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

Expression of IgD may use both DNA rearrangement and RNA splicing mechanisms

From a library of mouse sperm DNA, we have isolated two overlapping clones which contain the C(delta) gene. One of these clones also contains the C(mu) gene. The C(delta) gene is separated from the C(mu) membrane exons by approximately 2 kilobases (kb) of DAN. The C(delta) gene was identified by (a) hybridization to poly(A)(+)RNA prepared from the IgD-producing rat plasma cell tumor IR731, and (b) homology of a translated nucleotide sequence to the amino acid sequence of the human delta chain. The C(delta) gene spans 8 kb of DNA in the germ line. Plasmid subclones of the C(delta) gene were used as probes in Southern and RNA blot experiments. RNA blot analysis of cytoplasmic poly(A)(+)RNA from IR731 and a mu(+)delta(+) B-cell hybridoma revealed 1.6- and 2.7-kb delta mRNA species with different 3' ends, which presumably encode the secreted and membrane-bound forms, respectively, of the delta chain. Southern blot analysis of DNA from two mu(+)delta(+) lymphomas revealed that the C(delta) gene is in the germ-line configuration in each case. Restriction map analysis of C(mu) and C(delta) genomic clones isolated from a library of normal mu(+)delta(+) B-cell DNA also gave no evidence for DNA rearrangement in the region between the C(mu) and C(delta) genes. Taken together, these data suggest that IgD expression in mu(+)delta(+) B cells does not involve a V(H)-to-C(delta) DNA switch rearrangement. We propose that simultaneous expression of C(delta) and C(delta) with a single V(H) gene is mediated by two alternative routes of RNA processing of a primary nuclear transcript which contains the V(H), C(mu), and C(delta) genes. In contrast, analogous experiments with myeloma IR731 DNA revealed that the C(mu) gene has been deleted from the myeloma DNA and that the C(delta) gene has undergone DNA rearrangement, presumably including a switch recombination of the V(H) gene from the C(mu) to the C(delta) gene. These results indicate that two alternative mechanisms may be used in the expression of IgD molecules-RNA splicing in B cells and DNA rearrangement in plasma cells.

Cloning of mouse immunoglobulin epsilon gene and its location within the heavy chain gene cluster

Mouse immunoglobulin epsilon chain gene was cloned from DNA of a hybridoma producing anti-dinitrophenyl IgE, which was constructed by fusing a spleen cell of a BALB/c mouse with a variant clone of MOPC21 myeloma (IgG1 producer). Because a given active heavy chain constant region (CH) gene is linked to a heavy chain joining segment (JH) gene at its 5' side, the expressed C epsilon gene of the hybridoma was cloned from a phage library containing partial Sau3A digests of IgE hybridoma DNA by using a J gene fragment as a probe. Among 6 X 10(5) phages screened, five positive clones were obtained and three of them were identified as C epsilon gene clones by restriction mapping, Southern blot hybridization, R-loop formation, and partial nucleotide sequence determination. The determined nucleotide sequence predicted the amino acid sequence which resembles a part of the CH3 domain of human epsilon chain. The deletion profile of the C epsilon gene in various myelomas expressing different CH genes indicates that the C epsilon gene is located between the C gamma 2a and C alpha genes. The linkage (5'-epsilon-alpha-3') was directly confirmed by molecular cloning of the overlapping chromosomal segments from newborn mouse DNA.

Repetitive sequences in class-switch recombination regions of immunoglobulin heavy chain genes

Immunoglobulin class switch involves a unique recombination event that takes place at the region 5' to each heavy chain constant region gene during B lymphocyte differentiation. Such regions that are responsible for the class-switch recombination are defined as S regions (Kataoka et al., Proc. Natl. Acad. Sci. USA 77, 919, 1980). We have cloned a rearranged gamma 2b gene from a mouse myeloma (MPC11) and compared its structure with the germ line counterparts. The rearranged gamma 2b gene contained the 5' flanking region of the gamma 3 gene (S gamma 3 region) which are linked to the 5' flanking region of the gamma 2b gene (S gamma 2b region). We have determined nucleotide sequences surrounding the recombination site of the rearranged and germ line gamma 2b genes, which include the S gamma 2b and S gamma 3 regions. Both gamma 2b and S gamma 3 regions comprise tandem repetition of conserved units of 49 bp. Similar 49 bp repeating units are also found in the previously determined sequence of the S gamma 1 region in which class-switch recombination took place in MC101 myeloma. The nucleotide sequences of the S gamma 1, S gamma 2b and S gamma 3 repeating units share significant homology with each other. The S mu region, partial nucleotide sequence of which was previously determined, contains abundant short sequences such as AGCT, TGGG and AGCTGGGG which are shared in common by repeating sequences in S gamma regions. These results suggest that the recombination responsible for class switch from mu to gamma or from a gamma to another gamma, may be facilitated directly or indirectly by homology of repeating sequences in S regions.

Ordering of mouse immunoglobulin heavy chain genes by molecular cloning

We have determined the order of the mouse immunoglobulin gamma 1, gamma 2 b, gamma 2 a and epsilon genes by molecular cloning of overlapping chromosomal segments. The results clearly demonstrate that the order is 5'-gamma 1-(21 kilobases)-gamma 2b-(15 kilobases)-gamma 2a-(15 kilobases)-epsilon-3'. There seem to be no J regions at the 5' side of each constant region gene so far obtained except for the mu gene and these constant region genes seem to have repetitive sequences characteristic of switch (S) regions at their 5' side.

Linkage of the four gamma subclass heavy chain genes

The genes for the heavy-chain constant regions of the four gamma subclass immunoglobulins were identified in a set of overlapping mouse DNA fragments representing about 100 kilobase pairs (kb) of the mouse genome that was cloned from bacteriophage lambda libraries of BALB/c mouse embryo DNA. R-loop mapping studies show that the genes are located 5'-C gamma 3-34 kb-C gamma 1-21 kb-C gamma 2b-15 kb-C gamma 2a-3' and lie in the same transcriptional orientation. Two DNA segments, one of 19 kb and another of 15 kb, that surround the C gamma 2b and C gamma 2a genes, respectively, show considerable homology and implicate a tandem duplication mechanism in the evolution of this gene cluster.

Organization and expression of immunoglobulin genes in fetal liver hybridomas

The organization and expression of immunoglobulin genes were studied in a series of six hybridomas derived from the fusion of a nonproducing myeloma cell with cells from mouse fetal liver. These hybridomas, which exhibit several phenotypic characteristics of immature B lymphocytes, all have productively rearranged mu heavy chain genes and produce both the membrane and secreted forms of mu mRNA in a ratio of about 1:10. Significantly, none of the hybridomas has an unrearranged (germ line) allelic mu gene. Examination of the kappa light chain genes revealed that all six of the hybridomas contain unrearranged kappa loci and produce 8.4-kilobase transcripts containing kappa constant region sequences. None of the five hybridomas that exhibit a mu-only phenotype contains a rearranged kappa gene other than that derived from the myeloma parent. One hybridoma, which actively secretes kappa immunoglobulin, contains a rearranged kappa gene of fetal liver origin and synthesizes a distinctive kappa mRNA precursor in addition to the 8.4-kilobase transcript. These results demonstrate that rearrangement of heavy chain immunoglobulin genes normally occurs prior to that of light chain genes and further indicate that the transcriptional competence of the kappa constant region locus is established prior to the time of its rearrangement.

Cmu gene rearrangement of mouse immunoglobulin genes in normal B cells occurs on both the expressed and nonexpressed chromosomes

We have examined the organization of heavy-chain immunoglobulin genes on both the expressed and nonexpressed chromosomes of normal B lymphocytes from allotype heterozygous (BALB/c X C57BL/J)F1 mice. The C mu genes of BALB/c mice are on 12.4-kilobase EcoRI and 13.1-kilobase Kpn I restriction fragments, whereas those of C57BL/J mice are on 13.6-kilobase EcoRI and 14.3-kilobase Kpn I restriction fragments, allowing the examination of rearrangements on each chromosome independently. B lymphocytes from spleen and Peyer's patches expressing both IgD and IgM of the BALB/c allotype were isolated with a fluorescence-activated cell sorter. EcoRI and Kpn I restriction digests were hybridized with a C mu gene-containing probe. The C mu gene is present on both chromosomes. DNA rearrangements occur on both the expressed and nonexpressed chromosome within the 3.6-kilobase Kpn I/EcoRI restriction fragment containing the joining (JH) gene locus. We conclude that allelic exclusion of heavy-chain immunoglobulin gene expression is not mediated by JH-region DNA rearrangement of the expressed chromosome only. In contrast, analysis of the C kappa gene region from the same sorted B-cell DNA reveals a substantial quantity of germ-line context DNA. We also demonstrate that the deletions observed on the Eco RI fragment containing the C mu gene in myeloma cells and in C mu gene-containing recombinant DNAs do not usually occur in normally differentiating B lymphocytes and are likely to be confined to myeloma tumor cells.

Sequences of the joining region genes for immunoglobulin heavy chains and their role in generation of antibody diversity

To assess the contribution to immunoglobulin heavy chain diversity made by recombination between variable region (VH) genes and joining region (JH) genes, we have determined the sequence of about 2000 nucleotides spanning the rearranged JH gene cluster associated with the VH gene expressed in plasmacytoma HPC76. The active VH76 gene has recombined with the second germ-line JH gene. The region we have studied contains two other JH genes, designated JH3 and JH4. No other JH gene was found within the region 1000 nucleotides downstream from JH4. Between JH3 and JH4 there is a pseudo-JH sequence with substantial homology to the authentic JH genes. The four JH genes whose sequences now are known can account for all known JH amino acid sequences. The JH genes are more divergent than the Jk genes and vary in length, encoding either 15 or 17 amino acid residues. Because JH regions comprise part of the third hypervariable region (HV3), combinatorial VH--JH joining substantially augments VH diversity. Moreover, a VH gene can recombine with each JH gene at several positions, and either one or two germ-line JH codons can be excised. This JH truncation markedly reduces the length of HV3 and hence must alter antigen-binding specificity. We have also determined the sequence of the JH4 region in two different gamma 2a mRNAs and have found that each has suffered a point mutation (aspartate to asparagine) which would alter the charge of the antigen-binding site.

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.

Cloning of human immunoglobulin mu gene and comparison with mouse mu gene

We have cloned a 12 kb DNA segment containing human mu gene and its flanking sequence from human fetal liver DNA library using mouse mu gene as a probe. Partial nucleotide sequence determination shows that the cloned DNA contains the sequence encoding human mu chain. This is the first constant region gene of the human heavy chain that is cloned. We have compared human and mouse mu genes by heteroduplex analysis and Southern blot hybridization. The results clearly show that not only the sequence encoding the CH4 domain but also the 5'-flanking (S mu) sequence is conserved between human and mouse mu genes, suggesting that the nucleotide sequence in the S mu region has an important biological function, presumably a recognition signal for the class switch recombinant as proposed previously.

Cloned embryonic DNA sequences flanking the mouse immunoglobulin C gamma 3 and C gamma 1 genes

To investigate the DNA surrounding genes for immunoglobulin heavy chain constant (CH) regions, we have isolated two clones bearing a C gamma 3 gene and two bearing a C gamma 1 gene from a library of mouse embryo DNA fragments. The C gamma 3 clones span 8.6 kilobase pairs (kb) on the 5' side of the gene and 6.7 kb on its 3' side, while the C gamma 1 clones together span 13 kb of 5' flanking sequence and 2.5 kb of 3' flanking sequence. Restriction mapping of the C gamma 3 gene indicates that intervening sequences divide the gene into segments of domain size, as in other CH genes. Hybridization of clone fragments to restriction digests of mouse DNA indicates that both the C gamma 1 and C gamma 3 genes probably occur as single copies in the genome. Moreover, the entire cloned sequences on the 5' side of both genes appear to be unique in the genome, indicating that no large common sequences flank CH genes. Restriction data suggest that the C gamma 3 gene is 37-40 kb 5' to the C gamma 1 gene.

Organization of the sequences flanking immunoglobulin heavy chain genes and their role in class switching

We have used heteroduplex analysis to investigate the sequences surrounding the germline C gamma 1 and C gamma 3 genes, and to compare them with those surrounding the C mu gene. We detected an inverted pseudogene 5' to the C gamma 3 gene and 50-65% homologous to it. A 400 bp region of the C gamma 1 and C gamma 3 3' flanking sequences was conserved as strongly as the genes (65-80%), suggesting it may have a specific function. The sequences 5' to the C gamma 1 and C gamma 3 genes and possibly also the C mu gene are composed of tandem partially homologous repeats of a similar 250 bp unit, arranged in the case of the C gamma 1 gene, in 2-5 kb blocks of alternating orientation. These repeats comprised over 13 kb of the spacer region separating the C gamma 3 and C gamma 1 genes. Recombination sites for heavy chain class switching fell within these repeated sequences, suggesting that recombination between partially homologous blocks of repeat sequences 5' to CH genes generates the deletion responsible for class switching. This hypothesis was strongly supported by an examination of published nucleotide sequences around the recombination sites of rearranged C gamma 1 and C gamma 2b genes (1,2).

Helper and killer T cells do not express B cell immunoglobulin joining and constant region gene segments

We have analyzed four kinds of T cells for rearrangement and expression of immunoglobulin genes. These cells include: (a) whole thymus; (b) WEHI-22, a T-cell lymphoma; (c) HT-1, an major histocompatibility complex-restricted T helper line; and (d) CTLLi6, an H-2 alloreactive killer cell line. None of the B-cell joining and constant gene segments are rearranged in the T cells. The monoclonal cells do not express any C kappa, C lambda, Cmu or C alpha RNA species. Small amounts of C kappa, C alpha, and Cmu sequences are present in RNA prepared from the thymus, although the significance of this RNA for T-cell antigen receptor synthesis is uncertain. The data support the hypothesis that expression of B-cell joining and C gene segments is unnecessary for T-cell helper and T-cell killer activity.

Evolutionary approach to the question of immunoglobulin heavy chain switching: evidence from cloned human and mouse genes

We have used cloned mouse and human heavy chain genes to identify regions of conserved homology between mouse and man and between mu and alpha genes. Using heteroduplex mapping, we find that coding segments for homologous domains appear to have been well conserved between the two species, but the short intervening sequences that separate domains have diverged considerably. These studies also identify extensive regions of homology 5' to both mu and alpha constant region genes that are conserved between the two genes as well as between mouse and man. These segments encompass regions in which mu/alpha recombination occurs during the heavy chain class switch, and their extensive homology may be relevant to this process.

CH gene rearrangements in IgM-bearing B cells and in the normal splenic DNA component of hybridomas making different isotypes of antibody

To probe mechanisms operating at the CH gene locus during normal B lymphocyte differentiation, we have used cloned probes for the constant region genes Cmu, C gamma 1 and C alpha to analyze the immunoglobulin heavy chain genes of three kinds of cell populations in successive stages of B cell development. These are IGM-bearing B lymphocytes from the normal spleen of unprimed mice, hybridomas prepared by fusing spleen cells from antigen-primed mice with the SP2/O permanent cell line and selected to secrete one of five different isotypes (IgM, IgG3, IgG1, IgG2 and IgA) and a set of plasmacytoma lines. The IgM-bearing B cells carry Cmu genes with rearrangements between VH and JH genes on both chromosomes even though only one chromosome is expressed; clearly, allelic exclusion cannot be explained by the lack of CH gene rearrangement on the nonexpressed chromosome. The normal splenic DNA component of antibody-secreting hybridomas displays rearrangements between JH and Cmu genes as well as among CH genes other than Cmu, with concomitant deletion of CH genes 5' to those expressed. These CH rearrangements and deletions are likely to accompany the isotype switching process and may occur on both expressed and nonexpressed chromosomes. We used hybridomas (spleen-derived), which secrete primarily IgM, and plasmacytomas (gut-derived), which secrete primarily IgA, to represent plasma cells in early and late stages of differentiation, respectively. A direct comparison of hybridomas and plasmacytomas making the same products (IgG3 or IgG1) indicates that hybridomas display a low frequency (2/12) of nonexpressed C alpha gene rearrangements in contrast to the high frequency (7/10) displayed by plasma-cytomas. We propose that CH gene switching rearrangements and deletions may occur successively along the CH gene locus, involving any of the undeleted genes at each step. These can occur on both expressed and nonexpressed chromosomes during the normal clonal outgrowth of a B cell line in vivo, and would result in the accumulation of both productive and nonproductive rearrangements of the presumed last CH gene, C alpha.

Immunoglobulin gene rearrangement in immature B cells

Two types of immature B cells, namely fetal liver hybridomas and the leukemic cell line 70Z/3, both of which have cytoplasmic mu chains but no light chains, were examined for DNA rearrangements of their light chain and heavy chain immunoglobulin genes. In the fetal liver hybridomas, which were constructed from fetal liver cells and a tumor cell, no light chain gene rearrangement was observed, whereas in the 70Z/3 cell line a kappa light chain rearrangement probably occurred. The results suggest that, although the lack of light chain synthesis can be due to a lack of gene rearrangement, there may also be transcriptional regulation, which may also be important for the expression of light chain immunoglobulins in immature B cells.

Phase variation: evolution of a controlling element

Phase variation in bacteria is regulated by homologous recombination at a specific DNA site. This recombinational event causes the inversion of a 970-base-pair DNA sequence that includes the promoter necessary for transcription of a flagellar gene. The invertible segment is flanked by two sites that are necessary for the inversion and contains a gene (hin) whose product mediates the inversion event. The hin gene shows extensive homology with the TnpR gene carried on the Tn3 transposon. It is also homologous with the gin gene carried on bacteriophage mu. These relationships suggest that the phase variation system may have evolved by the association of a transposon with a resident gene and the subsequent specialization of these elements to regulate flagellar antigen expression.

DNA sequences mediating class switching in alpha-immunoglobulins

Immunoglobulin class switching involves specific DNA rearrangements of the gene segments coding for heavy chain constant regions (CH) during B lymphocyte differentiation. In two different cases of C mu to C alpha switching examined here (T15 and M603) and one taken from the literature (MC101), three different sites on the 5' side of C mu and three different sites on the 5' side of C alpha are joined together in the process of CH switching. The sequences surrounding the three germ-line C alpha sites of recombination are highly conserved blocks of 30 nucleotides that may serve as recognition sequences for CH switching to the C alpha gene. This putative recognition sequence is repeated 17 times in approximately 1400 nucleotides of the germ-line Calpha 5' flanking sequence. The lack of homology between this C alpha sequence and sequences reported for the C gamma 1 and C gamma 2b switch sites suggests that heavy chain switching is mediated by class-specific recognition sequences and, presumably, class-specific regulatory mechanisms. In addition, it appears that in one example (MC101) CH switching progressed from C mu to C alpha to C gamma 1. This switching pathway may present difficulties for the simple deletional model of CH switching.

An immunoglobulin deletion mutant with implications for the heavy-chain switch and RNA splicing

The IF2 immunoglobulin mutant is a DNA deletion of one coding segment and large sections of the flanking intervening sequences. The deletion results in a new splicing pattern and starts in a DNA region containing tandemly repeated sequences which may carry heavy-chain class switch signals.