Most kappa immunoglobulin mRNA in human lymphocytes is homologous to a small family of germ-line V genes

B cell receptor light chain repertoires show signs of selection with differences between groups of healthy individuals and SLE patients

We have developed a microarray to study the expression of L-chain V genes (V(L) genes) in healthy and SLE patient peripheral κ- and λ-sorted B cells. In all repertoires tested, one V(L) gene accounts for over 10% of all gene V(L) expression, consistent with positive selection acting on L-chains. While a few V(L) genes were highly expressed in all individuals, most V(L) genes were expressed at different levels. Some V(L) genes (5 out of a total of 78) were not detected. We attribute their absence from the repertoire to negative selection. Positive selection and negative selection were also found in SLE repertoires, but expression of V(L) genes was different; the differences point to less regulation of V(L) gene repertoires in SLE. Our data shows that V(L) gene expression is variable and supports a model where the L-chain repertoire is generated by both positive and negative selection on L-chains.

Molecular basis for the cross-reactive idiotypes on human anti-IgG autoantibodies (rheumatoid factors)

High titres of anti-IgG autoantibodies (rheumatoid factors, RF) are characteristic of patients with rheumatoid arthritis, Sjögren's syndrome, and mixed cryoglobulinaemia, and may contribute to immune complex formation and tissue damage. The monoclonal RFs from cryoglobulinaemia patients frequently display cross-reactive idiotypes. The genetic basis for the cross-reactive idiotypes on RF autoantibodies has not been determined. To clarify structural and genetic relationships among RFs from unrelated subjects, a series of anti-peptide antibodies have been generated that define primary sequence-dependent idiotypes on RF heavy and light chains. Multiple monoclonal and polyclonal RFs from unrelated individuals have been probed by Western blotting with the anti-idiotypic reagents. The results show that sequences in the kappa light chain variable region represent a common structural element among RF autoantibodies. This hypothesis is confirmed by the cloning and sequencing of the conserved germline variable region gene which encodes human RF kappa chains.

Occurrence of heavy chain of 7S IgM half-molecule whose NH2-terminal sequence is identical with that of kappa light chain sequence in patients with Waldenstrom macroglobulinemia

We report a rare case of a half molecule 7S IgM (HM 7SIgM) consisting of a unique mu heavy chain and kappa light chain found in blood and urine samples from a patient with primary Waldenstrom macroglobulinemia. A 64kDa abnormal immunoglobulin was detected in serum and urine by immunoblot method, and purified by a two-dimensional SDS-PAGE after separation from IgG and albumin fractions on gel filtration. NH2-terminal amino acid sequence analysis of the heavy chain revealed that residues 1-20 were identical to those of the NH2-terminal region of kappa light chain derived from the same patient. This sequence was then followed by a sequence that could not be identified by a computer homology search on the protein database. Using polypeptide segments obtained from the unique mu chain by digestion with endopeptidase, we identified a sequence spanning from residue 127 in the variable region of the known mu chain to residue 19 in the known CH1 domain and a sequence spanning from residues 67-82 in the heavy chain variable region class II. From these results, we concluded that the 64 kDa protein was an abnormal half molecule 7S IgM consisting of a kappa light chain and a unique mu heavy chain of 35 kDa polypeptide in which the NH2-terminal 20 amino acids were replaced by 20 amino acids derived from the sequence of kappa light chain in the NH2-terminal region.

Flanking and intragenic sequences regulating the expression of the rabbit alpha-globin gene

Despite their descent from a common ancestral gene and the requirement for coordinated, tissue-specific regulation, the alpha- and beta-globin genes in many mammals are regulated in distinctly different ways. Unlike the beta-globin gene, the rabbit alpha-globin gene is transiently expressed at a high level without an added enhancer in transfected erythroid and non-erythroid cells. By examining a series of alpha/beta fusion genes, we show that internal sequences of the rabbit alpha-globin gene (within the first two exons and introns) are required along with the 5' flank for this enhancer-independent expression. Furthermore, deletion of the introns of the alpha-globin gene, or replacement by introns of the beta-globin gene, results in severely decreased expression of the transfecting genes. Hybrid constructs between segments of the alpha-globin gene and a luciferase gene confirm that internal alpha-globin sequences are needed for high level production of RNA in transfected cells. The flanking and internal sequences implicated in regulation of the rabbit alpha-globin gene coincide with a prominent CpG-rich island and may comprise an extended promoter (including both flanking and intragenic sequences) that is active in transfected cells without an enhancer.

Defining the genetic origins of three rheumatoid synovium-derived IgG rheumatoid factors

A major diagnostic marker in most rheumatoid arthritis (RA) patients is the rheumatoid factor (RF), an autoantibody that binds to the Fc region of IgG. To delineate the Ig genes and the underlying mechanism for RF production in RA patients, we applied a systematic approach to define the genetic origins of three IgG RFs derived from the synovial fluid of two RA patients. The results show that two of three IgG RF have substantial numbers of somatic mutations in their variable (V) regions, ranging from 13 to 23 mutations over a stretch of 291-313 nucleotides, resulting in a frequency of 4.4-7.8%. However, one IgG RF has only one mutation in each V region. This result indicates that an IgG RF may arise from a germline gene by very few mutations. The mutations occur mainly in the complementarity-determining regions (CDRs), and the mutations in the CDRs often lead to amino acid substitutions. Five of the six corresponding germline V genes have been found to encode either natural autoantibodies or autoantibodies in other autoimmune disorders; and three of the six V genes have been found in fetal liver. Taken together with other results, the data show that (a) several potentially pathogenic RFs in RA patients arise from natural autoantibodies, and (b) only a few mutations are required to convert the natural autoantibodies to IgG RFs.

Immunophenotypic and idiotypic characterisation of the leukaemic B-cells from patients with prolymphocytic leukaemia: evidence for a selective expression of immunoglobulin variable region (IGV) gene products

B-cell prolymphocytic leukaemia (B-PLL) is a rare chronic lymphoproliferative disease characterised by a massive splenomegaly associated with a mild or no lymphadenopathy and a high leukocyte count, mostly representing prolymphocytic features. We have studied membrane expression of certain Ig VK and VH gene products in five patients with B-PLL using a panel of monoclonal anti-subgroup and anti-cross-reactive idiotype (CRI) antibodies. Membrane expression of leukocyte-associated markers has also been investigated. The leukaemic cells from four patients expressed VKIII and VKIIIb subgroup and sub-subgroup kappa light chains. The VKIIIb and VHI-associated CRI identified by the monoclonal antibodies (MoAb) 17-109 and G8 were co-expressed in one patient. No B-cells from the patients expressed the VHIII-associated CRI. The same pattern of CRI expression was observed in a serum paraprotein collected from one of the patients. These results suggest a biased selection for the IG VKIII and VKIIIb light chains in B-PLL.

Modulation and high frequency expression of autoantibody-associated cross-reactive idiotypes linked to the VHI subgroup in CD5-expressing B lymphocytes from patients with chronic lymphocytic leukaemia (B-CLL)

Leukaemic B cells from patients with chronic lymphocytic leukaemia (B-CLL) are known to express the pan T-cell marker CD5 and a restricted set of immunoglobulin (Ig) variable region heavy (VH) and light (VL) chains encoded by germline or minimally mutated germline genes. We have studied surface expression of certain VH and VK gene products on peripheral blood B lymphocytes from 23 patients with B-CLL, using a panel of monoclonal antibodies (MoAbs) recognizing germline encoded cross-reactive idiotypes (CRI) associated with VHI (G6, G8), VHIII (B6, D12), VKIIIb (17-109) and an epitope linked to the VKIII light chain subgroup (C7). While only 1.7-3.2% of peripheral blood B lymphocytes from normal individuals expressed the VHI-associated CRI (VHI-CRI), these CRI were expressed on virtually all the leukaemic B cells from 17-22% of the CLL patients. The VHIII-associated CRI (VHIII-CRI), however, were found in 8.5-13% of the CLL B cells. Fifty per cent of the IgMK-expressing CLL cells (7/14) expressed the VKIII light chain subgroup of which only one expressed the VKIIIb-associated CRI (VKIIIb-CRI), 17-109. The anti-VHI-associated CRI antibodies were used to study their regulatory effect on in vitro Ig synthesis by the leukaemic cells. A significant suppression of spontaneous and mitogen-driven Ig production was observed in all cases studied. These results demonstrate an over-expression of VHI and VKIII gene products in B-CLL and suggest that B cells expressing these CRI are particularly susceptible to lymphoproliferative stimuli. The anti-CRI antibodies can be used to modulate Ig production by the leukaemic cells and may be of potential value for selective immunotherapy.

Nucleotide sequence of the human autoantibody 2E7 specific for the platelet integrin IIb heavy chain

The platelet glycoprotein (GP) IIb-IIIa complex figures prominently as an immunogen in autoimmune (idiopathic) thrombocytopenic purpura (ITP). 2E7 is a human monoclonal IgM autoantibody, derived from splenocytes of a patient with ITP, that recognizes a specific octapeptide amino acid sequence, Phe-Asp-Gly-Tyr-Trp-Gly-Tyr-Ser, on the heavy chain of GPIIb. This represents the first precise identification of an epitope on GPIIb-IIIa recognized by a human antibody. In this study, we have isolated total mRNA from 2E7, synthesized the corresponding cDNA using reverse transcriptase, and amplified the immunoglobulin mu and kappa chain cDNA by the Taq 1 polymerase chain reaction (PCR) using specific primers. The 2E7 mu chain variable region is encoded by a VH3 gene segment that is 98% homologous to the germline gene VH1.9III, a D-gene that is not homologous to any of the germline D-genes reported to date, and a JH6 gene segment that is essentially germline. The heavy-chain sequence, save for the unique D-gene, is similar to that of a number of human autoantibodies. The 2E7 kappa variable region is encoded by a Vk1 gene segment linked to a Jk1 gene segment. The Vk1 sequence of 2E7, with the exception of one nucleotide, is identical to that of autoantibody HF2-1/17, a prototype of SLE-associated anti-DNA autoantibodies bearing the 16/6 idiotype. The single base substitution results in a relatively conservative exchange of Asp for Glu at position 70 of the protein sequence. Despite this near identity in sequence, 2E7 does not bind to either single-stranded or double-stranded DNA. From these results, we conclude that specificity of 2E7 is likely to reside in either or both the D-JH region (CDR3) of the mu chain and the Jk region (CDR3) of the kappa chain. In addition to the identification of a novel D-gene, we also provide evidence that the 2E7 VHIII gene is probably a prototype of a VHIII subfamily, that the germline Vk1 gene shared by 2E7 and autoantibodies of the 16/6 idiotype probably represents a separate Vk family, and that this Vk gene cannot itself attribute specificity for DNA.

Regulation of the relative abundances of c-myc mRNAs in human promyelocytic HL60 cells

Transcription of the c-myc gene is initiated mainly from two promoters, P1 and P2. By S1 nuclease analysis we found that there is 8 times more P2- than P1-initiated RNA in total RNA from HL60 cells. The half-lives of P1- and P2-initiated transcripts are 26 and 18 min, respectively, so the difference in the relative abundance of the mRNAs is not due to differences in their stabilities. The relative rates of transcription from the P1 and P2 promoters, estimated by in vitro nuclear run-on analysis, were found to differ by about 10-fold, sufficient to account for the difference in the steady-state levels of the two mRNAs. The abundance of c-myc mRNA changes dramatically during differentiation of HL60 cells. Dimethyl sulphoxide causes a very rapid reduction in total c-myc mRNA, while with phorbol ester a transient increase occurs followed by a more gradual decline. At no time during these dramatic alterations were significant changes detected in the relative abundance of P1- and P2-initiated mRNAs, or in their stabilities.

The V kappa gene repertoire in the human germ line

The question of how many V kappa gene segments exist in the human germ line was addressed. Seventy-five V kappa genes of the kappa locus and twenty-five V kappa genes localized outside of the locus ("orphons") had been cloned previously; 67 of the genes and 19 of the orphons had already been sequenced yielding 36 and 1 potentially functional V kappa genes, respectively, the remaining ones being pseudogenes. We now (a) determined the relative hybridization intensities of the cloned V kappa genes and orphons, (b) identified the bands in blot hybridizations of genomic DNA digests with the cloned genes and orphons, (c) determined the band intensities in the genomic DNA digests from two individuals and one cell line, (d) normalized the results with the help of the C kappa gene segment which is present in the haploid genome in one copy, (e) compared the genomic blot hybridization patterns with patterns of equimolar mixtures of the cloned V kappa genes and orphons, and (f) defined the bands and fractional intensities in bands that could not be assigned to cloned genes or orphons. From the resulting data we conclude that there are 5-7 still uncloned V kappa genes in germ-line DNA in addition to the 75 known V kappa genes and in addition to the 25 orphons 12-15 orphon candidates. It appears that the rheumatoid factor light chains of the Wa and 6B6.6 idiotypes are coded for by one V kappa III gene each. It is concluded that the kappa locus comprises no more than 50 potentially functional genes and no more than 85 V kappa genes altogether.

Premature termination of transcription can be induced on an injected alpha-tubulin gene in Xenopus oocytes

The Xenopus laevis alpha-tubulin gene X alpha T14, which is highly expressed during oogenesis, exhibits accurate and efficient transcription initiation when microinjected into X. laevis oocytes. However, we found previously in nuclease protection assays of transcripts from injected X alpha T14 that many protected fragments that were shorter than expected could be produced. We show here by exonuclease VII mapping, Northern (RNA) blotting, and gel fractionation of RNA that these fragments were caused by truncated transcripts that share the same initiation sites as mature transcripts but whose 3' ends are located in the 5' leader just 45 to 72 nucleotides downstream. We present evidence from the analysis of in vitro pulse-labeled RNA that these truncated transcripts are formed by premature transcription termination rather than by RNA processing. At low template levels, very little premature termination occurred, but as more DNA was injected, the proportion of transcripts that were prematurely terminated increased steadily, even at template levels at which the initiation machinery was unsaturated. At high template levels, most transcripts were prematurely terminated. These results suggest that some sort of saturable antitermination function operates in oocytes in a manner that is dependent on the number of appropriate templates available rather than on the number of polymerases that initiate transcription. They also suggest that measures of initiation frequency may not always be a reliable means of assessing the amount of transcription of injected genes in oocytes.

Structure of rearranged and germ-line rabbit V kappa genes indicated that the CDR3 is encoded by the V kappa gene

The third complementary-determining regions (CDR3) of rabbit kappa chains are unusually long and the length is more heterogeneous when compared to those of the mouse and the human kappa chains. To study how the rabbit kappa light (L) chain genes create diversity and generate CDR3, we analyzed the structure of a rearranged variable kappa gene (Vr) and the variable (Vg) and joining (Jg) regions of the putative precursor genes. Alignment of the Vr gene sequence with that of the Vg and Jg regions allowed precise determination of the recombination event. Five nucleotides between the recombination point and the J2 heptamer were deleted, indicating flexibility in the recombination producing rabbit kappa chains. The entire Vg is contained in the rearranged product demonstrating that neither a D element nor an N sequence addition are required for the CDR3 formation. Comparison of the Vr and the Vg gene sequences show base substitutions suggesting that somatic mutations may contribute to rabbit kappa L chain diversity.

Premature termination of transcription can be induced on an injected alpha-tubulin gene in Xenopus oocytes

The Xenopus laevis alpha-tubulin gene X alpha T14, which is highly expressed during oogenesis, exhibits accurate and efficient transcription initiation when microinjected into X. laevis oocytes. However, we found previously in nuclease protection assays of transcripts from injected X alpha T14 that many protected fragments that were shorter than expected could be produced. We show here by exonuclease VII mapping, Northern (RNA) blotting, and gel fractionation of RNA that these fragments were caused by truncated transcripts that share the same initiation sites as mature transcripts but whose 3' ends are located in the 5' leader just 45 to 72 nucleotides downstream. We present evidence from the analysis of in vitro pulse-labeled RNA that these truncated transcripts are formed by premature transcription termination rather than by RNA processing. At low template levels, very little premature termination occurred, but as more DNA was injected, the proportion of transcripts that were prematurely terminated increased steadily, even at template levels at which the initiation machinery was unsaturated. At high template levels, most transcripts were prematurely terminated. These results suggest that some sort of saturable antitermination function operates in oocytes in a manner that is dependent on the number of appropriate templates available rather than on the number of polymerases that initiate transcription. They also suggest that measures of initiation frequency may not always be a reliable means of assessing the amount of transcription of injected genes in oocytes.

Initiation and termination of human U1 RNA transcription requires the concerted action of multiple flanking elements

Sequences in the 5' flanking region of small nuclear RNA (snRNA) genes are responsible for recognition of 3' end signals. Formation of the pre-U1 3' end occurs at the downstream signal closest to the promoter, probably by transcription termination. We have analyzed promoter elements for their participation in formation of the 3' ends of pre-U1 RNA. To do this, a human U1 RNA gene with deletions in individual promoter elements was microinjected into Xenopus laevis oocytes and the resulting RNAs were analyzed by a nuclease S1 protection assay. Each of the promoter elements, except element B (the functional equivalent of a TATA box), was shown to be dispensable for recognition of the snRNA 3' end signal. This latter element was necessary, but not sufficient, for initiation of transcription; so its possible role in termination could not be assessed. Therefore, it is likely that recognition of the 3' end signal is an inherent feature of transcription complexes that initiate at an snRNA promoter.

An oocyte-expressed alpha-tubulin gene in Xenopus laevis; sequences required for the initiation of transcription

We have studied the expression of X alpha T14, a member of the alpha-tubulin multigene family in Xenopus laevis. Small amounts of X alpha T14 RNA are detectable in a range of cell types, but much higher levels are present in ovary and tissue culture cells. In oocytes X alpha T14 transcripts accumulate during early vitellogenesis but their level declines in more advanced stages. Faithful and efficient initiation of transcription occurred on cloned X alpha T14 injected into oocytes even at low template levels. We have examined the amount of transcript produced by various deletion mutants relative to a co-injected control gene. The presence of 200bp of DNA 5' and 53bp of DNA 3' to the initiation site sufficed for high levels of promoter activity, although maximum activity required 560 bp of 5' flanking DNA. The DNA between -200 and -60 was necessary for transcription in oocytes and contains several sequence motifs implicated in transcriptional regulation including three CCAAT boxes and a sequence resembling a heat shock element. An 8 bp deletion that removed the latter element from 5kb of 5'-flanking DNA reduced promoter activity by 60%.

GATAAG; a cis-control region binding an erythroid-specific nuclear factor with a role in globin and non-globin gene expression

An erythroid-specific nuclear protein factor binds to a sequence motif (GATAAG) which is present in the promoter region of the mouse alpha and beta major globin genes, and in the erythroid-specific promoter of the human porphobilinogen deaminase (PBG-D) gene. The protein activity is conserved across species, being found in mouse erythroleukaemia (MEL) cells, chicken erythrocytes, the human erythroid K562 and KMOE cell lines, but not in a variety of non-erythroid mouse tissues or in HeLa cells. Functional analysis of this element in the alpha globin gene promoter by stable transfection experiments show that the GATAAG motif resides in a 68 bp sequence which has a stimulatory effect on transcription in mouse erythroleukaemia but not fibroblast cells. The GATAAG motif is conserved in the promoters and 3' enhancers of a variety of globin and non-globin genes implying that it is a cis-element involved in the tissue-specific up-regulation of several genes that are co-expressed during erythroid cell differentiation.

Alternate structures and stabilities of c-myc RNA in a bursal lymphoma cell line

A bursal lymphoma cell line, BK25, had been shown to be haploid at the c-myc locus and to have undergone an alteration of chromatin structure upstream from the c-myc coding region. In BK25 DNA at least the 3' half of an ALV provirus is integrated 160bp upstream from exon 2. As a result of this integration event, the first and second exons are separated by at least 17 kb. Approximately 90% of c-myc transcription begins in the promoter of the ALV proviral long terminal repeat (LTR) and this mRNA has a half-life of approximately 25 minutes in actinomycin D chase experiments. Approximately 10% of c-myc transcription initiates at the normal promoter of c-myc. The latter message has an unusually long half-life of greater than 100 minutes. By contrast, in MSB-1 cells, which lack any c-myc rearrangements, transcription begins at the normal promoter in exon 1 and c-myc RNA has a half-life of approximately 15 minutes. These results suggest that factors in addition to the structure of the 5' end of chicken c-myc RNA determine its stability in vivo.

Structure and regulation of a lignin peroxidase gene from Phanerochaete chrysosporium

We have been investigating the structure and regulation of the lignin peroxidase genes from Phanerochaete chrysosporium. The gene for lignin peroxidase isozyme H8 was isolated and sequenced. The gene is split into nine exons and eight introns. The introns have consensus sequences both at the splice junctions and at an internal element which may be involved in the splicing mechanism. The promoter contains the eukaryotic consensus elements: a TATA box at -78 and a ACAAT box at -106. Transcription initiates downstream from these sequences as verified by S1 nuclease mapping. Induction of the genes for the lignin peroxidase isozymes during growth under nitrogen and under carbon limitation were compared by analyses of RNA and protein. The results indicate that the lignin peroxidase isozymes are differentially regulated in response to environmental stress.

The complete sequence of a frog alpha-tubulin gene and its regulated expression in mouse L-cells

A frog alpha-tubulin cDNA and a frog alpha-tubulin gene, closely related to the cDNA, were cloned and sequenced and the structure of the gene deduced. The gene was introduced into mouse L-cells in order to investigate the transcription and regulation of the gene. The gene was transcribed and there was processing of the transcripts. Furthermore, the gene displayed the correct autoregulatory feedback control.

Alternative splicing model for the synthesis and secretion of the 20 kilodalton form of rat growth hormone

The characterization of a 20 kilodalton (20 kD) variant of rat growth hormone is reported. The 20 kD variant from rat pituitary gland extracts was identified on Western immunoblots of polyacrylamide gels. It was also shown that pituitary tissue maintained in culture secretes the 20 kD form. A rat growth hormone cDNA fragment was used as a probe in S1 nuclease mapping experiments of rat pituitary poly (A) mRNA to detect the presence of two growth hormone mRNAs in the rat pituitary gland. The protected mRNAs correspond to the predicted sizes that would encode the 22 kD and 20 kD forms of growth hormone. The site of variation between the mRNAs maps to a potential alternative 3' splice site in the 5' end of exon 3 of the coding sequence. The results support the hypothesis that the 20 kD variant in rat is the product of an mRNA alternatively spliced in exon 3, as is the case for the human growth hormone.

The use of defined peptides in characterizing idiotypes

The structural correlates of idiotypes have been sought in several antibody systems. The cumulative results suggest that the hypervariable regions (or complementarity-determining regions) of the heavy and light chains are the structural basis of idiotypes. However, in most cases, it is exceedingly difficult to associate a particular idiotypic determinant with a specific amino acid sequence. Recently, synthetic peptides were used to induce antibodies specific for predefined determinants in intact proteins. These findings led us and others to use synthetic peptides corresponding to the hypervariable regions/complementarity-determining regions to induce anti-idiotypes. These novel anti-idiotypic antibodies are easy to prepare, and are ideal reagents for structural and genetic studies of antibody responses.

High-frequency expression of a conserved kappa light-chain variable-region gene in chronic lymphocytic leukemia

Malignant B lymphocytes from several patients with chronic lymphocytic leukemia (CLL) were examined for reactivity with murine monoclonal antibody 17.109. This antibody, prepared against the rheumatoid factor (RF) paraprotein Sie, recognizes a crossreactive idiotype on 48% of human IgM RF paraproteins, but does not react with IgM paraproteins without RF activity or substantially with normal pooled immunoglobulin. The 17.109-reactive idiotype is a marker for a kappa III variable-region gene, designated V kappa RF, that is conserved in outbred human populations. In a limited study of 31 CLL patients, the leukemic cells from 5 of 20 patients with kappa light chain-expressing CLL were recognized by the 17.109 monoclonal antibody. Despite having malignant cells specifically reactive with this antibody, patients with 17.109-positive CLL did not have elevated serum levels of circulating antibody bearing 17.109-reactive determinants. Total RNAs isolated from the CLL B lymphocytes, or from hybridomas produced by fusing the CLL cells with the WI-L2-729-HF2 cell line, were fractionated electrophoretically and examined by blot hybridization. Under stringent hybridization conditions capable of discerning a single base-pair mismatch, RNA from the 17.109-idiotype-positive CLL cells hybridized to synthetic oligonucleotide probes corresponding to framework and complementary-determining regions in the V kappa RF gene. The high frequency of the 17.109-associated idiotype and the V kappa RF gene in CLL suggests that the disease may arise from B lymphocytes that express a restricted set of inherited immunoglobulin variable-region genes with little or no somatic mutation.

Human immunoglobulin variable region genes: V kappa polymorphisms suggest variation in V-gene repertoires

The present study characterizes four potentially informative polymorphic bands of 5.2, 2.3, 1.9, and 1.2 kb, detected by Southern blot hybridization of Eco RI digests of human DNA using HK101/80 (an immunoglobulin V kappa I probe). These restriction fragment length polymorphisms (RFLP) show Mendelian segregation and they are linked to each other and to Km(1), the allotypic marker on the kappa constant region. There is strong linkage disequilibrium between the 2.3 and 1.2 kb polymorphisms. A 0.7 kb Pst I polymorphic band and a 2.9 kb Sac I polymorphic band were also identified; the latter may reflect a region of tandem repeats in the V kappa region. No bands representing the alternative forms of any of the polymorphic restriction sites were identified. This implies either that genes are missing from the V kappa repertoire or that such bands are hidden because of comigration of fragments due to conservation of restriction sites. Evidence for comigration of fragments was obtained from independent V kappa clones and suggests that dark bands on Southern blots of Pst I digests must often represent several superimposed genes which have conserved restriction sites. The demonstration of RFLP within the V kappa region provides circumstantial evidence for polymorphic variation in the repertoire of V kappa structural genes. The RFLP reported here should be useful as genetic markers in future studies on the immune response and disease susceptibility in man.

Novel promoter upstream of the human c-myc gene and regulation of c-myc expression in B-cell lymphomas

A new promoter of the human c-myc gene called P0, with multiple RNA start sites, was mapped over 500 bases upstream of the two previously identified promoters, P1 and P2. Sequencing full-length cDNA clones of P0 RNAs revealed two open reading frames upstream of that for the P64c-myc protein. P0 RNA is located on polyribosomes and released by puromycin, indicating that it functions as an mRNA. In vitro translation of RNA synthesized from the cloned cDNAs predicts that P0 transcripts are translated into a novel 12.5-kilodalton protein corresponding to the first open reading frame. The regulation of P0 RNA was studied in the B-cell lymphoma cell line Manca, in which only the translocated c-myc allele lacking exon 1 was thought to be active. However, we found that P0 transcription and the DNase I-hypersensitive site associated with this promoter persist on the untranslocated allele, even though P1/P2 transcription as measured by a nuclear runoff assay was repressed. These results suggest that allelic exclusion of c-myc expression in this B-cell lymphoma is caused by a repression of transcription which is specific to the P1/P2 promoters. We previously reported a block to elongation of transcription near the 3' end of exon 1 in the wild-type c-myc gene, which results in an excess of exon 1 over exon 2 transcription (5a). In contrast, we found that in the Daudi B-cell lymphoma, which retains exon 1 in the active allele, equimolar transcription of exons 1 and 2 occurs. This result suggests a model for the activation of c-myc in B-cell lymphomas.

The AAUAAA sequence is required both for cleavage and for polyadenylation of simian virus 40 pre-mRNA in vitro

The sequence AAUAAA is found near the polyadenylation site of eucaryotic mRNAs. This sequence is required for accurate and efficient cleavage and polyadenylation of pre-mRNAs in vivo. In this study we show that synthetic simian virus 40 late pre-mRNAs are cleaved and polyadenylated in vitro in a HeLa cell nuclear extract, and that cleavage in vitro is abolished by each of four different single-base changes in AAUAAA. In this same extract, precleaved RNAs (RNAs with 3' termini at the polyadenylation site) are efficiently polyadenylated. This in vitro polyadenylation reaction also requires the AAUAAA sequence.

Human kappa light chain subgroup analysis with synthetic peptide-induced antisera

All human kappa light chains belong to one of four subgroups, classified according to their amino acid sequences or by reactivity with adsorbed heteroantisera. The structural basis for the subgroup distinction by antisera is unknown. Therefore, to create anti-kappa subgroup antibodies with predefined specificity, we immunized rabbits with synthetic peptides which correspond to sequences within the first framework region of prototype kappa I, II, III, and IV light chains. The peptide-induced antisera recognized primary sequence-dependent kappa subgroup determinants. They correctly predicted the amino acid sequence in the first framework region of two kappa light chains. By Western immunoblotting and enzyme-linked immunoassay the antisera also identified previously typed, monoclonal light chains of different subgroups with complete specificity. These reagents, define a site of kappa subgroup distinction and represent a potent tool for the characterization of light chain heterogeneity.

Genetic basis for the cross-reactive idiotypes on the light chains of human IgM anti-IgG autoantibodies

The role of immunoglobulin structural genes in the generation of autoantibodies in humans has not been elucidated. Human monoclonal IgM anti-IgG autoantibodies (rheumatoid factors, RFs) from unrelated people often share idiotypic antigens. Antibodies against synthetic peptides have localized two of the shared idiotypic determinants to the second and third complementarity-determining regions of the kappa light chain. The reported sequences of several human RF light chains are remarkably homologous in these regions. Animal studies have shown that some shared idiotypic antigens represent serological markers for immunoglobulin variable (V)-region genes. Therefore, we hypothesized that human RF light chains derived from a single germ-line gene, designated V kappa-(RF), or from a small family of very closely related genes. In the present experiments, we have isolated and sequenced two human V kappa germ-line genes that encode kappa light chains, which are identical or closely related to the light chains of human RF. The data indicate that the shared idiotypic antigens on RF are phenotypic markers for a kappa V-region gene that is highly conserved in the human population. The results also imply that the light chains of IgM anti-IgG autoantibodies can be encoded by germ-line genes without any somatic mutation.

Novel promoter upstream of the human c-myc gene and regulation of c-myc expression in B-cell lymphomas

A new promoter of the human c-myc gene called P0, with multiple RNA start sites, was mapped over 500 bases upstream of the two previously identified promoters, P1 and P2. Sequencing full-length cDNA clones of P0 RNAs revealed two open reading frames upstream of that for the P64c-myc protein. P0 RNA is located on polyribosomes and released by puromycin, indicating that it functions as an mRNA. In vitro translation of RNA synthesized from the cloned cDNAs predicts that P0 transcripts are translated into a novel 12.5-kilodalton protein corresponding to the first open reading frame. The regulation of P0 RNA was studied in the B-cell lymphoma cell line Manca, in which only the translocated c-myc allele lacking exon 1 was thought to be active. However, we found that P0 transcription and the DNase I-hypersensitive site associated with this promoter persist on the untranslocated allele, even though P1/P2 transcription as measured by a nuclear runoff assay was repressed. These results suggest that allelic exclusion of c-myc expression in this B-cell lymphoma is caused by a repression of transcription which is specific to the P1/P2 promoters. We previously reported a block to elongation of transcription near the 3' end of exon 1 in the wild-type c-myc gene, which results in an excess of exon 1 over exon 2 transcription (5a). In contrast, we found that in the Daudi B-cell lymphoma, which retains exon 1 in the active allele, equimolar transcription of exons 1 and 2 occurs. This result suggests a model for the activation of c-myc in B-cell lymphomas.

The AAUAAA sequence is required both for cleavage and for polyadenylation of simian virus 40 pre-mRNA in vitro

The sequence AAUAAA is found near the polyadenylation site of eucaryotic mRNAs. This sequence is required for accurate and efficient cleavage and polyadenylation of pre-mRNAs in vivo. In this study we show that synthetic simian virus 40 late pre-mRNAs are cleaved and polyadenylated in vitro in a HeLa cell nuclear extract, and that cleavage in vitro is abolished by each of four different single-base changes in AAUAAA. In this same extract, precleaved RNAs (RNAs with 3' termini at the polyadenylation site) are efficiently polyadenylated. This in vitro polyadenylation reaction also requires the AAUAAA sequence.

A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells

The c-myc gene product is a nuclear protein expressed in a wide variety of cell types. It has been implicated in the control of normal cell growth as well as transformation, but its exact function is unknown. When the human promyelocytic leukaemia cell line HL60 is treated with retinoic acid, the cells differentiate into granulocytes, and there is a reduction in steady state c-myc RNA of more than 10-fold. Nuclear runoff assays show that this reduction is caused by a corresponding decrease in the transcription of exon 2. However, only a minor decrease in exon 1 transcription is observed upon differentiation. In undifferentiated HL60 cells there is an approximately 3-fold molar excess of exon 1 transcription over exon 2, and this excess increases to about 15-fold in differentiated cells. This observation suggests that a major component of c-myc transcriptional down-regulation in HL60 cells is at the level of elongation rather than at the level of initiation. The position of the elongation block was mapped to the region of the boundary between exon 1 and intron 1. During HL60 differentiation, a DNase I hypersensitive site in the chromatin about 300 bases downstream of the 5' end of of intron 1 increases in intensity relative to other sites, possibly reflecting events associated with the termination of transcription. Our runoff analysis also revealed transcription of both strands immediately upstream of exon 1 in HL60 cells. The sense strand transcription of this region produces a novel c-myc RNA which initiates several hundred bases upstream of the previously defined promoters and is found in a variety of cell types.

Structure and expression of a human subgroup II immunoglobulin kappa gene

We have determined the entire nucleotide sequence of an active immunoglobulin V kappa gene of the human subgroup II. Comparison of the main coding sequence of this gene to another member of this subgroup reveals germline sequence differences that occur not only in complementarity determining regions but also in framework regions. We find that at least two regions commonly associated with active immunoglobulin genes--the TATAA box and the decanucleotide TGATT-TCAT--are represented in this gene. The gene was expressed by permanent and transient DNA-mediated transfection in various cell lines. We have determined the precise site of transcriptional initiation using S1 analysis of gene transcripts and show that this site is the same in the transfected cell lines and in the cell line from which the gene was isolated.

Cloning and sequence determination of a human rheumatoid factor light-chain gene

The contribution of germ-line variable regions to autoantibody formation in humans is poorly understood. To study the gene structure of a human autoantibody, chronic lymphatic leukemia (CLL) cells from a patient with an IgM anti-IgG (rheumatoid factor, RF) paraprotein were utilized. The rearranged immunoglobulin gene encoding the kappa light chain for the RF was cloned, and the nucleic acid sequence of its variable region was determined. As demonstrated by Southern blot analysis using a kappa joining-region probe, the CLL cells, stable CLL-WIL2-729-HF2 RF-secreting hybridomas, and the cloned light-chain gene all had an identical restriction fragment containing the rearranged light-chain gene. The CLL RF light chains reacted weakly with an antipeptide antibody against a primary structure-dependent idiotype present on the light chains of the majority of IgM RF paraproteins. The nucleotide and predicted amino acid sequences of the CLL light-chain gene place it in the kappa III variable-region subgroup, and a comparison to known RF paraproteins reveals marked homology to the light-chain amino acid sequence of the IgM RF paraprotein Pom. Both Pom and the CLL light chain appear to identify a second kappa III gene or gene group that is able to encode RF paraprotein light chains.

Amino acid sequence of a light chain variable region of a human rheumatoid factor of the Wa idiotypic group, in part predicted by its reactivity with antipeptide antibodies

Antipeptide antisera were raised to the second and third complementarity-determining regions of the light chain derived from a human monoclonal IgM (Sie) which had antigammaglobulin activity and belonged to the Wa cross-reactive idiotypic group of human rheumatoid factors, two of whose members (Sie, Wo1) had been previously sequenced in our laboratory (Andrews and Capra, Biochemistry 20, 5816-5822, 1981). These antisera were found to react with the light chain of another human monoclonal IgM (Go1) that shared the Wa idiotype while antipeptide antisera made to the third CDR of the Sie heavy chain failed to react. The amino acid sequence of the variable region of the Go1 light chain was found to be highly homologous to the light chain of Sie from which the synthetic peptides were derived, particularly in the framework regions and the second and third CDR. This study illustrates that antipeptide antisera are valuable and specific probes for determining the relationship between molecules which exhibit similar antigen binding or idiotypic specificities and, furthermore, such antisera are able to predict amino acid sequences with surprising precision.

A rapid and simple procedure for the preparation of homogeneously labeled DNA probes

This report describes a novel technique for the preparation of homogeneously labeled DNA probes. The procedure uses a heteroduplex intermediate, which is directly prepared from a double-stranded plasmid, and therefore requires neither sub-cloning of the fragment of interest into a specialized vector nor the use of a synthetic primer. The technical advantages of the procedure are demonstrated by preparation of a probe able to determine the precise location and efficiency of utilization of the polyadenylation site used during transcription of the rat preproinsulin II gene in a transfected avian cell line.

Molecular defects in a human immunoglobulin kappa chain deficiency

The molecular basis of a human immunoglobulin deficiency characterized by the complete absence of kappa chains has been investigated by nucleotide sequence analyses of a patient's kappa constant region (C kappa) genes. Both of his C kappa genes had a single point mutation, resulting in the loss of the invariant tryptophan from one allele and of an invariant cysteine from the other allele. These results indicate that neither of the patient's C kappa alleles encoded a kappa chain that could form a stable intradomain disulfide bond, although peculiarities in the expression of kappa chains in the patient's family suggest that other factors may be involved.

cDNA of the immunoglobulin kappa chain of an Epstein-Barr virus-transformed human lymphoid cell line: partial sequence determination and bacterial expression

We report the isolation, nucleotide sequence determination, and bacterial expression of a partial cDNA for the immunoglobulin kappa chain from the Epstein-Barr virus-transformed human lymphoid cell line GM131. The cDNA, cloned in pBR322 by use of oligo(dG) X oligo(dC) tails, yields two Pst I fragments of 250 and 600 base pairs (bp). Various restriction enzyme fragments of the cDNA were subcloned in the vectors M13 mp10 and M13 mp11 for sequence analysis. As a result of instability of the 250-bp M13 subclones, the base sequence of the 250-bp Pst I fragment could not be determined. The 600-bp Pst I fragment contains coding sequences for part of the variable (V) region (residues 78-95) and all of the joining (J) (residues 96-108) and constant (C) regions (residues 109-212) and extends 148 bp into the 3' flanking region. Although the C- and 3'-flanking-region sequences are identical to germ-line sequences, the J-region sequence does not correspond to any of the five human germ-line J regions. The sequence is most similar to that of J4, with three base changes resulting in one silent mutation and two amino acid substitutions, at residues 103 (Lys----Tyr) and 106 (Ile---Met). The silent mutation appears to be the result of RNA splicing between the J and the C regions. The V-region sequence differs from published V-region germ-line sequences at several codons and from the more common amino acid sequences at two positions, residues 91 and 93. At these positions, histidine residues are found in place of the more common tyrosine and serine, respectively. None of the four amino acid substitutions observed for the GM131 kappa-chain are unique, suggesting that the changes, which most likely contribute to antigenic specificity, are compatible with antibody structure and function. The 600-bp Pst I fragment was subcloned in two prokaryotic expression vectors, pATH11 and pUC8. In both instances, a kappa-chain fusion protein detectable by immunoblotting was produced.

Human immunoglobulin kappa light chain genes of subgroups II and III

The first complete sequences of functionally rearranged VK genes (abbreviations ref. 1) of subgroups II and III are reported. The genes have been cloned from lymphoid cell lines synthesizing KII or KIII light chains as evidenced from immunochemical analyses with anti-VK subgroup-specific antisera. These data, together with the sequence of a KIV gene (described in the accompanying paper) and those of previously published KI genes make possible a comparison of genes representative of the four known V region subgroups of human K light chains. The VKII gene is distinguished from the VKI, VKIII, and VKIV genes by a much longer intron within the leader sequence: 426 bp vs ca. 120-220 bp. Blot hybridization experiments with human DNA digests using probes from the KII and KIII genes and from the respective upstream regions help to define subgroup specific probes and hybridization conditions.

A large section of the gene locus encoding human immunoglobulin variable regions of the kappa type is duplicated

The structure of a new segment of the gene locus encoding the variable regions of human immunoglobulins of the Kappa type (VK) has been elucidated. This segment (cluster B) encompasses six VK sequences, which belong to three different subgroups and which are arranged in the same transcriptional orientation. Part of cluster B was found to be very similar to another region of the VK gene locus, which was cloned previously (cluster A). Sequence differences between the homologous region of clusters A and B range from 0.2% to 3.7% depending on the position of the VK sequences. The divergence is in the same range for genes and pseudogenes. Hybridization experiments with DNAs from different individuals clearly demonstrate that the two segments are located at different positions within the VK locus and do not represent allelic variants. The sequence homology between clusters A and B is higher than the homology of both clusters to an allelic variant, which is represented by a DNA segment that had been isolated from another individual. These results, together with a report in the literature of two other homologous regions in the VK locus, make it very likely that a major part of even the whole locus is duplicated. In this case, VK gene numbers would be higher than previously estimated on the basis of hybridization studies. An inverse orientation of VK gene clusters would explain published data on rearrangement products in B-cells if an inversion-deletion mechanism is assumed.

A sequence downstream of A-A-U-A-A-A is required for formation of simian virus 40 late mRNA 3' termini in frog oocytes

The 3' terminus of simian virus 40 late mRNA is formed by nucleolytic cleavage of an mRNA precursor. In this report we show that efficient cleavage requires a sequence in the 3' flanking region, "downstream" of the highly conserved A-A-U-A-A-A sequence. This sequence is not required for polyadenylylation itself or for accurately positioning the 3' terminus that is formed.

Aberrant recombination events in B cell lines derived from a kappa-deficient human

We have analyzed the structure of Ig kappa chain genes in B cell lines derived from a human individual who cannot synthesize any kappa chains, and whose Igs all contain lambda chains (1). We have characterized secondary DNA recombination events at two kappa alleles which have undergone misaligned V-J recombinations. One such secondary recombination has joined the flanking sequences of a V kappa and a J kappa 2 gene segment as if it were the reciprocal product of a V-J kappa 2 recombination, and resulted in the displacement of the recombined VJ kappa 1 gene segments from the C kappa locus. The non-rearranged form of the V kappa fragment which had recombined with the J kappa 2 flank was cloned. Nucleotide sequencing of this fragment identified a V kappa gene that differed by at least 38% from all previously sequenced human V kappa genes. The other V-J kappa segment analyzed has undergone a secondary recombination at a different site from that described above, at a site within the intervening sequence between the J kappa and C kappa gene segments, similar to the location of secondary recombinations which have occurred in lambda + B cell lines from mice and humans (2,3). These results prove that multiple recombinations can occur at one J kappa-C kappa locus.

Possible involvement of human D minigenes in the first complementarity-determining region of kappa light chains

The nucleotide sequences of the complementary strands of two human diversity region (D) minigenes, D2 and D4, show stretches of homology with two human variable region kappa chain (V kappa) genes, NG9 and HK101, respectively, in the first complementarity-determining region. In one V kappa sequence, the homology includes the 5' flanking region of D minigenes, which may comprise a recombinase recognition signal. It is thus conceivable that gene conversions involving D minigenes may contribute to V kappa diversity.