Linking of the human immunoglobulin VK and JKCK regions by chromosomal walking

A 9.1-kb gap in the genome reference map is shown to be a stable deletion/insertion polymorphism of ancestral origin

We show a mute 9.1-kb gap in the human genome reference map, unraveled by RDA studies, to be a worldwide deletion/insertion polymorphism of stable type. The molecular and population data presented suggest its origin from a unique ancestral transposition event in chromosomal region 22q11.2, overlapping the IglambdaV genes at about 450 kb from the cluster of the IglambdaJ-C genes. These findings are not meant to be just another report of a polymorphic marker suitable for population studies. Rather, we wish to stress that a large number of inborn mute gaps may be spread all over the genome and that the many RDA-detected microdeletions already available are efficient tools for the discovery of this otherwise hidden category of genetic variation. Apart from their possible impact on expression of structural genes, mute gaps must be filled for the reference map of our genome to be truly completed.

Association of KM genotype with bullous pemphigoid

Association of kappa light chain immunoglobulin allotypes with bullous pemphigoid was examined in 101 Caucasian patients. Km alleles were determined by polymerase chain reaction amplification followed by restriction enzyme digestion. The frequency of Km(3)/Km(1,2)kappa light-chain genotype was found to be significantly associated with the disease, while that of the Km(3)homozygous genotype was significantly higher in patients with both anti-BPAG1 and anti-BPAG2 autoantibodies.

Molecular modeling study of the multidrug resistance modifiers cis- and trans-flupentixol

Recent drug-membrane interaction and quantitative structure-activity relationship studies of thioxanthenes and related compounds acting as multidrug resistance (MDR) modifiers pointed to the importance of the stereoisomery for their MDR reversing activity. Therefore a molecular modeling study of trans-(T) and cis-flupentixol (C) was performed in order to elucidate the observed discrepancy between equal binding potency to P-glycoprotein and different MDR reversing activity of the two stereoisomers. The results show that the 2 to 3-fold difference in MDR reversing activity of T compared to C might be related to a different orientation of the molecules in the membrane lipid environment. From the conformations generated by the SYBYL systematic search procedure those comprising local energy minima were selected and further optimized with semiempirical quantum chemistry methods. From the optimized conformations those that corresponded to 1H NMR results on drug conformations in lipid environment were selected for further molecular modeling studies. The electrostatic and lipophilic fields of T and C were compared in order to identify molecular properties related to the activity difference. The results show that the electrostatic fields of the drugs when similar in shape are dissimilar and that the lipophilic and hydrophilic regions are clearer separated in T in comparison with C. This imposes a better fitting of T compared to C to membrane lipid environment in accordance with the observed higher interaction strength of T with phospholipids.

Searching for non-V kappa transcripts from the human immunoglobulin kappa locus

The 76 V kappa (variable) gene segments of the human immunoglobulin kappa locus (Ig kappa) were cloned in two contigs. Within each contig the distances between the genes range from a few hundred bp to 31 kb. We have now studied the question of whether transcripts are produced from intergenic regions, from regions near the kappa locus or from V kappa orphon regions. RNAs from several cell lines were converted to cDNAs which were then hybridized to the cosmid and phage lambda clones of the locus and of the orphon regions; the conditions were chosen such that the hybridization of transcripts with repetitive elements was minimized. The expression of a rearranged V kappa gene in a lymphoid cell line was readily detected. Also, a region 46 kb downstream from C kappa (constant) and a cDNA clone from a non-lymphoid cell line hybridizing to this region were studied in some detail. No transcripts were found, however, to be derived from the intergenic regions of the germ-line kappa locus which is in keeping with current ideas on the evolution of the V kappa multigene family.

The ribose 5-phosphate isomerase-encoding gene is located immediately downstream from that encoding murine immunoglobulin kappa

The immunoglobulin kappa locus (Ig kappa) is active only in the B-lymphocyte cell lineage. By exon-trapping we found a gene situated downstream from the murine Ig kappa locus. This gene encodes a protein with 53% sequence identity to the ribose 5-phosphate isomerase A (RPI-A) of Escherichia coli and is therefore likely to be the murine homologue (mRPI) of this enzyme. We confirmed this assumption by showing that a glutathione S-transferase (GST)::mRPI fusion protein has enzymatic activity and that an anti-mRPI antibody detects a protein of the predicted mass of RPI (33 kDa). Cloning and sequencing of the human counterpart show that the RPI gene is evolutionarily conserved. The expression of mRPI is not influenced by the rearrangement status of the Ig kappa locus in B cells and mRPI is expressed in all tissues. We thus show that two genes with very different expression patterns, a housekeeping gene and a gene expressed in a tissue-specific manner, can be located on a chromosome in close proximity to each other.

Analysis of the promoter of the human prostatic acid phosphatase gene

From the analysis of two overlapping cosmid clones prepared from human genomic DNA libraries, a contig of 44 kb containing a 5' portion of the PAP gene and 17 kb of the upstream region was established. It was characterized by restriction mapping and sequence analysis of 2.5 kb upstream of the initiation codon. Two major transcription initiation sites were found to be located around 56 and 91 bp upstream of the initiation codon, as determined by nuclease S1 and primer extension mapping. Expression of the PAP gene was measured by Northern blots in the androgen responsive LNCaP cell line. It was found to be induced 2-3-fold by the addition of the synthetic androgen mibolerone to the cells. The induced mRNA levels were approx. 10-times lower than those for the prostate-specific antigen (PSA) in LNCaP cells.

The immunoglobulin kappa locus-or-what has been learned from looking closely at one-tenth of a percent of the human genome

The immunoglobulin kappa locus and its immediate surroundings, which are described in the present report, comprise 3 Mb of DNA, i.e., 0.1% or one per mill of the 3000 Mb of the human genome. Based on the work of our group during the past 12 years, we can now (1) depict in much detail the structure of the kappa locus with its 76 V kappa genes and pseudo genes, five J kappa elements and one C kappa gene; (2) specify the size of the germ-line repertoire of kappa light chains, which is one of the sources of the practically unlimited antibody diversity; (3) assign the known transcription products (studied as cDNAs) and kappa proteins to certain germ-line V kappa genes and attribute the differences in sequences to hypermutation and, to a lesser extent, to allelic variation; (4) analyze the hypermutation patterns which may contribute to the understanding of this enigmatic process; (5) describe the V kappa-J kappa rearrangements for half of the V kappa genes by a deletion mechanism and for the other half by a mechanism involving inversions of Mb-sized (i.e., 0.5 mm long) DNA fragments; (6) define various regulatory and other conserved sequence elements; (7) get clues as to the variation of the structure of the kappa locus in different individuals and populations, including a haplotype with only half the number of V kappa genes; (8) interpret many aspects of the evolution of the kappa locus in terms of duplications, insertions, deletions and gene conversions; (9) attribute the formation of the 24 V kappa orphons (i.e., genes outside the locus), whose sequences were determined, to pericentric inversions and other transposition processes; (10) answer a series of questions of biomedical interest; and (11) contribute 12.5 Mb of restriction maps, 1.8 Mb of clones and 250 kb of sequences to the elucidation of the human genome.

The V kappa genes of the L regions and the repertoire of V kappa gene sequences in the human germ line

Only 14 of the 25 V kappa genes and pseudogenes had been found before as parts of the L regions. The cloning and linking described in the accompanying report allowed us now to assign to Lp or Ld some V kappa genes which had been found before on scattered clones. In addition the sequences of several still unknown genes are reported here, thus completing the publication of the V kappa genes of the kappa locus as far as they are potentially functional or have only one or two 1-bp defects. Of the V kappa genes of the kappa locus, 32 are potentially functional, 16 have minor defects, 3 have both potentially functional and slightly defective alleles and 25 are pseudogenes which amounts to a repertoire of 76 V kappa-related gene sequences. The V kappa genes of the L regions are, within the subgroups, particularly similar to each other, which is in part due to common evolutionary origins and in part caused by gene conversion-like events. One donor-acceptor pair could be clearly identified, since converted and not-converted alleles of the acceptor gene were found. In other cases the duplicates of the converted genes served as non-converted controls.

The human immunoglobulin kappa locus. Characterization of the partially duplicated L regions

The L regions are parts of the C kappa proximal (p) and distal (d) copies of the human immunoglobulin kappa locus and are therefore called the Lp and Ld regions. The two regions with their 25 V kappa genes and pseudogenes have now been cloned, thus completing the cloning of the kappa locus. Lp has been linked to the neighboring Ap and B regions, while Ld was linked to Ad. There is good evidence that at the other side of Ld, i.e. towards the centromere, the end of the locus has been reached. Most of the cloning and linking was achieved by chromosomal walking, employing cosmid and phage lambda clones. No such clones could be found for three small gaps. Two of them were closed by a polymerase chain reaction strategy; the third one was characterized by genomic blot hybridization experiments and eventually bridged by a yeast artificial chromosome clone. Early in evolution, a stretch of about 25 kb which comprised three V kappa genes near the 5' end of the L region precursor must have been duplicated, such that the later duplication of large parts of the kappa locus resulted in the appearance of two very similar three-gene regions in each, Lp and Ld. Two deletions in the central parts of the L regions, on the other hand, must have occurred after the duplication of the locus, since they are found in Lp and Ld in different positions.

Creation of mice expressing human antibody light chains by introduction of a yeast artificial chromosome containing the core region of the human immunoglobulin kappa locus

We have previously described a strategy for integrating selectable marker genes into yeast artificial chromosomes (YACs) to facilitate their transfer into embryonic stem (ES) cells. Here we apply this technology to create mice carrying the core region of the human immunoglobulin (Ig) kappa light chain locus. A YAC was isolated which contains a 300 kb insert spanning three V kappa segments, the J kappa cluster, the C kappa region and extending downstream of the Kde element. After modification of this YAC to integrate the selectable neo marker gene, the YAC was introduced into ES cells by protoplast fusion. Several ES cell clones were obtained which appeared to harbor one complete copy of the YAC while retaining little or no other yeast DNA. The ES cells were injected into blastocysts and the chimaeric mice were shown to rearrange the introduced human light chain genes with the resultant production of antibodies containing human kappa light chains in the serum.

The immunoglobulin kappa locus: polymorphism and haplotypes of Caucasoid and non-Caucasoid individuals

The immunoglobulin kappa locus has previously been characterized by comparing the restriction patterns of the DNA of 23 Caucasoid individuals and defining various polymorphisms and haplotypes. This study has now been extended to a group of 28 Blacks and another group of 13 individuals of different ethnic origins. The predominant haplotype of the Caucasoid group, called haplotype N, was also found frequently in the other groups. Some of the restriction fragment length polymorphism markers typical of haplotype G, on the other hand, were seen 2-3 times more frequently in the black than in the Caucasoid group. Haplotype 11, which is characterized by the absence of about half of the variable gene segments (V kappa) and which had been observed in 3 out of 46 Caucasoid alleles, has been found twice in the 82 alleles of the two new groups. A number of new polymorphisms was detected and new haplotypes were defined, although the structure of the immunoglobulin kappa locus seems generally to be well conserved among different populations.

V kappa gene segments rearranged in chronic lymphocytic leukemia are distributed over a large portion of the V kappa locus and do not show somatic mutation

The structure of the human V kappa locus has been thoroughly investigated, but how the germ-line V kappa gene segment repertoire is actually sampled in kappa chain gene rearrangements is not known. In order to begin to answer this question we have polymerase chain reaction (PCR) amplified the rearranged V kappa genes from 26 kappa-expressing cases of chronic lymphocytic leukemia (CLL), followed by cloning and sequencing of the PCR product. All four V kappa gene families were represented amongst rearranged genes. In 25 out of 32 cases, the sequence of the rearranged gene matches perfectly that of 1 of 11 different known germ-line V kappa genes, indicating that no somatic mutation has occurred. Of the remaining 7 rearranged V kappa genes, 4 differ from known germ-line genes by only one or two amino acid residues; and 3 differ from each other and from all known sequences by 5 or more residues, suggesting that somatic mutation has occurred in these 3 cases. We conclude that: (a) in at least three-quarters of cases the rearranged genes are unmutated; (b) there is preferential usage of individual V kappa genes but not of V kappa gene families; and (c) the V kappa genes used are widely dispersed in the V kappa locus.

Immunoglobulin kappa light chain germ-line transcripts in human precursor B lymphocytes

B lymphoblastoid cell lines (BLCL), established from bone marrow and peripheral blood mononuclear cells from two severe combined immunodeficiency (SCID) patients, manifested a complete absence of genomic rearrangements of the immunoglobulin (Ig) heavy (H) and light (L) chain loci. The BLCL contained germ-line transcripts of the Ig kappa region locus of approximately 1.2 kilobase (kb). By cDNA cloning and sequence analysis the transcripts were shown to consist of a C kappa segment, a J kappa 1 gene segment, 160 base pairs (bp) of J kappa 1 5' intervening sequence, containing the heptamer/nonamer recombination recognition sequences and at the 5' end a 523-bp segment designated human kappa zero, The first 206 bp of this 5' segment were homologous to the reported murine kappa zero region. Genomic restriction mapping and DNA sequence analysis demonstrated that the human kappa zero segment is located approximately 4 kb upstream of J kappa 1. The kappa zero segment contains a putative promoter region with an OCT2 binding site, and has a splice donor site to accomplish splicing to an acceptor site 160 bp upstream of J kappa 1. Expression of the kappa zero gene segment was found in BLCL derived from normal fetal bone marrow, in which both Ig kappa loci were in the germ-line configuration. These findings indicate that the described transcripts are not only present in SCID, but also in normal developing pre-B lymphocytes. The expression of germ-line Ig kappa L chain transcripts may be associated with the locus becoming accessible to gene rearrangement.

Ongoing V kappa-J kappa recombination after formation of a productive V kappa-J kappa coding joint

V kappa genes of man can recombine with the J kappa gene segments either by an inversion or by a deletion mechanism. Back-to-back fusion products of the respective recombination signal sequences (signal joints) are retained on the chromosome after the formation of a V kappa-J kappa coding joint by an inversion. Our knowledge of the structure of the human kappa locus and the application of the polymerase chain reaction allowed us now to establish a direct relationship between different kappa recombination products in the lymphoid cell line JI. Two consecutive inversions fully explain the existence of two coding joints and two signal joints on the same chromosome of this cell line. Although the initially formed coding joint is productively rearranged and expressed, a second V kappa-J kappa rearrangement took place which leads to an aberrant joint. In this process a J kappa gene segment of the signal joint that had been created in the first V kappa-J kappa joining was used as the recombination target. The sequence of the two rearrangements is unequivocal since a product of the first (productive) reaction is a partner in the second (aberrant) one.

Polymerase chain reaction-based genotyping for allotypic markers of immunoglobulin kappa shows allelic association of Km with kappa variable segment

Allotypic markers of immunoglobulin kappa (Km) may be determined using a novel method of amplification of the constant segment (C kappa) (IGKC) by polymerase chain reaction (PCR) followed by restriction enzyme digestion. Restriction sites in the C kappa PCR product correlate with allotypic differences among Km(1), Km(1,2), and Km(3) alleles. An AccI site in the PCR product correlates with Km(3); and presence or absence of a MaeII site correlates with the Km(1) or Km(1,2) allele, respectively. Km allelic frequencies were determined in a Caucasian population and compared to genotypic frequencies of nearby polymorphic markers. Among unrelated individuals with rheumatoid arthritis (RA) and controls, there is no evidence of allelic association between CD8A and polymorphic markers of the immunoglobulin kappa region [a V kappa (IGKV) BglII polymorphism about 24 kb centromeric to C kappa, Km allotype, and a SacI polymorphism 3.5 kb telomeric to the C kappa segment]. Similarly, there is no allelic association of the SacI C kappa polymorphism with Km or with the BglII V kappa polymorphism. However, there is evidence of allelic association of V kappa B3 and Km, specifically between the V kappa BglII 2.2-kb allele and Km(3) and also between the V kappa 3.5-kb allele and Km(1,2). Therefore, Km typing by PCR-based methods suggests the presence of allelic association between polymorphisms within the coding region of the C kappa segment and the nearest V kappa segment.

The human immunoglobulin kappa locus. Characterization of the duplicated A regions

The central regions of the kappa locus, the so-called A regions, have been fully characterized on cosmid and phage lambda clones. The regions, which are parts of the C kappa-proximal and -distal copies of the locus and are, therefore, called Ap and Ad regions, comprise about 140 kb each and contain together 30 V kappa genes and pseudogenes. The A regions have been linked on their 5' sides to the O regions and on their 3' sides to the L regions. Chromosomal walking has eliminated a previous gap in the Ap region. Detailed restriction maps of the Ap and Ad regions and the sequences of 9 V kappa genes are reported. Four events, which have occurred in evolution probably after the duplication of the A region, were identified: the insertion of an Alu element in Ad; the insertion of part of a LINE element in Ap; the deletion of a 17.5-kb fragment including one V kappa gene from Ap; the sequence divergence of duplicated V kappa gene regions which ranges among the five pairs studied here from 0 to 14 bp per kb and converted two genes to pseudogenes while their duplicates stayed functional. An analysis of the A regions of the lymphoid cell lines RPMI 6140 and GM607 confirmed the previous finding that the V kappa-J kappa rearrangement in these cell lines had occurred by deletion and inversion mechanisms, respectively. Thus, the structural data contribute to the understanding of the evolution and the functioning of the A regions of the kappa locus.

Variable-constant segment genotype of immunoglobulin kappa is associated with increased risk for rheumatoid arthritis

OBJECTIVE

To further investigate the association of rheumatoid arthritis (RA) with a particular genotype identified by a restriction site polymorphism near the constant segment of immunoglobulin kappa (C kappa).

METHODS

The frequencies of genomic DNA polymorphisms detected within or near C kappa (the most C kappa-proximal variable segment [V kappa] B3 and a T lymphocyte marker [CD8A]) were determined by Southern blotting and hybridization. The frequencies of coding-region polymorphisms of C kappa (Km allotypes) were determined by amplification by polymerase chain reaction followed by restriction enzyme digestion.

RESULTS

Although the frequencies of B3, Km, and CD8A genotypes were not different between RA and normal control populations, more individuals were homozygous for both C kappa and B3 in the RA group (relative risk 2.2, P less than 0.01), especially in the DR4-negative RA subgroup (relative risk 3.9, P less than 0.001).

CONCLUSION

The homozygous genotype of an approximately 30,000-base region including the C kappa segment confers an elevated risk for RA, particularly in the DR4-negative subgroup.

Genetic studies of four highly homologous rheumatoid factor-associated Vk genes in rheumatoid arthritis patients and normal individuals

Rheumatoid factors (RFs) are autoantibodies directed against IgG molecules. They are present in increased quantity in most patients with rheumatoid arthritis (RA), and are implicated in tissue damage in this disease. Paradoxically, recent studies of RFs have revealed that these autoantibodies are likely a physiological component of the immune system, and may play a role in the development and function of the B cell repertoire. Previously, we found that a significant fraction of RA patients express RF bearing the 6B6.6 cross-reactive idiotype, which is a phenotypic marker of the Humkv328-like genes. In order to elucidate the possible genetic factors that may contribute to the abnormal production of RFs in RA patients, we studied restriction fragment length polymorphisms (RFLP) of four highly homologous RF-related kappa light chain variable region (Vk) genes (i.e. Humkv328, Humkv328h2, Humkv328h5 and Humkv329) in RA patients and normal controls. The results show that kv328, kv328h2 and kv329 are likely to be alleles of the kv328 locus, while kv328h5 is a highly homologous Vk gene residing in a separate locus; and that deletion in one copy of either the kv328 or the kv328h5 loci, but not both loci, occurs in several individuals. However, the frequencies of various RFLP patterns of these two Vk gene loci are similar in patients and normals.

Polymorphisms and haplotypes in the human immunoglobulin kappa locus

By comparing the restriction patterns of the DNA from 23 unrelated individuals 16 polymorphisms were defined which allowed us to differentiate between the duplicated copies Op, Ap, Lp and Od, Ad, Ld of the kappa locus (p for the C kappa proximal, d for the distal copy). Some of these duplication-differentiating polymorphisms or DDP revealed also allelic differences between individuals; they are therefore restriction fragment length polymorphism (RFLP) markers at the same time. Three RFLP in the single copy B-J kappa-C kappa region were included into the study. Three basic haplotypes were derived from the combined genotype data, haplotypes N, G and 11. The latter haplotype in which the whole distal copy of the kappa locus is missing was found three times among the 46 haploid genomes studied. The genotypes of the family members of an individual who is homozygous for haplotype 11 are consistent with Mendelian inheritance. Haplotypes N and G are distinguished from each other by eight RFLP markers. Six additional haplotypes, which were found in one or several individuals each, can be derived from the basic haplotypes N and G by hypothetical recombination and/or mutation events.

The human immunoglobulin kappa locus. Characterization of the duplicated O regions

Two large regions of the human immunoglobulin kappa locus, the so-called O regions, have been characterized on cosmid and phage lambda clones. The two regions are very similar but not identical duplicates belonging to the C kappa proximal (p) and the distal (d) copies of the kappa locus. The Op and Od regions comprise contigs of 90 and 120 kb, respectively, and contain 20 V kappa genes and pseudogenes which have been sequenced. Three pairs of V kappa genes were found to be practically identical in the duplicates while allotypic differences, at least for two of the genes, are considerable. The similarities between the duplicate genes may be related to the fact that the two copies of the kappa locus are arranged in a palindrome-like fashion with the 5' sides of the O regions pointing towards each other (C kappa J kappa B Lp Ap Op-Od Ad Ld). This may have contributed to equalizing the sequences. Beyond Op and Od no further V kappa genes were found within about 80 kb. Instead, repetitive DNA sequences have been localized there, the structures of which suggest that they may have been involved in the evolution of the V kappa gene-containing regions. The V kappa pseudogene containing W regions, that had been transposed in evolution from the short to the long arm of chromosome 2 by a pericentric inversion, may have been derived from the O regions according to structural homologies between defined sections of the O and W regions.

V lambda and J lambda-C lambda gene segments of the human immunoglobulin lambda light chain locus are separated by 14 kb and rearrange by a deletion mechanism

We have cloned a region of 124 kb of the human immunoglobulin lambda light chain locus on chromosome 22 encompassing seven V lambda and seven J-C lambda gene segments. No further C lambda gene segment was found in a region of 35 kb downstream of C lambda 7, which encodes the Ke+Oz- isotype. The C lambda proximal V lambda gene segment V lambda III. 1 is located 14.5 kb upstream of C lambda 1. The five sequenced V lambda genes have the same transcriptional orientation as the J-C lambda gene segments which is likely to be true for the majority of the V lambda gene segments in the human lambda locus and which suggests a deletion mechanism for DNA rearrangement. This is supported by hybridization of V lambda gene probes to germ-line and rearranged DNA from lambda light chain-producing cell lines. Sequences of 23 cDNA clones allow to establish a V lambda subgroup classification based on nucleic acid sequence data and an estimate of the J-C lambda usage.

Induced rearrangement of kappa genes in the BLIN-1 human pre-B cell line correlates with germline J-C kappa and V kappa transcription

The human pre-B acute lymphoblastic leukemia cell line, BLIN-1, has been previously shown to undergo kappa light chain rearrangement in vitro, making it a valuable resource for analyzing pre-B to B cell differentiation. We have examined the recombination potential of BLIN-1 by characterizing several independently derived kappa-expressing subclones for DNA rearrangement and V kappa gene usage. Analysis of five kappa-expressing subclones (all having the same heavy chain rearrangement) demonstrated independent kappa light chain rearrangement events by DNA hybridization analysis. Northern blot analysis using probes recognizing the four different V kappa families revealed that two subclones used the most proximal V kappa (V kappa IV), one subclone used a V kappa I, and one subclone used a V kappa II. By polymerase chain reaction analyses, we detected transcripts from rearranged V-J-C kappa genes as well as transcripts from germline J-C kappa and V kappa in BLIN-1 cells induced to rearrange the kappa locus. kappa germline transcripts were also detected in normal developing B cell populations in fetal liver and bone marrow. Our collective results indicate that: (a) BLIN-1 can be induced to rearrange the kappa locus, and this correlates with the expression of germline kappa locus transcripts that may play a role in activating or targeting gene rearrangement; and (b) active rearrangement and usage of V genes representing different kappa families suggest that, like in the mouse, repertoire diversification in humans occurs in the presence of a fixed heavy chain rearrangement.

Megabase inversions in the human genome as physiological events

The genes of the immunoglobulin kappa light chains are assembled during B-cell differentiation by somatic recombination of one of the V kappa (variable) gene segments and the J kappa-C kappa (joining-constant) gene region. This seems to occur by deletion of the DNa between V kappa and J kappa-C kappa if they are arranged in germ-line DNA in the same transcriptional polarity or by inversion of a fragment containing the V kappa gene if the polarities are opposite. We have cloned 75 V kappa genes and pseudogenes of the human kappa locus and linked them in large contigs. There seem to be no more than 85 such genes, less than 50 of these being potentially functional. Thirty-eight of the cloned genes have the same transcriptional polarity as J kappa-C kappa and are part of the so-called J kappa proximal cluster; 35 genes in a distal cluster (the result of a duplication event in evolution) have a polarity that was suggested to be opposite to the one of J kappa-C kappa. We now show that the V kappa genes of the proximal cluster rearrange by a deletion mechanism whereas the others join J kappa-C kappa by inversion of megabase-sized DNA fragments.

The mouse immunoglobulin kappa light-chain genes are located in early- and late-replicating regions of chromosome 6

The murine immunoglobulin kappa (kappa) light-chain multigene family includes the constant region (C kappa), joining-region genes, and approximately 30 kappa-variable (V kappa) region families. The entire region occupies an estimated 1,000 to 3,000 kilobases, and some V kappa families have been linked by recombinant inbred mapping. The C kappa gene and 14 V kappa families replicated differently among cell lines of lymphoid and nonlymphoid origin. In nonlymphoid cells, the C kappa gene replicated earlier than the V kappa families. A transition from replication during the second third of S phase for the C kappa gene to later replication during S for V kappa families was observed. The V kappa family (V kappa 21) that maps closest to the C kappa gene, replicated during the first half of the S phase; most of the other V kappa families replicated during the second half of S, and some replicated during the last quarter of the S phase. In lymphoid cells, the kappa locus replicated earlier in the pre-B than in the B-cell lines. In one pre-B-cell line, 22D6, the kappa genes examined replicated at the beginning of the S phase. In the B-cell lines, the EcoRI segment containing the transcribed gene replicated near the beginning of the S phase. Other V kappa families replicated within the first two-thirds of S phase. Some linked V kappa families replicated at similar times. In the B-cell lines, a transition from replication at the beginning of S for the transcribed C kappa and V kappa genes and surrounding DNA sequences to later replication for the other V kappa families was observed. However, in contrast to the non-lymphoid cell lines, the replication of this locus occurred predominantly during the first half of S. The kappa locus contains both early- and late-replicating genes, and early replication is usually associated with transcriptional activity. The results are discussed with respect to the organization of transcriptionally active chromatin domains.

The mouse immunoglobulin kappa light-chain genes are located in early- and late-replicating regions of chromosome 6

The murine immunoglobulin kappa (kappa) light-chain multigene family includes the constant region (C kappa), joining-region genes, and approximately 30 kappa-variable (V kappa) region families. The entire region occupies an estimated 1,000 to 3,000 kilobases, and some V kappa families have been linked by recombinant inbred mapping. The C kappa gene and 14 V kappa families replicated differently among cell lines of lymphoid and nonlymphoid origin. In nonlymphoid cells, the C kappa gene replicated earlier than the V kappa families. A transition from replication during the second third of S phase for the C kappa gene to later replication during S for V kappa families was observed. The V kappa family (V kappa 21) that maps closest to the C kappa gene, replicated during the first half of the S phase; most of the other V kappa families replicated during the second half of S, and some replicated during the last quarter of the S phase. In lymphoid cells, the kappa locus replicated earlier in the pre-B than in the B-cell lines. In one pre-B-cell line, 22D6, the kappa genes examined replicated at the beginning of the S phase. In the B-cell lines, the EcoRI segment containing the transcribed gene replicated near the beginning of the S phase. Other V kappa families replicated within the first two-thirds of S phase. Some linked V kappa families replicated at similar times. In the B-cell lines, a transition from replication at the beginning of S for the transcribed C kappa and V kappa genes and surrounding DNA sequences to later replication for the other V kappa families was observed. However, in contrast to the non-lymphoid cell lines, the replication of this locus occurred predominantly during the first half of S. The kappa locus contains both early- and late-replicating genes, and early replication is usually associated with transcriptional activity. The results are discussed with respect to the organization of transcriptionally active chromatin domains.

A segment of human Vh gene locus is duplicated

In humans, the kappa light chain variable region gene (Vk) locus evolved in part by duplications of four large segments. Similarly, some portions of the human heavy chain constant region gene locus are duplicated. Recently, we found that the Humhv3005 Vh gene is highly homologous to the reported 1.9III gene. Subsequently, restriction fragment length polymorphism study of the human Vh locus with a 1.6-kb EcoR1 fragment downstream of the hv3005 gene (termed hv3005/E1.6) suggested that the hv3005 and the 1.9III Vh loci might be generated by duplication from a common-ancestor Vh gene segment. To assess this possibility, we mapped the 15-kb region of the isolated hv3005 clone, beginning from 2 kb upstream, and sequenced the adjacent Vh4 gene (designated Humhv4005) located 10 kb downstream of the hv3005 gene. The result showed that hv4005 shared 99% homology with the 1.9II gene, located about 11 kb downstream of the 1.9III gene. Taken together, these data demonstrate that the hv3005-hv4005 region and the 1.9III-1.9II region arose by a duplication of a common ancestor Vh gene segment.

Direct evidence for intrastrand DNA inversion of kappa immunoglobulin gene segments in two murine plasmacytomas

The products of kappa immunoglobulin gene recombination have been characterized in two murine plasmacytomas to examine the relationship between V-J products and reciprocal elements. By cloning, sequencing, hybridization, and application of the polymerase chain reaction, we have established the direct relationship of the kappa recombination products in these cells. The results provide stronger support for the intrastrand mechanism of kappa gene recombination as well as demonstrating a role for secondary, corrective recombinations.

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.

Three breakpoints of variant t(2;8) translocations in Burkitt's lymphoma cells fall within a region 140 kilobases distal from c-myc

The variant translocations t(2;8) in Burkitt's lymphoma cells join band q24 of chromosome 8, distal from c-myc, to the Igkappa locus, with considerable variation in the location of the breakpoints on chromosome 8. We report the cloning and molecular characterization of a chromosome 8 region, distal from the c-myc locus, which encompasses the breakpoints of the Burkitt's lymphoma cell lines BL64, BL21, and LY91 within 11 kilobase pairs, termed provisionally bvr-1 (Burkitt's variants' rearranging region 1). Using probes from the c-myc, the bvr-1, and the human pvt-1 loci obtained by chromosome walking coupled with pulsed-field gel electrophoresis, we have constructed a physical map of the region 3' of c-myc. We map bvr-1 and pvt-1 about 140 and 260 kilobase pairs, respectively, distal from c-myc.

Three breakpoints of variant t(2;8) translocations in Burkitt's lymphoma cells fall within a region 140 kilobases distal from c-myc

The variant translocations t(2;8) in Burkitt's lymphoma cells join band q24 of chromosome 8, distal from c-myc, to the Igkappa locus, with considerable variation in the location of the breakpoints on chromosome 8. We report the cloning and molecular characterization of a chromosome 8 region, distal from the c-myc locus, which encompasses the breakpoints of the Burkitt's lymphoma cell lines BL64, BL21, and LY91 within 11 kilobase pairs, termed provisionally bvr-1 (Burkitt's variants' rearranging region 1). Using probes from the c-myc, the bvr-1, and the human pvt-1 loci obtained by chromosome walking coupled with pulsed-field gel electrophoresis, we have constructed a physical map of the region 3' of c-myc. We map bvr-1 and pvt-1 about 140 and 260 kilobase pairs, respectively, distal from c-myc.

Rearrangement by inversion of a T-cell receptor delta variable region gene located 3' of the delta constant region gene

We have located a T-cell receptor variable (V) delta gene segment immediately 3' of the delta constant (C) region gene and 5' to the known joining (J) alpha gene segments. This V delta gene is in the opposite transcriptional polarity to C delta and has rearranged to C delta by inversion in a gamma/delta-expressing hybridoma, DN7.3. This V delta gene is commonly rearranged in adult but not fetal gamma/delta-expressing thymocytes and has not been observed among alpha gene rearrangements reported to date. The reciprocal joining sequence isolated from this cell line contains N region nucleotides between the recombination signal sequences, in contrast to previously analyzed reciprocal joints. The results are discussed in the context of models accounting for ordered V gene usage during lymphocyte development.

Anti-DNA antibodies, autoimmunity and the immunoglobulin repertoire

The advent of hybridoma and recombinant DNA technology about a decade ago has allowed a detailed analysis the structure, properties and molecular genetics of antibodies. These techniques, combined with studies of idiotypes and of Abelson-transformed and other cell lines, have resulted in major findings which are of particular importance to both the normal immune system and to autoimmunity. The rearrangement and expression of antibody genes in the normal immune system are discussed first, as a background for an appreciation of the significance of the molecular genetics of autoantibodies. We then turn to autoantibody genes, with an emphasis on anti-DNA antibodies and their role in the autoimmune disease, systemic lupus erythematosus. A model for the genetics of lupus which includes a possible role for Ig genes is considered.

Correct in vivo splicing of the mouse immunoglobulin kappa light-chain pre-mRNA is dependent on 5' splice-site position even in the absence of transcription

In transcripts from the rearranged mouse immunoglobulin kappa light-chain locus, the intron separating the variable (V) plus joining (J) exon from the constant (C) exon contains up to three additional J regions, each with a functional 5' splice site. Previously, HeLa cells transfected with DNA encoding kappa light chains have been shown to mimic kappa-producing lymphocytes in splicing exclusively to the upstream-most 5' splice site, whereas selectivity is lost when kappa transcripts containing two more J regions are incubated in HeLa cell or lymphocyte nuclear extracts. Here we demonstrate that the fidelity of in vivo splicing depends on neither V-J rearrangement, the instability of erroneously splicing transcripts, nor a hierarchy of J-region 5' splice site utilization. Analysis of the splicing of presynthesized kappa transcripts injected into Xenopus oocytes demonstrates the correct 5' splice-site selection is independent of transcription. Implications for in vitro studies of regulated splice-site pairing are discussed.

The J kappa proximal region of the human K locus contains three uncommon V kappa genes which are arranged in opposite transcriptional polarities

The structure of one of the V kappa gene-containing regions of the locus coding for the human immunoglobulin light chains of the kappa type is described. This so-called B region contains three genes: B1, B2 and B3. According to its sequence B1 is a pseudogene which does not fit well into the present subgroup classification. In lymphoid cell lines the B1 gene region is frequently deleted. B2 and B3 are the previously reported EV15 and V kappa IV genes. The transcriptional polarity of the B1 gene is found to be opposite to one of the B2 and B3 genes. This observation together with the fact that the B region is proximal to the J kappa C kappa gene segment leads to the conclusions to the mechanism of the V kappa-J kappa recombination and allows us to explain the formation of the recombination products in a particular cell line by two consecutive inversions.