Contribution of immunoglobulin heavy-chain variable-region genes to antibody diversity

Differential reactivity of germ line allelic variants of a broadly neutralizing HIV-1 antibody to a gp41 fusion intermediate conformation

Genetic factors, as well as antigenic stimuli, can influence antibody repertoire formation. Moreover, the affinity of antigen for unmutated naïve B cell receptors determines the threshold for activation of germinal center antibody responses. The gp41 2F5 broadly neutralizing antibody (bNAb) uses the V(H)2-5 gene, which has 10 distinct alleles that use either a heavy-chain complementarity-determining region 2 (HCDR2) aspartic acid (D(H54)) or an HCDR2 asparagine (N(H54)) residue. The 2F5 HCDR2 D(H54) residue has been shown to form a salt bridge with gp41 (665)K; the V(H)2-5 germ line allele variant containing N(H54) cannot do so and thus should bind less avidly to gp41. Thus, the induction of 2F5 bNAb is dependent on both genetic and structural factors that could affect antigen affinity of unmutated naïve B cell receptors. Here, we studied allelic variants of the V(H)2-5 inferred germ line forms of the HIV-1 gp41 bNAb 2F5 for their antigen binding affinities to gp41 linear peptide and conformational protein antigens. Both V(H)2-5 2F5 inferred germ line variants bound to gp41 peptides and protein, including the fusion intermediate protein mimic, although more weakly than the mature 2F5 antibody. As predicted, the affinity of the N(H54) variant for fusion-intermediate conformation was an order of magnitude lower than that of the D(H54) V(H)2-5 germ line antibody, demonstrating that allelic variants of 2F5 germ line antibodies differentially bind to gp41. Thus, these data demonstrate a genetically determined trait that may affect host responses to HIV-1 envelope epitopes recognized by broadly neutralizing antibodies and has implications for unmutated ancestor-based immunogen design.

Genetic diversity of the human immunoglobulin heavy chain VH region

The human immunoglobulin heavy chain VH region is one of the most complex regions in the human genome. The high level of diversity of this region has been shown by a number of studies. However, because of the limitations of the conventional experimental methods, it has been difficult to learn the extent of the diversity and the underlying mechanisms. This review describes a number of new genetic approaches developed in the authors' laboratory. By using these approaches, significant progress has been made in assigning different VH sequences to their respective loci, in learning the diversity of gene segment number and composition among the VH haplotypes, and in learning VH gene segment organization in individual haplotypes. Information obtained toward this direction could help in understanding the mechanisms underlying VH region diversity and the biological impact of the VH region diversity.

Diversity of the immunoglobulin heavy chain in the Atlantic salmon (Salmo salar L.) is contributed by genes from two parallel IgH isoloci

Immunoglobulin heavy chain (IgH) variable (V) region cDNAs from the Atlantic salmon, Salmo salar L., have been isolated and analysed with respect to diversity and transcription of the two parallel IgH isoloci in this species. A total of nine V(H) families were defined according to the 80% identity criterion, of which seven were highly related (>80% identity) to the V(H) families defined in rainbow trout and arctic charr. The variability of the CDR1 and 2 was low, although mutational hot-spot consensus sequences were accumulated in these regions. The CDR3 showed largest variability, expressing at least eight different groups of D motifs diversified by fusion of the D motifs, possible N and P nucleotide insertions and exonuclease activity. Presumably functional transcripts expressing D motifs in all three reading frames were identified for two of the motifs. The cDNAs were mapped to either of the two parallel loci, and sequence analysis revealed that the repertoire of V(H) segments was contributed by transcription of genes from both of the IgH isoloci. Transcription of genes from both isoloci generated no obvious effects on variability in the CDR3 of the Atlantic salmon IgH chains, although one additional J(H)-segment with altered N-terminal was generated by the process of duplication and divergence. Thus, the issue of biological significance of the two IgH isoloci remains unclear.

Characterization of a murine immunoglobulin VH gene segment in subgroup III: a new member of the 7183 gene family

A new gene for the variable region of the immunoglobulin heavy chain (VH gene) has been isolated from BALB/c adult liver DNA using a cDNA plasmid probe containing a mouse VH sequence. The complete nucleotide sequence of this germline gene (VH10-19), shows that it belongs to the 7183 gene family. The VH gene appears to contain an intervening 104-base-long sequence and displays the same recombination signal sequences that those observed in the germline 81X. The presence of an internal heptamer at the 3' end of the VH10-19 coding region let an alternative recombination event that could increase the representation of this gene in the immature repertoire.

Molecular and serological diversity of anti-DNA autoantibodies from NZB and (NZB X NZW) F1 mice

We have carried out an analysis of the serological and molecular diversity of a panel of monoclonal anti-DNA autoantibodies and serum autoantibodies from NZB and (NZB X NZW) F1 mice, in an attempt to obtain insights into the mechanisms responsible for the development of systemic autoimmune disease. Our data show that the autoantibodies are quite diverse. A dominant, binding-site idiotope on one of our monoclonal autoantibodies is expressed at variable levels in anti-DNA binding antibodies in the sera of both NZB and (NZB X NZW) F1 mice, but on none of the other monoclonal autoantibodies in our panel. We have cloned and sequenced the heavy chain variable region (VH) gene of one anti-DNA hybridoma and by hybridization have determined the VH and V kappa gene segments expressed by 14 others. All of the autoantibodies express members of known V gene subfamilies. A total of four different VH and at least six V kappa subfamilies are expressed by the hybridomas. Thus, a broad spectrum of the total murine Ig repertoire is represented in the anti-DNA autoantibodies present in these strains.

A VH gene is located within 95 Kb of the human immunoglobulin heavy chain constant region genes

Using cosmids covering about 117 Kb upstream of the human immunoglobulin chain C mu gene, we have identified a potentially functional VH gene, belonging to the VHVI subgroup. This VHVI gene is only about 95 Kb from the C mu gene and is probably the first functional VH segment of the Igh locus. These results illustrate the proximity of the human VH, DH and JH segments involved in creation of the complete heavy chain genes.

Human immunoglobulin heavy-chain-variable (VH) region gene families defined by hybridization with cloned human and murine VH-genes

The Southern DNA hybridization technique was used to determine the organization of human immunoglobulin heavy-chain-variable region (VH) gene families and the extent of polymorphism within these families. Human DNA was digested with a restriction enzyme and then hybridized to a cloned human or murine VH gene. Six human and six murine genes were used. Hybridization patterns seen in the human genes fell into three groups, which corresponded to the Kabat subgroup assignments based on sequence. When DNA from different individuals was compared, polymorphism was demonstrated in each of the three gene families. The VH II family demonstrated a higher degree of polymorphism than the others. Hybridization with the murine probes, each of which represented a different murine VH-gene family, revealed six distinct patterns of hybridization. Five of the probes detected all or a portion of one of the previously defined human families. The sixth probe, 36-60, yields a unique pattern of hybridization, suggesting a fourth VH-gene family. Dot hybridizations show that 36-60 does not hybridize with human VH-genes representing each of the known families, further supporting this possibility.

Generation of diversity of the beta chain of the human T-lymphocyte receptor for antigen

Human T-cell receptor beta-chain (Ti beta) genes are formed by the rearrangement of variable (V), diversity (D), and joining (J) gene segments. A comparison of the nucleotide and deduced amino acid sequences of the variable regions of six human Ti beta cDNAs reveals that they display a level of homology similar to that shared by human immunoglobulin heavy chain V genes. In contrast to immunoglobulin V regions, which contain three discrete regions of hypervariability, the Ti beta V regions display a more widely distributed pattern of variability. Southern blot analyses show that most human Ti V beta gene families contain one to three members. However, a single family containing at least eight members is identified. This analysis allows the identification of at least 15 human Ti V beta germ-line genes. The sequence data show that at least one germ-line Ti beta J gene is used preferentially in Ti beta cDNAs. Moreover, they suggest the presence of at least four human germ-line Ti beta D genes. At least three mechanisms are involved in generating the diversity of human Ti beta genes: (i) the combinatorial rearrangement of different V, D, and J genes; (ii) imprecise V-D-J joining, including V-D joining in any of three translational reading frames; and (iii) the addition of extra nucleotides at the V-D-J joints (N-region diversity).

Complete nucleotide sequences of three VH genes in Caiman, a phylogenetically ancient reptile: evolutionary diversification in coding segments and variation in the structure and organization of recombination elements

Complete nucleotide sequences are described for three caiman (Caiman crocodylus crocodylus) immunoglobulin VH genes (C3, E1, and G4) that hybridize with a murine VH probe. The E1 and G4 genes are physically linked (intergenic distance, approximately equal to 6.5 kilobases) in the same transcriptional orientation but are not directly contiguous with the C3 gene. When the coding segments, including both framework and complementarity-determining regions, of these genes and the murine probe sequences are compared by metric analysis, it is apparent that the caiman genes are only slightly more related to each other than to the mammalian sequence, consistent with significant preservation of nucleotide sequence over an extended period of phylogenetic time. Based on the presence of transcriptionally critical 5' sequences and the absence of terminator codons, frameshift mutations, or other recognizable alterations, the genes do not appear to be pseudogenes. The E1 gene, however, is distinguished from other VH genes because (i) the spacer region within the 3' recombination signal sequence is 12 base pairs, typical of VK genes but not of VH genes, which possess 22- to 23-base-pair spacers and (ii) a near-perfect VH recombination signal sequence is present within the intervening sequence that splits the segment encoding the leader. These studies establish VH gene multiplicity in a species that arose prior to mammalian radiation and provide a description of differences in the configuration and location of recombination elements associated with an otherwise potentially functional gene.

Genetic polymorphism at the kappa chain locus in mice: comparisons of restriction enzyme hybridization fragments of variable and constant region genes

Variable (V kappa) and constant (C kappa) region genes of the mouse kappa light chain have been compared in inbred strains and in geographically isolated or genetically separated populations of mice by Southern blot analysis of endonuclease-restricted germline DNA. In most cases, the C kappa gene is found on a single restriction fragment while the V kappa genes of the V kappa 19 and V kappa 21 groups are each found on several (6-18) fragments. The restriction fragment (RF) patterns of V kappa 19 and V kappa 21 groups are both polymorphic when compared among inbred mouse strains. Southern blot patterns of V kappa 21 and V kappa 19 of inbred strains are also found among some geographically isolated populations of mice, suggesting that inbred strains acquired kappa loci from different subspecies. Some populations of geographical isolates show V kappa 21, V kappa 19, and C kappa contexts similar to inbred mice while more distantly related species within the genus Mus and laboratory rats show no apparent similarity in context to inbred strains. Variable region genes determining the RF patterns of V kappa 19 and V kappa 21 appear to be linked to each other and to the C kappa and Lyt-3 loci.

Effect of somatic mutation within translocated c-myc genes in Burkitt's lymphoma

Our previous studies of a translocated c-myc gene in the Raji Burkitt's lymphoma cell showed somatic mutations in exons 1 and 2. We have extended these observations to two other translocated c-myc genes and find a common occurrence of mutation in the noncoding exon 1. We also found that in Raji cells, unlike other Burkitt's lymphoma cell lines, the normal allele of the c-myc gene is transcribed as well as the translocated gene. These results support a model in which c-myc oncogene activation in Burkitt's lymphoma occurs by disruption of a normal transcriptional control mechanism in which the c-myc protein is itself involved.

Structural relationships among mouse and human immunoglobulin VH genes in the subgroup III

The mouse VHIII subgroup is composed of four families which share sequence homology. We isolated a VH germ-line genomic clone, which cross hybridizes with a cDNA probe from one of these families, derived from a myeloma secreting an antigalactan antibody. We report here the nucleotide sequence of the cross hybridizing gene and show that very likely it has an anti-sheep red blood cell specificity. Comparison of its nucleotide sequence with those of the three other VHIII families shows that these genes share segmental homologies of variable lengths. This suggests that interchanges of sequence blocks between VH genes could be an important evolutionary mechanism for diversifying the germ-line repertoire. The strong homology (82%) with human VHIII genes suggests that efficient antibody sequences are strongly conserved. This conservation of homology is particularly striking when compared to the more limited homology (63%) between mouse and human C kappa genes.

Immunoglobulin diversity: analysis of the germ-line VH gene repertoire of the murine anti-GAT response

A cDNA clone was constructed from a mRNA encoding an anti-GAT (Glu60 Ala30 Tyr10) BALB/c monoclonal antibody heavy chain. Its sequence, covering codons -5 to 162 and therefore encompassing the complete V-D-J region, was determined. Surprisingly, the sequence of the VH gene-encoded region was almost identical with that of the BALB/c VH anti-HNP (4-hydroxy-3-nitrophenyl) acetyl VH region, suggesting that the same VH germ-line might be used to encode two heavy chains contributing to antibodies of discrete specificities. A specific VH probe was derived and annealed to Eco RI and Bg1 II restriction fragments of liver (unrearranged) DNA extracted from the BALB/c, DBA/2 and C57BL/6 mouse strains that differ in their H chain allotypes. Under stringent conditions, only a few bands were identified by Southern blotting. The different patterns observed suggest that the VH anti-GAT repertoire differs between these strains even though their various anti-GAT antibodies express the same public idiotypic specificities.

Complete nucleotide sequence of an immunoglobulin VH gene homologue from Caiman, a phylogenetically ancient reptile

Immunoglobulin variable (V) gene regions typify extensive multigenic families in terms of overall size, chromosomal arrangement and presence of large numbers of apparent pseudogenes. A unique mechanism of somatic reorganization involving recombination of VH, D and JH or VL and JL segments accompanies the differentiation of lymphoid cells and together with somatic mutation and other types of recombination accounts for V-region diversity. Although these processes have been well characterized in higher mammals, little is known concerning their origin and diversification during phylogenetic time. Previously, we described the blot-hybridization characteristics of murine VHIII probes with restriction enzyme-digested genomic DNA isolated from several phylogenetically critical species, including Caiman crocodylus, a modern representative of an ancient reptilian subclass. Here we have used a murine probe, S107V, to select homologous clones from a library of Caiman genomic DNA constructed in a lambda bacteriophage. The complete nucleotide sequence of a Caiman gene homologous to the murine VH gene and its adjacent 5' and 3' region is described. Comparison of the sequence with mammalian prototypes shows evidence of considerable organizational and structural homology extending outside the presumed VH-coding region and including elements believed to be involved in somatic recombination. Inferences about the evolution of this multigenic family can now be extended to the level of phylogenetic class.

Somatic generation of antibody diversity

In the genome of a germ-line cell, the genetic information for an immunoglobulin polypeptide chain is contained in multiple gene segments scattered along a chromosome. During the development of bone marrow-derived lymphocytes, these gene segments are assembled by recombination which leads to the formation of a complete gene. In addition, mutations are somatically introduced at a high rate into the amino-terminal region. Both somatic recombination and mutation contribute greatly to an increase in the diversity of antibody synthesized by a single organism.

Genetic and temporal control of neonatal antibody expression

Two hybridoma cell lines were established with B cells derived from neonatal BALB/c spleen cells. The anti-dinitrophenyl (DNP) antibodies derived from these lines were characterized with respect to their isotype, affinity, and isoelectric point. Antiidiotypic reagents were prepared that permit an analysis of the representation of antibodies sharing idiotype with these two hybridomas in the developing and mature B cell pool of BALB/c mice (Igha) and other murine strains. One of the two antibodies, TF2-36, was found to be indistinguishable from 14% of anti-DNP monoclonal antibodies derived in fragment culture from spleen cells of 1-4-d-old BALB/c donors. B cells expressing this idiotype were found to represent approximately 2% of the anti-DNP-specific repertoire after the 1st wk of neonatal development and into adulthood. The second hybridoma antibody, TF2-76, was found to be expressed at very low levels during the first several days of neonatal development; however, B cells expressing this idiotype increased in frequency during the 2nd wk of neonatal development representing 7% of all DNP-responsive B cells 12-13 d after birth. The proportion of B cells expressing this idiotype also decreased to approximately 2% in adults. The relatively late appearance of B cells bearing this idiotype was confirmed by their susceptibility to tolerance induction after the 1st wk of neonatal development. Both the early neonatal clonotype, TF2-36, and the late neonatal antibody clonotype, TF2-76, were found to be expressed in a similar fashion in F1 mice constructed between Igha and Ighb parentals, but both were expressed at very low levels during the development of Ighb mice. Thus, the control of the magnitude of expression of these neonatal clonotypes appears to be associated with the Igh locus.

The generation of antibody diversity

By their nature, antibody molecules exhibit a wide range of binding specificities. The antigen-binding properties of the antibody reside entirely in the amino-terminal portion of the molecule, termed the variable domain. Structurally, the combining site specificity is determined by the amino-acid residues within 6 short lengths, 3 each in the heavy and light chains, of usually variable sequence. The hypervariability of 2 of these lengths arises from the somatic recombination of short gene segments into a single stretch of mRNA which encodes the entire variable region of 1 polypeptide chain. For example, a V gene segment that codes for most of the variable portion of a light chain, can combine with one of a number of much shorter J gene segments to create the complete variable region gene. In heavy chain genes, a third element, the D gene segment, increases the potential for diversity even further. A mechanism has been proposed by which variability occurs at the point where 2 gene segments join. Thus, a large part of the generation of antibody diversity occurs in the somatic recombination of small genetic elements.

Organization and evolution of immunoglobulin VH gene subgroups

The organization and evolution of immunoglobulin variable region genes was studied by comparing human and mouse heavy chain variable region (VH) genes. We show that a VH gene subgroup constitutes a physically linked multigene family separated from another VH subgroup. We mapped the VHIII gene subgroup to be 3' to the VHII gene subgroup based on deletion of VH genes after V-D-J rearrangement. The results indicate that the human VHIII gene subgroup underwent a significant gene expansion as compared to the mouse VHIII subgroup. Amino acid sequence data indicate that human VHIII genes correspond to only a small subset of mouse VHIII genes. Human VHIII genes contain a shorter intron and are two codons shorter than most BALB/c mouse VHIII genes. The nature of nucleotide substitutions between VH genes within a species (human) is similar to that between genes of different species (human/mouse). Both contain approximately 50% silent substitutions.

Multiple components in restriction enzyme digests of mammalian (insectivore), avian and reptilian genomic DNA hybridize with murine immunoglobulin VH probes

High molecular weight genomic DNAs isolated from an insectivore, Tupaia, and a representative reptilian, Caiman, and avian, Gallus, were digested with restriction endonucleases transferred to nitrocellulose and hybridized with nick-translated probes of murine VH genes. The derivations of the probes designated S107V (1) and mu 107V (2,3) have been described previously. Under conditions of reduced stringency, multiple hybridizing components were observed with Tupaia and Caiman; only mu mu 107V exhibited significant hybridization with the separated fragments of Gallus DNA. The nick-translated S107V probe was digested with Fnu4H1 and subinserts corresponding to the 5' and 3' regions both detected multiple hybridizing components in Tupaia and Caiman DNA. A 5' probe lacking the leader sequence identified the same components as the intact 5' probe, suggesting that VH coding regions distant as the reptilians may possess multiple genetic components which exhibit significant homology with murine immunoglobulin in VH regions.

Simple DNA sequences in homologous flanking regions near immunoglobulin VH genes: a role in gene interaction?

Five closely related immunoglobulin VH genes (subgroup II) were compared by sequencing of several kb of DNA. In three of the genes homology greater than 75% was found along an area of 4 kb that includes the coding region. The homology in flanking regions is only slightly lower than that in the coding sequences. Two other genes, which are located on the same EcoRI fragment, show high homology to the first three genes in the coding and immediately flanking regions. In more distant flanking regions no homology is found with the first three genes. This indicates that their evolutionary history differs from that of the other three genes. A region of simple DNA sequence composed of repetitive TCC and TCA elements was found at a distance of approximately 380 bp upstream from the initiator ATG of these VH genes. This region is the site where the two sets of genes abruptly start to diverge. The structure of the simple DNA sequence in the various VH genes suggests that it may be involved in gene interaction. We propose that both simple DNA sequences and homology in flanking regions serve a function in the correction of VH genes, which seem to be rather free to diverge and drift into pseudogenes. A correction mechanism may help this gene family to maintain its two major features, multiplicity and diversity.

Functional significance and evolutionary development of the 5'-terminal regions of immunoglobulin variable-region genes

The 5'-terminal sequence of the kappa light-chain gene expressed in MPC11 plasmacytoma cells was definitively determined by analysis of both the kappa mRNA and the gene from which it is transcribed. The distance between the cap site and the translation initiation codon is only 3 nucleotides, and in a minor variant only 2 nucleotides, considerably less than that found in other species of nucleus-derived mRNA. S1 nuclease protection experiments with MPC11 nuclear RNA indicate that the cap sites are coincident with the transcriptional start sites, suggesting that the 5'-terminal heterogeneity is caused by imprecision in transcriptional initiation. A comparison of the 5'-terminal structure of the MPC11 V kappa gene with that of several other V genes indicates that the length of the first exon, which is composed of the 5' untranslated region which is composed of the 5' untranslated region and a sequence encoding most of the signal peptide, is highly conserved. Within this set of examples, the 5' untranslated region varies from 3 to 33 nucleotides, and the signal-peptide-coding block from 46 to 76 nucleotides. This analysis has also provided insight into the genetic origins for two anomalous properties of the MPC11 light chain.

Somatic mutation in genes for the variable portion of the immunoglobulin heavy chain

The size of the gene pool potentially encoding antibodies to p-azophenyl arsonate has been examined. A heavy chain-specific full-length complementary DNA clone has been constructed with the use of messenger RNA from a hybridoma that produces antibodies to the arsonate hapten and bears nearly a full complement of the determinants comprising the cross-reactive idiotype (CRI). The sequences of both the complementary DNA clone and the corresponding immunoglobulin heavy chain have been independently determined. A probe for the variable region gene was prepared from the original heavy chain complementary DNA clone and used to analyze, by Southern filter hybridization, genomic DNA from both A/J (CRI positive) and BALB/c (CRI negative) mice. Approximately 20 to 25 restriction fragments containing "germline" variable region gene segments were detected in both strains, and many are shared by both, Since 35 CRI-positive heavy chains have been partially sequenced thus far and 31 are different, the results of the hybridization analysis suggest that somatic mutation events involving the variable region gene segments of the heavy chain play a role in the origin of the amino acid sequence diversity seen in this system.

Single amino acid substitution altering antigen-binding specificity

S107, a phosphocholine-binding myeloma protein, has been cloned in soft agar, and an antigen-binding variant has been isolated and characterized. The variant does not bind phosphocholine attached to carrier or as free hapten in solution but does retain antigenic determinants (idiotypes) of the parent. Chain recombination experiments suggest that the defect in binding is entirely in the heavy chain. Amino acid sequence analysis showed a single substitution--glutamic acid to alanine at position 35--in the first hypervariable or complementarity-determining region. In terms of the three-dimensional model of the phosphocholine-binding site, glutamic acid-35 provides a hydrogen bond to tyrosine-94 of the light chain that appears to be critical for stability of this portion of the binding site. The removal of this bond and the presence of the smaller alanine side chain is thus consistent with the loss in binding activity. These results suggest that small numbers of substitutions in antibodies, such as those presumably introduced by somatic mutation, may in some situations be effective in altering antigen-binding specificity.

Organization, structure, and assembly of immunoglobulin heavy chain diversity DNA segments

We have identified, cloned, and sequenced eight different DNA segments encoding the diversity (D) regions of mouse immunoglobulin heavy-chain genes. Like the two D segments previously characterized (16, 17), all eight D segments are flanked by characteristic heptamers and nonamers separated by 12-bp spacers. These 10 D segments, and several more D segments identified but not yet sequenced, can be classified into three families based on the extent of sequence homology. The SP2 family consists of nine highly homologous D segments that are all 17-bp long and clustered in a chromosomal region of approximately 60 kb. The FL16 family consists of up to four D segments, two of which were mapped in the 5' end region of the SP2-D cluster. The two FL16D segments are 23 and 17 bp long. The third, the Q52 family, is a single-member family of the 10-bp-long DQ52, located 700 bp 5' to the JH cluster. We argue that the D-region sequences of the majority of heavy chain genes arise from these germline D segments by various somatic mechanisms, including joining of multiple D segments. We present a specific model of D-D joining that does not violate the 12/23-bp spacer rule.

Transcriptional regulation of immunoglobulin V genes

The relative transcriptional activity of rearranged and unrearranged (germline) VK genes in secreting plasmacytoma cells was assessed by two independent methods. Measurements of V sequence abundance by hybridization kinetic (Rot) analysis indicated that the steady state content of transcripts from a rearranged VK gene is at least 16,000-fold greater than that from an unrearranged VK gene. Direct measurements of transcriptional activity in isolated nuclei indicated that this difference is due, in large part to a difference in transcription rate. Since the primary sequences of V genes and their 5' flanking regions are not altered during rearrangement, these results suggest that VK gene transcription might be controlled by elements on the 3' side of the VK genes or at the CK locus, perhaps via an influence on chromatin structure.

Polymorphism of germ-line immunoglobulin VH genes correlates with allotype and idiotype markers

The polymorphic nature of the immunoglobulin VH genes was investigated by Southern blot analysis of liver DNA of sixteen different mouse strains and hybridization with VH probes. Differences in restriction enzyme pattern (REP) were observed and six different patterns of restriction fragments were found for the sixteen strains analyzed. No equivalent polymorphism was observed in another multigene family, the actins. The six patterns correlate with immunoglobin constant region allotypes (Igh-1). Experiments with Igh-1-congenic strains suggest that the VH REP is linked to immunoglobulin constant region haplotype. Mouse strains which share inherited idiotypes also share identical VH restriction pattern. This provides a structural basis for the genetic linkage between idiotypes and allotypes. It also indicates that different strains carry different VH gene repertoires, which may be the basis for the expression of different inherited idiotypes in various strains. We propose that a VH group in a set of linked genes that are coinherited as a cluster with the constant region genes and that VH and Ch can be regarded as an extended haplotype.

Mouse heavy chain variable regions: nucleotide sequence of a germ-line VH gene segment

We have constructed a library of Balb/c mouse embryo DNA in the vector Charon 4A. The library was searched for sequences homologous to the VH region of a cloned cDNA of the UPC10 heavy chain mRNA. In this paper, we describe the structure and the partial nucleotide sequence of one of such clones (VH441). The nucleotide sequence of this germ-line gene indicates that it encodes amino-acids 1-98 of the X44 and J601 galactan-binding VH regions, but that it differs from the UPC10 VH segment by four single base changes. The VH gene appears to contain a 101 bases long intervening sequence within a precursor sequence identical to the precursor sequence of UPC10. The 3' non coding sequence of the V gene contains the two conserved sequences found in embryonic V DNA segments, CACAGTG and ACATGAACC, separated by 23 nucleotides and a sequence CACTGTG separated by 33 nucleotides from the first heptamer.

Diversity of germ-line immunoglobulin VH genes

The sequences of four embryonic mouse immunoglobulin VH genes have been compared. All genes end at codon 98 and code for a hydrophobic signal peptide of 19 residues interrupted at codon -4 by an intron of 83 base pairs. Substitutions occur in all gene segments but at a significantly higher frequency in the hypervariable regions. The data suggest an evolutionary basis for the diversity of immunoglobulin genes. Divergence resulted also in a termination codon in two of the genes, suggesting that part of the V gene repertoire cannot be expressed unless some correction mechanism is available.

Human V kappa immunoglobulin gene number: implications for the origin of antibody diversity

To assess the relative contributions of germline versus somatically mutated genes in the human immune system, we have examined the size of the kappa light-chain variable region (V kappa) gene pool. Two cloned kappa subgroup 1 (V kappa 1) gene probes detected the same family of 15 to 20 crosshybridizing restriction fragments in human DNA, whereas flanking region probes detected fewer hybridizing fragments. Most of the hybridizing bands represent single-copy genes, as judged by a "'gene titration" experiment. Furthermore, the number of hybridization bands is a good estimate of the haploid gene number, since we observed little polymorphism of restriction sites in the V kappa locus of eight unrelated people. A cloned V kappa 3 probe hybridized to essentially the same 15--20 genes in human DNA as the V kappa 1 probes. These results strongly suggest that a discrete family of 15--20 genes constitutes a large proportion of the V genes from three of the four V kappa subgroups. The small number of V kappa genes in the human genome supports the idea that somatic mutation plays a major role in the origin of antibody diversity in man.

Identification of D segments of immunoglobulin heavy-chain genes and their rearrangement in T lymphocytes

The finding that the diversity (D) and joining (JH) but not the variable (VH) DNA segments of mouse immunoglobulin heavy-chain genes are joined in the DNA of some cloned cytolytic T cells, led to identification and sequencing of three different D DNA segments. Two segments identified on the embryo DNA carry on both the 5' and 3' sides two sets of characteristic sequences separated by a 12-base pair spacer, which have been implicated as recognition signals for a recombinase. The third segment, identified in a form joined with a JHDNA segment in a T cell, carries the recognition signal on the 5' side. These results support the 12/23-base pair model for somatic generation of immunoglobulin V genes, and rule out the possibility that the cytolytic T cells use assembled VH, D and JH sequences to encode their antigen receptors.

Human immunoglobulin variable region genes--DNA sequences of two V kappa genes and a pseudogene

The study of immunoglobulin genes at the molecular level can allow us to elucidate the origin of antibody diversity. Investigations of immunoglobulin gene structure in the mouse have shown that light chains are encoded by three gene segments: the C gene encoding the constant region and the V and J genes encoding the variable region. In antibody-producing cells the V and J genes join together to create a complete immunoglobulin gene. No data are available on the structure of human light chain variable region genes, but the variable regions of over 150 human kappa light chain proteins have been sequenced and they comprise four distinct subgroups. Here we report the complete DNA sequences of three human kappa variable region (V kappa) genes isolated from fetal liver DNA. The sequences demonstrate that two non-allelic genes encoding subgroup I proteins have more than 90% nucleotide homology in both proteins coding and non-coding regions. Comparison of these human genes with two complete DNA sequences of mouse V kappa genes shows that V kappa gene structure is highly conserved between the two species, which suggests that V kappa genes rearrange during the differentiation of human lymphocytes by a very similar mechanism to that in the mouse. The sequence of a defective V kappa gene is also described--this gene is unable to code for a functional immunoglobulin due to substitutions, deletions and insertions in its sequence. It is analogous to the pseudogenes of globin and Xenopus 5S RNA.

Transcripts of the immunoglobulin C mu gene vary in structure and splicing during lymphoid development

Two classes of transcripts of the mouse immunoglobulin mu constant region (C mu) gene can be distinguished. Whereas B cells contain mu mRNAs of 2.4 and 2.7 kilobases (kb), many T lymphoma, Abelson pre-B lymphoma, and myeloid tumor cell lines contain polyadenylylated RNA species bearing C mu sequences (C mu RNAs) of 1.9, 2.1, 2.3, and 3.0 kb. Production of C mu RNAs, unlike mu mRNAs, does not require recombination with the joining region (JH) locus. To define the structure of C mu RNAs, RNA from representative cell lines was fractionated by gel electrophoresis, transferred to diazobenzyloxymethyl paper, and tested for hybridization with 23 DNA fragments that collectively span a chromosomal mu gene, cloned from a plasmacytoma. All the C mu RNAs bear sequences derived from each of the four C mu domains, but none contain the intervening sequences separating domains; thus each represents a spliced RNA species. The 1.9-kb C mu RNA contains the 3' sequence characteristic of secreted mu chain, whereas the longer species bear that of membrane-bound mu chin. Hence C mu RNAs and mu mRNAs are equivalent throughout the C mu and 3' terminal regions. They differ markedly, however, in their 5' regions, because the 3.0-and 2.3-kb C mu RNAs bear sequences from within the conventional JH-C mu intervening sequence. Because these sequences are several kb from C mu, this region must contain at least one hitherto unsuspected splice site. C mu RNAs may not express immunological diversity, because no evidence was found that they bear variable regions. T and pre-B lymphoid and myeloid cells contain equivalent C mu RNA species, which coexist with mu mRNAs in some pre-B and B lymphoid lines. C mu RNA expression appears to reflect an activated state of the C mu gene common to cells at early stages of T, B, and myeloid development.

Cloned human and mouse kappa immunoglobulin constant and J region genes conserve homology in functional segments

The human immune system offers special advantages for study of the development and evolution of the immune response. A variety of human cell lines are available that are arrested at various stages of development, and human genes provide a convenient evolutionary point of comparison with the already well characterized genes of the mouse. In this paper, we describe the procedure we have used to clone the human kappa chain genes in both germline and rearranged configurations. We have taken advantage of distantly related probes derived from the mouse and nonstringent conditions of hybridization to find the human genes among phage lambda recombinants formed with partially purified genomic restriction fragments of human DNA. In addition to establishing a physical map of the human kappa C and J regions, we have determined the entire sequence of a germline human constant region gene (the Inv3 allele) and two of its J segments, as well as the V/J recombination site of an active human kappa chain gene. For purposes of comparison, we also determined the sequence of the chromosomal mouse constant region gene and its flanking sequences. Although mouse and human sequences have changed extensively during the 70 million years since the two species diverged. significant blocks of homology have been conserved selectively. Some of these have obvious significance in terms of DNA and RNA splicing reactions. By forming heteroduplex structures between mouse and human genes we were able to identify four human J regions that are much more stringently conserved throughout their coding sequences than are the C region genes. In addition, the middle j structure (J3) of the mouse (which is thought to be inactive) appears to be missing from the human genome.

Structure and multiplicity of genes for the human immunoglobulin heavy chain variable region

Several genes for the variable region of immunoglobulin heavy chains (VH genes) have been isolated from human fetal liver DNA by using a cDNA plasmid probe containing a mouse VH sequence. The detectable VH genes are separated by 12-16 kilobases of DNA, and hybridization experiments show about 23 hybridizing VH genes in DNA of three different individuals. The complete nucleotide sequence of one of these human VH genes shows that it belongs to the human VHIII subgroup. The VH gene appears to contain an intervening sequence (104 bases in length) within a precursor sequence, between residues -4 and -5. The precursor sequence is itself 19 codons in length. The 3' end of the V gene seems to be at codon 93 or 94, and this is followed by the conserved sequences C-A-C-A-G-T-G and G-A-C-A-C-A-A-A-C-C. The presence of these sequences suggests that similar enzymatic mechanisms are involved in the integration of V genes in both heavy and light chains.

Two types of somatic recombination are necessary for the generation of complete immunoglobulin heavy-chain genes

At least two types of somatic recombination are necessary for the generation of a complete immunoglobulin gamma 2b gene from germ-line DNA sequences. The first type of recombination consists of the assembly of three separate DNA segments, each encoding a different part of the variable region. The second type of recombination replaces the exons coding for the constant region of the mu chain with those coding for the same region of the gamma 2b chain. The DNA sequencing studies suggest that the two types of recombination operate by different mechanisms.

Somatic rearrangements forming active immunoglobulin mu genes in B and T lymphoid cell lines

We have cloned an active gene for an immunoglobulin mu heavy (H) chain, bearing the variable (VH), joining (JH), and constant (C mu) sequences expressed in the IgM-secreting mouse plasmacytoma HPC-76. The mu gene was formed by somatic recombination between a VH gene and one of several JH genes, which are located about 7.7 kilobase pairs from the C mu gene in embryo DNA. The JH-C mu intervening sequence has suffered a deletion of about 2.7 kilobase pairs in HPC-76. Because the delection encompasses sequences required to switch an expressed VH-JH gene from C mu to another CH gene, it may represent a mechanism for "freezing" a lymphocyte clone at the stage of IgM expression. For the second (inactive) C mu allele in HPC-76, the entire joining and switch regions have been deleted; functional inactivation of one allele may thus represent one mechanism by which a lymphocyte clone restricts expression to a single allele (allelic exclusion). Probes generated from the cloned mu gene allowed examination of the JH locus in B, Abelson "pre-B," and T lymphoma cell lines and a myeloid line, all of which cotain RNA species bearing C mu sequences. The B and pre-B lines exhibited recombination within both alleles of the JH locus, suggesting that both alleles may be expressed in some cells. The absence of the JH gene 5' to the recombination sites favors a deletion mechanism for VH-JH joining. Recombination within the JH locus was also detected in two out of four T lymphoma lines, but not in the myeloid line. This indicates that the mechanism by which B cells generate immunoglobulin diversity is operational in some T cells. Lines that synthesize mu RNA without JH rearrangement may have activated the C mu gene directly or have undergone recombination at a more distant locus.