if any, rearrangements. However, using more sensitive approaches, it was possible to detect transcripts originating from the rearranged chi 2 locus. In contrast, in B cells isolated from a Basilea rabbit, which cannot express chi 1 chains, Southern blots revealed the rearrangement of the chi 2 genes, whereas the chi 1 rearranged fragments were barely detectable. These results could be explained either by preferential rearrangement of genes at the chi 1 locus or by clonal amplification of only cells producing chi 1. Furthermore, results of Southern blot analysis provide evidence that V-J recombination may be accompanied by an inversion of the intervening DNA region.

Linked genetic markers of the rabbit kappa light chain are not linked to the Tcr beta chain genes

In order to investigate linkage, we used serum allotypes of the two rabbit C kappa isotypes and restriction fragment length polymorphisms (RFLPs) of the genes for V kappa, C kappa, and T-cell receptor C beta. The inheritance of these genetic markers was studied through backcross and F2 matings. Southern analysis and hybridization of genomic DNA with a C kappa probe detected a 5 kb Pst I fragment linked to expression of the K2bas1 allotype and the presence of the kappa 1bbas gene and a 6.6 kb Pst I fragment linked to the expression of the K1b9 allotype, the presence of the kappa 2bas2 gene and lack of expression of the K2bas1 allotype. A V kappa probe detected a 1.3 kb Eco RI fragment linked to the presence of the kappa 1bbas gene and expression of the K2bas1 allotype. In contrast, the 9 or 14 kb Eco RI RFLP (C beta a or C beta b) detected with a Tcr beta chain probe segregated independently from C kappa allotypes and RFLPs. It has previously been found that C kappa and C beta are also unlinked in man, whereas in the mouse they are linked at a distance of approximately 8 centimorgans.