DNA elements are asymmetrically joined during the site-specific recombination of kappa immunoglobulin genes

A shuttle vector system for the investigation of immunoglobulin gene hypermutation: absence of enhanced mutability in intermediate B cell lines

Somatic hypermutation focused to the rearranged V(D)J segment of the immunoglobulin (Ig) loci contributes substantially to antibody gene diversification. However, neither the precise B cell subset subject to hypermutation nor the molecular mechanism(s) involved is known. One model proposes that Ig segments may be uniquely susceptible to DNA nicking and subsequent error-prone repair during a specific B cell developmental stage. We describe an SV40-based shuttle vector system for testing such a model. Plasmids containing two distinct Ig segments juxtaposed to the supF marker gene have been passaged through cell lines representing intermediate stages of B cell development, rescued and screened for marker gene mutations. To date we have not demonstrated enhanced supF mutation in any cell line examined, irrespective of the adjacent Ig segment. Thus, these cell lines exhibit normal DNA repair mechanisms and no evidence of increased endonuclease activity on the Ig segments tested. The feasibility of this system will allow similar experiments using other Ig target sequences exposed to a broader range of B cells.

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

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

V(D)J recombination in mouse thymocytes: double-strand breaks near T cell receptor delta rearrangement signals

In the murine T cell receptor delta locus, V(D)J recombination events frequently involve the D2 and J1 elements. Here we report the presence of double-strand breaks at recombination signals flanking D2 in approximately 2% of thymus DNA. An excised linear species containing the sequences between D2 and J1 and a circular product of the joining of D2 and J1 recombination signals were also found. Although broken molecules with signal ends were detected, no species with coding ends could be identified. Observation of these broken molecules in thymus, but not in liver or spleen, provides the first direct evidence for an association between specific cleavage of chromosomal DNA and recombination in mammalian cells, and supports a breakage-reunion model of V(D)J recombination.

Three lymphoid-specific factors account for all junctional diversity characteristic of somatic assembly of T-cell receptor and immunoglobulin genes

The somatic diversity immunoglobulin and T-cell receptor diversity is largely provided by the junctional variation created during site-specific rearrangement of separately encoded gene segments. Using a transient transfection assay, we demonstrate that the recombination activating genes Rag1 and Rag2 direct site-specific rearrangement on an artificial substrate in poorly differentiated as well as in differentiated nonlymphoid cell lines. In addition to a high frequency of precise recombination events, coding joints show deletions and more rarely P-nucleotide insertions, reminiscent of immunoglobulin and T-cell receptor junctions found in fetal tissues. N-region insertions, which are characteristic of adult junctional diversity, are obtained at high frequency upon transfection of a terminal deoxynucleotidyltransferase expression vector together with Rag1 and Rag2. These results show that only three lymphoid-specific factors are needed to generate all types of junctional diversity observed during lymphoid development.

Assembly of IgH CDR3: mechanism, regulation, and influence on antibody diversity

The most variable portion of immunoglobulin molecules is the third complementarity determining region (CDR3) of the heavy chain. This is simply because CDR3 encompasses the region of the rearranged gene where the three gene segments (VH-DH-JH) are joined. Since imprecisions exist in the recombinase reaction, significant differences can be generated at the sites of recombination. This results in the generation of antigen receptor molecules which can differ in their antigen specificity even though they derive from the same germline information. In sum, the significance of the inaccuracy in recombination is that antibodies which are reactive to different antigens can be derived from identical genetic information. This explains how the immune system (using only a limited amount of genetic information) can generate antibodies to virtually any antigen. Though the basic phenomenon of VH-DH-JH assembly has been appreciated for years, two recent findings demonstrate that the generation of CDR3 is more complex than originally believed. First, junctional modification is not a stochastic process as was initially presumed, but is in part developmentally regulated. Second, it has now been well documented that more complex recombinations (for example VH-DH-DH-JH, VH-DH-invDH-JH, etc.) are involved in generating the third hypervariable region of the heavy chain. Not only do these unusual rearrangements--which break the so-called "12/23" recombination rule--occur, but interestingly, certain predicted rearrangements (even some which do follow the "12/23" recombination rule) cannot be demonstrated and apparently do not occur. To date, there is no adequate explanation for the lack of these predicted recombinations. These results have important implications for both the generation of antibody diversity and the recombinase reaction itself.

V(D)J recombination: evidence that a replicative mechanism is not required

We examined a series of extrachromosomal DNA substrates for V(D)J recombination under replicating and nonreplicating conditions. Complete and partial replications were examined by monitoring the loss of prokaryote-specific adenine methylation at 14 to 22 MboI-DpnI restriction sites (GATC) on the substrates. Some of these sites are within 2 bases of the signal sequence ends. We found that neither coding joint nor signal joint formation requires substrate replication. After ruling out replication as a substrate requirement, we determined whether replication had any effect on the efficiency of V(D)J recombination. Quantitation of V(D)J recombination efficiency on nonreplicating substrates requires some method of monitoring the entry of substrate molecules into the cells. We devised such a method by monitoring DNA repair of substrates into which we had substituted deoxyuridine for 10 to 20% of the thymidine nucleotides in the DNA. The substrates which enter the lymphoid cells were repaired efficiently in vivo by the eukaryotic uracil DNA repair system. Upon plasmid harvest, we distinguished repaired (entered) from unrepaired (not entered) plasmids by cleaving unrepaired molecules with uracil DNA glycoylase and Escherichia coli endonuclease IV in vitro. This method of monitoring DNA entry does not appear to underestimate or overestimate the amount of DNA entry. By using this method, we found no significant quantitative effect of DNA replication on V(D)J recombination efficiency.

V(D)J recombination: evidence that a replicative mechanism is not required

We examined a series of extrachromosomal DNA substrates for V(D)J recombination under replicating and nonreplicating conditions. Complete and partial replications were examined by monitoring the loss of prokaryote-specific adenine methylation at 14 to 22 MboI-DpnI restriction sites (GATC) on the substrates. Some of these sites are within 2 bases of the signal sequence ends. We found that neither coding joint nor signal joint formation requires substrate replication. After ruling out replication as a substrate requirement, we determined whether replication had any effect on the efficiency of V(D)J recombination. Quantitation of V(D)J recombination efficiency on nonreplicating substrates requires some method of monitoring the entry of substrate molecules into the cells. We devised such a method by monitoring DNA repair of substrates into which we had substituted deoxyuridine for 10 to 20% of the thymidine nucleotides in the DNA. The substrates which enter the lymphoid cells were repaired efficiently in vivo by the eukaryotic uracil DNA repair system. Upon plasmid harvest, we distinguished repaired (entered) from unrepaired (not entered) plasmids by cleaving unrepaired molecules with uracil DNA glycoylase and Escherichia coli endonuclease IV in vitro. This method of monitoring DNA entry does not appear to underestimate or overestimate the amount of DNA entry. By using this method, we found no significant quantitative effect of DNA replication on V(D)J recombination efficiency.

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

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

Virus-transformed pre-B cells show ordered activation but not inactivation of immunoglobulin gene rearrangement and transcription

Virus-transformed pre-B cells undergo ordered immunoglobulin (Ig) gene rearrangements during culture. We devised a series of highly sensitive polymerase chain reaction assays for Ig gene rearrangement and unrearranged Ig gene segment transcription to study both the possible relationship between these processes in cultured pre-B cells and the role played by heavy (H) chain (mu) protein in regulating gene rearrangement. Our analysis of pre-B cell cultures representing various stages of maturity revealed that transcription of each germline Ig locus precedes or is coincident with its rearrangement. Cell lines containing one functional rearranged H chain allele, however, continue to transcribe and to rearrange the allelic, unrearranged H chain locus. These cell lines appear to initiate but not terminate rearrangement events and therefore provide information about the requirements for activating rearrangement but not about allelic exclusion mechanisms.

Structure of extrachromosomal circular DNAs generated by immunoglobulin light chain gene rearrangements

Recombination at the immunoglobulin kappa or lambda light chain locus generates extrachromosomal circular DNAs. We have isolated circular DNAs from adult mouse spleen cells and prepared a circular DNA clone library. We characterized four J kappa-positive and one J lambda 1-positive clones. The J kappa-clones contained both coding and signal joints of V kappa-J kappa joining, and the J lambda 1-clone contained a signal joint of V lambda 1-J lambda 1 joining. Genomic organization of the V kappa gene families used in these joints suggested the excision of circular DNA preceded by inversion. A specific dinucleotide (P) insertion in the coding joint was observed in two clones. Three coding joints were out of frame and one clone had an in-frame coding joint, although possibly combined with a pseudo-V kappa gene. These kappa-positive circular DNAs are possibly excised from the chromosome by secondary recombinations which replace non-productive primary rearrangements.

Analysis of junctional diversity during B lymphocyte development

Immunoglobulin rearrangement is central to generating antibody diversity because of heterogeneity generated during recombination by deletion or addition of nucleotides at coding joints by the recombinase machinery. Examination of these junctional modifications revealed that the addition of nongermline-encoded nucleotides was more prevalent in adult versus fetal B cells, thus partially limiting the fetal antibody repertoire. In contrast, deletion of nucleotides occurs equivalently in B cells at different stages of development and at different points in B cell ontogeny. Finally, the bias in murine immunoglobulins for one DH segment reading frame occurs at the DHJH intermediate.

Wild-type V(D)J recombination in scid pre-B cells

Homozygous mutation at the scid locus in the mouse results in the aberrant rearrangement of immunoglobulin and T-cell receptor gene segments. We introduced a retroviral vector containing an inversional immunoglobulin rearrangement cassette into scid pre-B cells. Most rearrangements were accompanied by large deletions, consistent with previously characterized effects of the scid mutation. However, two cell clones were identified which contained perfect reciprocal fragments and wild-type coding joints, documenting, on a molecular level, the ability of scid pre-B cells to generate functional protein-coding domains. Subsequent rearrangement of the DGR cassette in one of these clones was accompanied by a deletion, suggesting that this cell clone had not reverted the scid mutation. Indeed, induced rearrangement of the endogenous kappa loci in these two cell clones resulted in a mixture of scid and wild-type V-J kappa joints, as assayed by a polymerase chain reaction and DNA sequencing. In addition, three immunoglobulin mu- scid pre-B cell lines showed both scid and wild-type V-J kappa joins. These experiments strongly suggest that the V(D)J recombinase activity in scid lymphoid cells is diminished but not absent, consistent with the known leakiness of the scid mutation.

Wild-type V(D)J recombination in scid pre-B cells

Homozygous mutation at the scid locus in the mouse results in the aberrant rearrangement of immunoglobulin and T-cell receptor gene segments. We introduced a retroviral vector containing an inversional immunoglobulin rearrangement cassette into scid pre-B cells. Most rearrangements were accompanied by large deletions, consistent with previously characterized effects of the scid mutation. However, two cell clones were identified which contained perfect reciprocal fragments and wild-type coding joints, documenting, on a molecular level, the ability of scid pre-B cells to generate functional protein-coding domains. Subsequent rearrangement of the DGR cassette in one of these clones was accompanied by a deletion, suggesting that this cell clone had not reverted the scid mutation. Indeed, induced rearrangement of the endogenous kappa loci in these two cell clones resulted in a mixture of scid and wild-type V-J kappa joints, as assayed by a polymerase chain reaction and DNA sequencing. In addition, three immunoglobulin mu- scid pre-B cell lines showed both scid and wild-type V-J kappa joins. These experiments strongly suggest that the V(D)J recombinase activity in scid lymphoid cells is diminished but not absent, consistent with the known leakiness of the scid mutation.

Limits on heavy chain junctional diversity contribute to the recurrence of an antibody variable region

Antibody V region structural diversity in the mouse is generated, in part, by the combinatorial joining of different gene segments, as well as by the "imprecision" of these joining events. The same two gene segments can be joined at different locations, and nucleotides can be deleted or added de novo to the segment junction. While it is clear that such junctional processes are a major contributor to V region diversity, the mechanisms that generate this diversity are poorly understood. Here I present sequences in the VH-D-JH region of 34 VH genes that are composed of the same three VH gene segments. In combination with a single V kappa-J kappa pair, these VH genes encode a family of V regions that are recurrently expressed in the immune response of A/J mice to p-azophenylarsonate (Ars). The germline sequences of the three constituent gene segments for these VH genes are known, making it possible to determine the origin of the nucleotides in junctional regions. An examination of the frequency and type of nucleotides present in these regions provides insight into the properties of the segment joining mechanism. In addition, the data suggest that recurrent expression of the anti-Ars V regions which these VH genes partially encode is due not only to antigenic selection, but to the high probability with which these VH genes are formed during B cell differentiation.

Corrective recombination of mouse immunoglobulin kappa alleles in Abelson murine leukemia virus-transformed pre-B cells

Previous characterization of mouse immunoglobulin kappa gene rearrangement products cloned from murine plasmacytomas has indicated that two recombination events can take place on a single kappa allele (R. M. Feddersen and B. G. Van Ness, Proc. Natl. Acad. Sci. USA 82:4792-4797, 1985; M. A. Shapiro and M. Weigert, J. Immunol. 139:3834-3839, 1987). To determine whether multiple recombinations on a single kappa allele can contribute to the formation of productive V-J genes through corrective recombinations, we have examined several Abelson murine leukemia virus-transformed pre-B-cell clones which rearrange the kappa locus during cell culture. Clonal cell lines which had rearranged one kappa allele nonproductively while maintaining the other allele in the germ line configuration were grown, and secondary subclones, which subsequently expressed kappa protein, were isolated and examined for further kappa rearrangement. A full spectrum of rearrangement patterns was observed in this sequential cloning, including productive and nonproductive recombinations of the germ line allele and secondary recombinations of the nonproductive allele. The results show that corrective V-J recombinations, with displacement of the nonproductive kappa gene, occur with a significant frequency (6 of 17 kappa-producing subclones). Both deletion and maintenance of the primary (nonfunctional) V-J join, as a reciprocal product, were observed.

Corrective recombination of mouse immunoglobulin kappa alleles in Abelson murine leukemia virus-transformed pre-B cells

Previous characterization of mouse immunoglobulin kappa gene rearrangement products cloned from murine plasmacytomas has indicated that two recombination events can take place on a single kappa allele (R. M. Feddersen and B. G. Van Ness, Proc. Natl. Acad. Sci. USA 82:4792-4797, 1985; M. A. Shapiro and M. Weigert, J. Immunol. 139:3834-3839, 1987). To determine whether multiple recombinations on a single kappa allele can contribute to the formation of productive V-J genes through corrective recombinations, we have examined several Abelson murine leukemia virus-transformed pre-B-cell clones which rearrange the kappa locus during cell culture. Clonal cell lines which had rearranged one kappa allele nonproductively while maintaining the other allele in the germ line configuration were grown, and secondary subclones, which subsequently expressed kappa protein, were isolated and examined for further kappa rearrangement. A full spectrum of rearrangement patterns was observed in this sequential cloning, including productive and nonproductive recombinations of the germ line allele and secondary recombinations of the nonproductive allele. The results show that corrective V-J recombinations, with displacement of the nonproductive kappa gene, occur with a significant frequency (6 of 17 kappa-producing subclones). Both deletion and maintenance of the primary (nonfunctional) V-J join, as a reciprocal product, were observed.

The chromosome translocation (11;14)(p13;q11) associated with T cell acute leukemia. Asymmetric diversification of the translocational junctions

The t(11;14)(p13;q13) translocation associated with T cell acute lymphocytic leukemia generates two abnormal chromosomes, designated 11p+ and 14q-. To investigate the mechanism of t(11;14)(p13;q11) formation, we analyzed the translocation junctions of 11p+ and 14q- from two patients. The 11p+ junctions consisted of precise fusions of a pseudo recombination signal from chromosome 11 and the downstream recombination signal of the TCR D delta 2 gene segment from chromosome 14. In contrast, the 14q- junctions from both patients were diversified by random loss and addition of nucleotides at the translocation site. This asymmetric pattern of junctional diversification is typical of normal Ig/TCR gene rearrangement, and therefore implies that the t(11;14)(p13;q11) translocation arose due to aberrant activity of the Ig/TCR recombinase.

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

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

Junctional sequences of T cell receptor gamma delta genes: implications for gamma delta T cell lineages and for a novel intermediate of V-(D)-J joining

Nucleotide sequences of a large number of V-(D)-J junctions of T cell receptor (TCR) gamma and delta genes show that most fetal thymocytes express on their surface one of just two gamma delta TCRs known to be expressed by epidermal gamma delta T cells (s-IEL) or intraepithelial gamma delta T cells associated with female reproductive organs (r-IEL). In contrast, gamma delta TCRs expressed on adult thymocytes are highly diverse as a result of multiple combinations of gene segments as well as junctional deletions and insertions, indicating that developmental time-and cell lineage-dependent mechanisms exist that control the extent of gamma delta TCR diversity. In addition, this study revealed a new type of junctional insertion (P nucleotides), which led to a new model of V-(D)-J joining generally applicable to immunoglobulin and TCR genes.

Purification and characterization of a protein that binds to the recombination signal sequence of the immunoglobulin J kappa segment

A protein that binds to the recombination signal sequence (RS) of the immunoglobulin J kappa segment was purified almost to homogeneity from the nuclear extract of a murine pre-B cell line 38B9. A similar binding protein was found in lymphoid cell lines but not in non-lymphoid cell lines. The binding activity was associated with a polypeptide with a molecular weight of 60,000. DNase I footprinting analysis demonstrated that this binding protein interacted with the heptamer and several 3' bases close to the heptamer. The Kd value of the J kappa RS binding protein to the J kappa RS was 1 nM. One base substitution in the heptamer of the J kappa RS greatly reduced the affinity of the J kappa RS binding protein. The high specificity of the binding site of the J kappa RS binding protein suggests that this protein may be involved in V-J recombination.

Dynamics of early B lymphocyte precursor cells in mouse bone marrow: proliferation of cells containing terminal deoxynucleotidyl transferase

Three populations of early B lymphocyte precursor cells lacking mu heavy chains have been defined in mouse bone marrow, based on immunofluorescence labeling for terminal deoxynucleotidyl transferase (TdT) and B220 glycoprotein, as detected by monoclonal antibody 14.8 (TdT+14.8- cells; TdT+14.8+ cells; TdT-14.8+ cells). We have now analyzed the frequency, size distribution, proliferation and production rates of TdT+ cells in mouse bone marrow. These formed well-defined populations of medium-sized cells, the TdT+14.8+ cells tending to be larger than TdT+14.8- cells (modal cell diameters in cytocentrifuge preparations; 10.0 microns and 9.0 microns, respectively). Some TdT+ cells (1%-2%) were normally in metaphase, the TdT being dispersed through the cytoplasm. After inducing mitotic arrest with vincristine, the incidence of TdT+ cells in metaphase increased linearly from 2 to 4 h, indicating a turnover of 5.1%/h for TdT+14.8- cells and 9.0%/h for TdT+14.8+ cells. Subtraction of turnover data for TdT+14.8+ cells from those previously obtained for 14.8+ mu- cells gave values for the population of TdT-14.8+ cells. The calculated daily turnover of cells in the three compartments increased progressively (TdT+14.8-, 2.5 x 10(6) cells; TdT+14.8+, 5.0 x 10(6) cells; TdT-14.8+, 36.0 x 10(6) cells), accompanied by a shortening of the average apparent cell cycle time (TdT+14.8-, 20 h; TdT+14.8+, 11 h; TdT-14.8+, 8 h). The results demonstrate a progressive expansion of cell production at three putatively successive stages of early B lymphocyte development before the expression of mu chains. The findings contribute to a kinetic model of primary B cell genesis in mouse bone marrow.

NBP, a protein that specifically binds an enhancer of immunoglobulin gene rearrangement: purification and characterization

Immunoglobulin and T-cell receptor (TCR) genes are encoded in discrete germ line DNA segments that are joined by site-specific recombination during lymphocyte development. These DNA rearrangements are mediated by conserved heptamer and nonamer DNA sequence elements that lie near the sites of recombination. In this paper we show that the nonamer element coincides with the recognition site for a specific DNA-binding protein: mutations within the nonamer sequence, but not outside of it, decrease affinity for the binding protein by 300- to 1000-fold. Deletion of the binding site for the protein results in at least a 50-fold decrease in recombination frequency in vivo. By a combination of conventional and recognition site affinity chromatography, we have achieved greater than 20,000-fold purification of the protein from calf thymus, with an overall yield of 22%. The purified protein, which we now call nonamer-binding protein (NBP), has an apparent molecular weight of 63,000 and a frictional ratio of 1.27, suggesting that it exists as a globular monomer in 0.5 M NaCl. Our observations suggest that NBP is a component of the recombinational apparatus.

Comparison of filler DNA at immune, nonimmune, and oncogenic rearrangements suggests multiple mechanisms of formation

Extra nucleotides (termed filler DNA) are commonly found at the junctions of genetic rearrangements in mammalian cells. The filler DNA at immune system rearrangements, which are called N regions, are generated at VDJ joints primarily by terminal deoxynucleotidyl transferase. However, the origin of filler DNA at genetic rearrangements in nonlymphoid cells is uncertain. In an analysis of more than 200 junctions that arose by circularization of transfected linear DNA (D. B. Roth and J. H. Wilson, Mol. Cell. Biol. 6:4295-4304, 1986), we found 18 junctions with extra nucleotides exactly at the point of circularization. Analysis of these 18 junctions indicated that nonlymphoid cells could add extra nucleotides to the ends of duplex DNA. The characteristics of the extra nucleotides at these junctions and at 31 other rearrangement junctions from nonlymphoid cells were quite similar, suggesting that many genetic rearrangements may pass through a stage with free DNA ends. A comparison of the filler DNA at these 49 nonimmune system rearrangements with 97 N regions derived from immune system rearrangements suggested that lymphoid and nonlymphoid cells use different mechanisms for insertion of filler DNA, as expected from the absence of detectable terminal deoxynucleotidyl transferase in cells from nonlymphoid tissues. The filler DNAs at a smaller group of 22 translocations associated with cancer had features in common with both immune and nonimmune system rearrangements and therefore may represent a mixture of these two processes. Mechanisms that might account for the presence of filler DNA in nonlymphoid cells are discussed.

Comparison of filler DNA at immune, nonimmune, and oncogenic rearrangements suggests multiple mechanisms of formation

Extra nucleotides (termed filler DNA) are commonly found at the junctions of genetic rearrangements in mammalian cells. The filler DNA at immune system rearrangements, which are called N regions, are generated at VDJ joints primarily by terminal deoxynucleotidyl transferase. However, the origin of filler DNA at genetic rearrangements in nonlymphoid cells is uncertain. In an analysis of more than 200 junctions that arose by circularization of transfected linear DNA (D. B. Roth and J. H. Wilson, Mol. Cell. Biol. 6:4295-4304, 1986), we found 18 junctions with extra nucleotides exactly at the point of circularization. Analysis of these 18 junctions indicated that nonlymphoid cells could add extra nucleotides to the ends of duplex DNA. The characteristics of the extra nucleotides at these junctions and at 31 other rearrangement junctions from nonlymphoid cells were quite similar, suggesting that many genetic rearrangements may pass through a stage with free DNA ends. A comparison of the filler DNA at these 49 nonimmune system rearrangements with 97 N regions derived from immune system rearrangements suggested that lymphoid and nonlymphoid cells use different mechanisms for insertion of filler DNA, as expected from the absence of detectable terminal deoxynucleotidyl transferase in cells from nonlymphoid tissues. The filler DNAs at a smaller group of 22 translocations associated with cancer had features in common with both immune and nonimmune system rearrangements and therefore may represent a mixture of these two processes. Mechanisms that might account for the presence of filler DNA in nonlymphoid cells are discussed.

V(D)J recombination: a functional definition of the joining signals

Two conserved DNA sequences serve as joining signals in the assembly of immunoglobulins and T-cell receptors from V-, (D)-, and J-coding segments during lymphoid differentiation. We have examined V(D)J recombination as a function of joining signal sequence. Plasmid substrates with mutations in one or both of the heptamer-spacer-nonamer sequences were tested for recombination in a pre-B-cell line active in V(D)J recombination. No signal variant recombines more efficiently than the consensus forms of the joining signals. We find the heptamer sequence to be the most important; specifically, the three bases closest to the recombination crossover site are critical. The nonamer is not as rigidly defined, and it is not important to maintain the five consecutive As that distinguish the consensus nonamer sequence. Both types of signals display very similar sequence requirements and have in common an intolerance for changes in spacer length greater than 1 bp. Although the two signal types share sequence motifs, we find no evidence of a role in recombination for homology between the signals, suggesting that they serve primarily as protein recognition and binding sites.

Novel rearrangements at the immunoglobulin D locus. Inversions and fusions add to IgH somatic diversity

IgH rearrangements (VH-D, D-JH) are central to the generation of antibody diversity. The majority of the diversity seen in the third hypervariable region is generated by the D segment and at the joints formed by both junctional and N segment variation during D-JH and VH-D rearrangements. The mechanisms that regulate rearrangement are thought to obey the 12/23 rule, wherein D-D or VH-JH rearrangements are precluded. Here, we present evidence that D-D fusions do in fact occur, either as direct or inverted rearrangements. The fused D segments so generated may be fully capable of proceeding in subsequent D-JH and VH-D rearrangements. The resultant VH-D-D-JH recombinations add another dimension to the potential repertoire of IgH V regions by increasing the level of combinatorial diversity and by providing additional sites for N region variation.

Excision products of immunoglobulin gene rearrangements

We have isolated circular DNAs from splenocytes of euthymic and athymic mice, and prepared the DNA libraries of 1.5 X 10(6) clones. Hundreds of clones homologous to immunoglobulin (Ig) heavy chain segments (DSP2 and DQ52-JH) or light chain segments (J kappa and J lambda) have been identified. Southern hybridization predicted that three of 12 euthymic mouse clones homologous to DQ52-JH and four of 10 athymic mouse clones homologous to DSP2 contained reciprocal recombination products of D-J joining. Some of these clones were characterized by sequencing: two clones contained the precise excision product of the recombination of a DSP2 segment with either JH2 or JH3 segment; two clones showed imprecise ligation of the DSP2-JH2 coding joint and precise ligation of the DFL16.1-JH3 reciprocal joint in the same molecule. They seem to represent a replacement of the pre-existing DSP2-JH2 rearrangement by joining an upstream DFL16 segment to a downstream JH3 segment. The presence in extrachromosomal DNA of a reciprocal recombination product of DH-JH joining is consistent with the view that immunoglobulin genes, like T cell receptor (TCR) genes, can be rearranged in B cell lineage by the looping-out and excision of chromosomal DNA.

Novel strand exchanges in V(D)J recombination

We describe novel products of V(D)J recombination in which signal sequences become joined to coding elements, in contrast to the standard reaction whose products are junctions of two signal sequences or two coding elements. In this variant reaction, the recombination machinery evidently recognizes signal sequences and introduces strand breaks at the normal positions, but then connects the elements in unusual combinations. The lack of fixed directionality indicates that recombination sites are not uniquely aligned when strand exchange occurs. The discovery of these variant junctions suggests a model for the evolution of the antigen receptor loci.

Stable propagation of the active transcriptional state of an immunoglobulin mu gene requires continuous enhancer function

Enhancer sequences control the expression of the immunoglobulin mu heavy chain gene. In this study we examined whether the active transcriptional state of the mu gene can be propagated from mother to daughter cells after deletion of its enhancer. A mu gene that contains the enhancer flanked by D and J recombination signals was stably introduced into pre-B cells, resulting in mu gene transcription. Subsequent deletion of the enhancer from the transfected gene by D-to-J joining reproducibly resulted in switching off of mu expression. Moreover, transcriptional inactivation occurred although the mu gene was found to be hypomethylated prior to deletion of the enhancer. We conclude that the enhancer does not confer upon the mu gene "memory" of its active transcriptional state. Thus, the enhancer seems to be required both for establishment and for maintenance of mu gene expression.

Alternative V kappa gene rearrangements in a murine B cell lymphoma. An explantation for idiotypic heterogeneity

Idiotype variants of 38C13, a murine B cell lymphoma, have been isolated by immunoselection with antiidiotype mAbs. The V region genes for the kappa light chains and mu heavy chains expressed by these tumor cells were sequenced and compared. There was no evidence for V region somatic point mutation in this tumor. However, while the heavy chain genes were all identical, the light chain genes were all different. The light chain genes of each variant were derived from the V kappa-Ox1 gene family and joined to J kappa 4, whereas the light chain gene of the parental tumor was derived from the V kappa 9 family and joined to J kappa 2. Two of the variants used the identical V kappa gene but differed by the inclusion of a variable number of additional nucleotides in the V/J joint. Thus, the idiotypic heterogeneity of this B cell lymphoma arises as a consequence of alternative light chain rearrangements rather than point mutation. This process repetitively uses members of the same V kappa gene family. Two of the variants use the identical V kappa and J kappa gene segments but differ by the presence of extra nucleotides at the V kappa/J kappa joint.

Lymphoid V(D)J recombination: nucleotide insertion at signal joints as well as coding joints

The coding regions of antigen receptor genes assembled by variable-diversity-joining region [V(D)J] recombination are known in many cases to have undergone deletions of several nucleotides and also to contain insertions of noncoded nucleotides at the recombined junction (the coding joint). By using extrachromosomal recombination substrates to transfect lymphoid cell lines, we show that the signal joint (the fusion of the corresponding recognition signal sequences) can also contain insertions; however, nucleotide loss from the signals is very rare. The frequency of nucleotide addition varies among pre-B-cell lines in a manner proportional to their content of terminal deoxynucleotidyltransferase. We also find frequent nucleotide additions (and deletions) at coding joints, but in this case there is no strong correlation with the level of terminal deoxynucleotidyltransferase activity. Inserts at both signal and coding joints are rich in G + C, consistent with the base utilization preference of this enzyme.

Unusual immunoglobulin gene rearrangement leads to replacement of recombinational signal sequences

An unexpected immunoglobulin gene rearrangement, signal sequence replacement, was observed in which the recombinational signal sequences of a VH gene segment are fused intact to the 5' end of a DJH element. Nucleotides are not lost from the signal sequences, but they may be lost from the DJH coding sequence. Signal sequence replacement may result from the alternative resolution of an intermediate in VH-to-DJH recombination. This type of rearrangement provides a means to alter the targeting of immunoglobulin gene segments and suggests a mechanism for the occurrence of VH-JH junctions in vivo. Signal sequence replacement may represent an additional pathway for the generation of antibody diversity.

The defect in murine severe combined immune deficiency: joining of signal sequences but not coding segments in V(D)J recombination

Pre-B and pre-T cell lines from mutant mice with severe combined immune deficiency (scid mice) were transfected with plasmids that contained recombination signal sequences of antigen receptor gene elements (V, D, and J). Recovered plasmids were tested for possible recombination of signal sequences and/or the adjacent (coding) sequences. Signal ends were joined, but recombination was abnormal in that half of the recombinants had lost nucleotides from one or both signals. Coding ends were not joined at all in either deletional or inversional V(D)J recombination reactions. However, coding ends were able to participate in alternative reactions. The failure of coding joint formation in scid pre-B and pre-T cells appears sufficient to explain the absence of immunoglobulin or T cell receptor production in scid mice.

Structure of extrachromosomal circular DNAs excised from T-cell antigen receptor alpha and delta-chain loci

Small polydisperse circular (spc) DNA was isolated from mouse thymocytes, fragmented by HindIII digestion and cloned into the vector. Sixty DNA clones were randomly selected from the 10,400 phage library. The average size of insert was one-fifth of the original circular molecule. Twenty spc-DNA clones were homologous to DNA probes derived from T-cell antigen receptor (TCR) alpha-chain loci. We have characterized nine clones by DNA sequencing; they contain new germline sequences of the TCR alpha-chain variable (V alpha) and joining (J alpha) gene segments and the products out of the recombination of a V alpha with a J alpha gene segment. An additional four spc-DNA clones carried a new rearranging gene of the TCR delta-chain that is located between V alpha and J alpha genes. At least nine of 60 DNA clones carried the recombination junction of a heptamer-heptamer head-to-head structure expected from an excised product of V-J joining. This shows that most extrachromosomal circular DNAs in the thymus are formed by a sequence-dependent recombination mechanism. We suggest that a functional T-cell receptor V alpha gene can be constructed by somatic random rearrangements through successive looping-out, excision and deletion.

The scid gene encodes a trans-acting factor that mediates the rejoining event of Ig gene rearrangement

Homozygous mutation at the scid locus in the mouse impairs lymphoid development and results in animals deficient in B and T cells. We found that immunoglobulin heavy-chain gene rearrangement was blocked at the D-JH stage in Abelson-transformed scid pre-B cell lines. Examination of the recombinational junctions indicated that the correct gene elements (D and JH) were assembled, as shown by the presence of D region and JH-region DNA on the breakpoint restriction fragments cloned from the genome of the scid cell lines. All rearrangement events were accompanied by deletions of varying sizes such that none of the rearrangements resulted in the production of functional immunoglobulins. The breakpoints of the rearrangement events did not correspond to the utilization of a novel heptamer-nonamer recombination signal but probably arose by nonspecific deletion from distal JH and D heptamer-nonamer signals in the process of recombination. scid pre-B cell lines were infected with a recombinant retrovirus (DGR) containing Ig joining signals. Aberrant rearrangements were observed in DGR DNA that was integrated randomly throughout the mouse genome, which suggested that the mutation in scid mice encodes a trans-acting factor that is part of the lymphoid gene recombination machinery.

Evidence that the intervening sequence was excised as a linear molecule during D beta-J beta rearrangement in T-cell receptor beta chain gene loci

In a previous paper (Proc. Natl. Acad. Sci. USA 84: 4264, 1987) we reported an unusual DNA rearrangement in T-cell receptor beta chain gene loci in cells from a patient with human T-cell leukemia. A D beta 1-J beta 2.3 junction was found on one chromosome, while the other chromosome kept the germline configuration. Although the DNA fragment located between the D beta 1 and J beta 2.3 loci should have disappeared from the cells, it was found on chromosome 6 as an inserted segment. We have now determined the nucleotide sequences bordering both sides of the inserted segment. The signal sequence for D beta-J beta rearrangement at the 5' side of J beta 1.2 gene seems to have been used for the insertion. The 3' end of the inserted segment corresponded to the edge of the signal heptamer at the 5' side of J beta 2.3 which was used for the initial D beta 1-J beta 2.3 joining. This indicates that, during D beta-J beta rearrangement, the intervening sequence was excised as a linear molecule.

Rearrangement of exogenous immunoglobulin VH and DJH gene segments after retroviral transduction into immature lymphoid cell lines

A model substrate for the joining of Ig VH and DJH elements has been constructed in a retroviral vector carrying a selectable marker whose expression is independent of the arrangement of the resident Ig gene segments. The substrate was introduced into lymphoid and nonlymphoid cells, and site-specific recombination between the VH and DJH elements was monitored by a direct hybridization assay. Joining of the exogenous gene segments was observed in cell lines representative of three distinct stages in early B cell differentiation. Rearrangement was not observed in three cell lines derived from mature B cells, or in a fibroblastoid cell line. The VH and DJH elements were initially arranged so that the VH-DJH junction and the recombined flanking sequences could be recovered after rearrangement. By molecular cloning and nucleotide sequence determination, VH-DJH junctions formed upon rearrangement of the substrate were found to resemble closely similar junctions in functional H chain genes. The joining of VH and DJH elements was observed to be asymmetric; loss of nucleotides occurred at the coding joints, but not at the junctions between flanking sequences. Our results suggest that Ig H and L chain gene segments are joined by a common mechanism that is more active in B cell precursors than in mature B cells. These observations provide further evidence that the rearrangement of Ig gene segments occurs by a nonreciprocal recombinational mechanism. The model substrate described here is likely to be of use in defining the nucleotide sequences that mediate rearrangement and in examining the developmental specificity of this process.

A pre-B cell nuclear protein that specifically interacts with the immunoglobulin V-J recombination sequences

DNA-nuclear protein interactions were studied with synthetic recombination signal sequences (RSSs) for immunoglobulin V-J joining. With a gel retardation assay, a DNA-binding protein that specifically interacts with RSSs was detected in nuclear extracts from a pre-B cell line, 38B9. This protein was found in all the recombination-competent pre-B cell lines tested in this study, but not in myeloma, mature T cell, monocyte, or fibroblast cell lines. DNA footprint analysis with dimethyl sulfate demonstrated that the 7-mer region of the RSS was strongly protected when complexed with the binding protein. Furthermore, a single base substitution in the 7-mer region totally abolished the binding. The molecular mechanism of V-J joining is discussed in the context of the RSS-binding protein.

Increased frequency of N-region insertion in a murine pre-B-cell line infected with a terminal deoxynucleotidyl transferase retroviral expression vector

The role of terminal deoxynucleotidyl transferase (TdT) in the insertion of N regions into the junctional sites of immunoglobulin genes was investigated. Pre-B-cell lines capable of continuous rearrangement of immunoglobulin light-chain genes and differing only in the presence or apparent absence of TdT were derived by infecting cells with a TdT retroviral expression vector or a control vector. The cell lines were then superinfected with a retrovirus-based artificial immunoglobulin gene rearrangement substrate. The substrate was allowed to rearrange in the cell lines and the rearranged proviruses were rescued from the cell lines. Nucleotide sequence analysis of the V-J junctions of the proviral rearranged genes showed a fivefold greater frequency of N-region insertion in proviruses rescued from the TdT+ cell lines than in those rescued from the TdT- cell lines, so that at least 50% of the rearrangements that occurred in the presence of TdT had N regions. It is thus evident that TdT can stimulate N-region insertion, and the enzyme is presumably directly responsible for adding nucleotides at V-J and other immunoglobulin and T-cell receptor gene junctions.

Two pairs of recombination signals are sufficient to cause immunoglobulin V-(D)-J joining

The minimum sequence requirements for antigen receptor V-(D)-J joining were studied by constructing recombination-substrates containing synthetic recombination signals and introducing them into a recombination-competent pre-B cell line. Two sets of heptamer (CACTGTG) and nonamer (GGTTTTTGT) sequences were shown to be sufficient to cause the V-(D)-J joining, if the 12- and 23-base pair spacer rule is satisfied. A point mutation in the heptamer sequence, or a change in the combination of the two spacer lengths, drastically reduced the recombination.

Development of the primary antibody repertoire

The ability to generate a diverse immune response depends on the somatic assembly of genes that encode the antigen-binding portions of immunoglobulin molecules. In this article, we discuss the mechanism and control of these genomic rearrangement events and how aspects of this process are involved in generating the primary antibody repertoire.

DNA inversion within the apolipoproteins AI/CIII/AIV-encoding gene cluster of certain patients with premature atherosclerosis

The genes coding for apolipoproteins (apo) AI, CIII, and AIV, designated APOA1, APOC3, and APOA4, respectively, are closely linked and tandemly organized in the long arm of the human chromosome 11. A DNA rearrangement involving the genes encoding apoAI and apoCIII in certain patients with premature atherosclerosis has been associated with deficiency of both apoAI and apoCIII in the plasma of these patients. Structural characterization of the genes for apoAI and apoCIII in one of these patients indicates that this rearrangement consists of a DNA inversion containing portions of the 3' ends of the apoAI and apoCIII genes, including the DNA region between these genes. The breakpoints of this DNA inversion are located within the fourth exon of the apoAI gene and the first intron of the apoCIII gene. Thus, this DNA inversion results in reciprocal fusion of the apoAI and apoCIII gene transcriptional units. Expression of these gene fusions in cultured mammalian cells results in stable mRNA transcripts with sequences representing fusions of the apoAI and apoCIII mRNAs. These results indicate that absence of transcripts with correct apoAI and apoCIII mRNA sequences causes apoAI and apoCIII deficiency in the plasma of these patients and suggest that these apolipoproteins are involved in cholesterol homeostasis and protection against premature atherosclerosis.

Developmental stage specificity of the lymphoid V(D)J recombination activity

We have examined the level of immunoglobulin gene V(D)J recombination activity in a number of cell lines derived from lymphoid or nonlymphoid lineages. The assay we employed uses extrachromosomal DNA as substrate and thereby avoids difficulties associated with the use of chromosomally integrated substrates. The recombination activity decreases during B-lymphoid development. It is highest at the earliest stages of committed B-cell differentiation and then falls progressively, reaching undetectable levels at the mature B-cell stage. The activity is also present in multipotential progenitors of myeloid cells and in pre-T cells but not mature T cells. No activity was found in several nonhematopoietic cell lines. Recombination was seen only among substrate molecules which had replicated in the eukaryotic cells. Several possible interpretations of this result are discussed.

Increased frequency of N-region insertion in a murine pre-B-cell line infected with a terminal deoxynucleotidyl transferase retroviral expression vector

The role of terminal deoxynucleotidyl transferase (TdT) in the insertion of N regions into the junctional sites of immunoglobulin genes was investigated. Pre-B-cell lines capable of continuous rearrangement of immunoglobulin light-chain genes and differing only in the presence or apparent absence of TdT were derived by infecting cells with a TdT retroviral expression vector or a control vector. The cell lines were then superinfected with a retrovirus-based artificial immunoglobulin gene rearrangement substrate. The substrate was allowed to rearrange in the cell lines and the rearranged proviruses were rescued from the cell lines. Nucleotide sequence analysis of the V-J junctions of the proviral rearranged genes showed a fivefold greater frequency of N-region insertion in proviruses rescued from the TdT+ cell lines than in those rescued from the TdT- cell lines, so that at least 50% of the rearrangements that occurred in the presence of TdT had N regions. It is thus evident that TdT can stimulate N-region insertion, and the enzyme is presumably directly responsible for adding nucleotides at V-J and other immunoglobulin and T-cell receptor gene junctions.

High-frequency deletional rearrangement of immunoglobulin kappa gene segments introduced into a pre-B-cell line

We describe an immunoglobulin gene recombination indicator in which a specific rearrangement via deletion results in the acquisition of a dominant phenotype. The indicator consists of the Escherichia coli xanthine/guanine phosphoribosyltransferase (gpt) gene, whose translation is prevented by the presence of an upstream initiation codon out of frame with respect to the gpt coding sequence. Flanking this barrier initiation codon are the heptamer-spacer-nonamer recognition sequences from a kappa chain variable region (V kappa) and from a kappa chain joining region (J kappa). A proper V-J joint results in the deletion of the translational barrier and allows expression of the selectable marker. When tested by transfection into fibroblasts, no rearrangements were detected and the presence of the barrier initiation codon was sufficient to completely abolish gpt expression in these cells. Similarly, no rearrangements were detected after transfer of the test gene into myeloma cells. However, when the construct was introduced into the pre-B-cell line 38B9, greater than 80% of the transfected cells showed evidence of a specific rearrangement. These rearrangements were associated with the translation of gpt, although no selection for its expression was needed. DNA sequence analysis of six different V-J joints revealed that the rearrangement proceeded with a high degree of accuracy. These results indicate that only very minimal DNA sequences (21 base pairs 5' of the V heptamer and 4 base pairs 3' of its nonamer; less than 45 base pairs 5' of the J nonamer and 3' of its heptamer) are required for efficient rearrangement and provide formal proof that kappa gene segments can rearrange by a deletional mechanism.

N segment insertion and region-directed somatic hypermutation in a kappa gene of a t(2;8) chromosomal translocation

A detailed molecular analysis of both reciprocal recombination products of the variant t(2;8) chromosomal translocation of the Burkitt lymphoma derived cell line JI and their germline counterparts was carried out. The breakpoint on chromosome 8 is localized 28 kb to the 3' side of the c-myc protooncogene, the breakpoint on chromosome 2 was found to be within an aberrantly rearranged VK gene (abbreviations ref. 1). Novel features of the immunoglobulin moiety involved in this process include insertion of extra nucleotides in the V-J junction which have the characteristics of a N segment as it has been found up to now only in heavy chain and T cell receptor genes; the occurrence of somatic mutations in 8q+ and not in 2p-. These data allow a reconstruction of the course of events in the cell line JI; remarkable sequence regularities at the chromosomal breakpoints consisting of symmetrically placed dinucleotides and elements related to the hepta- and nonanucleotide recombinase recognition sequences are discussed in the context of the translocation mechanism.