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The Journal of Immunology, 2000, 164: 1916-1924.
Copyright © 2000 by The American Association of Immunologists

Heavy Chain Diversity Region Segments of the Channel Catfish: Structure, Organization, Expression and Phylogenetic Implications1 ,2

J. Russell Hayman and Craig J. Lobb3

Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216


   Abstract
Top
 Abstract
Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Circular DNA, derived from lymphocytes of juvenile channel catfish, was used to construct {lambda} libraries that were screened to identify the products of immunoglobulin DH-JH excision events. Clones were characterized that contained DH to JH recombination signal joints. The signal joints represented 23-bp recombination signal sequences (RSS) identical to germline JH segments that were adjacent to DH 12-bp RSS elements. DH flanking regions within the clones were used to probe a genomic library. Three germline DH gene segments containing 11–19 bp coding regions flanked by 12-bp RSS elements with conserved heptamers and nonamers were identified. The DH locus is closely linked to the JH locus, and Southern blots indicate that the DH segments represent different single member gene families. Analysis of H chain cDNA shows that each germline DH segment was expressed in functional VDJ recombination events involving different JH segments and members of different VH families. Several aspects of CDR3 junctional diversity were evident, including deletion of coding region nucleotides, N- and P-region nucleotide additions, alternate DH reading frame utilization, and point mutations. Coding region motifs of catfish DH segments are phylogenetically conserved in some DH segments of higher vertebrates. These studies indicate that the structure, genomic organization, and recombination patterns of DH segments typically associated with higher vertebrates evolved early in vertebrate phylogeny at the level of the bony fish.


   Introduction
Top
 Abstract
 Introduction
Materials and Methods
 Results
 Discussion
 References
 
During mammalian B cell development, H chain V region gene recombination occurs in two steps. Initial recombination between DH and JH gene segments forms the rearranged DJ, which subsequently recombines with a VH gene segment to form the rearranged VDJ. Recombination between gene segments is mediated by recombinase enzymes that recognized the recombination signal sequences (RSS)4 adjacent to the gene segment coding regions. Recombination may occur when one segment has a 23-bp spacer and the other has a 12-bp spacer (the 12/23 rule) (1, 2, 3, 4). During recombination, sequence variation occurs as a result of junctional formation. Nucleotides at the ends of the coding regions may be deleted, and there may be insertion of nontemplated nucleotides (N-region additions). If nucleotides are not deleted from the coding region, nucleotides palindromic to the end of the coding region may also be added to the coding sequence (P-region additions). Through these mechanisms and in concert with somatic mutation, the inherent structural diversity of expressed H chain V regions arises (reviewed in Ref. 4).

There are three apparent roles served by DH segments. Fundamentally DH segments serve to bridge VH and JH segments and are required to provide combinatorial diversity. Second, DH segments contribute sequence diversity to the H chain complementarity-determining region 3 (CDR3) region. Lastly, the expression of the rearranged DJ segment may provide B cell regulatory function by preventing utilization of H chains with D regions in alternate reading frames. These regulatory mechanisms, known to occur in the mouse (5) but not in humans (6), are dependent upon the presence of initiation codons found upstream of murine DH segments.

Phylogenetic studies have shown that the structure of VH and JH segments is conserved in lower vertebrates, but information on the structure, organization, and function of DH segments is limited. In the chicken, the H chain locus contains multiple VH gene segments, only 1 of which is functional, a single JH gene segment, and 16 DH gene segments (7, 8, 9). Fifteen of the DH segments are highly homologous suggesting that these arose by duplication. The D segments lack upstream initiation codons, are flanked on both sides by RSS elements containing a 12-bp spacer, and P-, but not N-nucleotides, are observed at the DJ and VDJ junctions (9). In Xenopus, the only amphibian presently examined, only one complete sequence of a DH segment is known, but cDNA evidence indicates that other DH segments are likely present. This element is flanked on both sides by RSS elements with 12-bp spacers, and the potential coding region is 6 nt in length. cDNA studies suggest that DH segments are a more important source of diversity in adults rather than tadpoles (10, 11).

In the horned shark, H chain gene segments are closely linked within multiple gene clusters (12). The general organizational pattern of the segments within these clusters is V-D1-D2-J-C. The VH and JH segments have 23-bp RSS spacers located downstream and upstream, respectively, of their coding sequences. In >99% of these clusters, the D1 segment is flanked by 12- and 23-bp RSS spacers, whereas the D2 segment is flanked on both sides by 12-bp RSS spacers. There are 200 or more different gene clusters, and in about half of these clusters germline-joined VD or VDJ segments exist. In the other clusters, recombination appears restricted to segments within a cluster and both the D1 and D2 segments appear to be utilized (13). The sequences of the D1 and D2 segments in different clusters are highly conserved which suggests that shark DH gene segments encode only limited CDR3 structural diversity.

Studies with the channel catfish have provided insight into the early evolutionary patterns of Ig gene organization and genetic diversity. The genomic organization of H chain gene segments in the catfish, a teleost (bony) fish, is different from that known in sharks. The Cµ gene, which encodes the predominant serum Ig and Ab of catfish (14, 15), exists as a single genomic copy (16, 17), a general conclusion that has been extended to other teleost fish (18, 19, 20, 21). In addition, it has been shown that VH gene families extensively diverged at the level of the bony fish. Southern blot studies indicate an extensive genomic VH repertoire consisting of at least seven catfish VH gene families, which represent >120 different gene segments (22). Members of these different families are interspersed with one another in the locus and are closely linked. Each of the sequenced VH members has a typical RSS with a 22- to 24-bp spacer located downstream of the coding region (23). Studies on the JH locus of the catfish also indicate structural and organizational patterns similar to those found in higher vertebrates. Nine JH gene segments (designated JH1 through JH9) are tightly clustered within a 2.2-kb region located immediately upstream from Cµ. Each JH segment appears to be functional, and each contains an RSS element with a 22- to 24-bp spacer located immediately upstream of the coding region (24, 25).

These studies indicate that catfish VH and JH gene segments would not be expected to undergo VJ joining without violating the 12/23 rule of recombination (3). In addition, earlier cDNA analyses revealed sequence diversity within the H chain CDR3 region that was not encoded by VH or JH segments suggesting, that DH segments must contribute to CDR3 diversity in the catfish (26). However, at this point DH segments have not been identified in bony fish. With these studies showing that the structure and organization of VH and JH gene segments co-evolved with single-copy C region genes, it was important to determine whether DH segments are present, and if so to determine their structure and genomic organization. This report characterizes DH segments of the channel catfish and provides new insights into the early evolutionary patterns of Ig gene organization and the mechanisms of CDR3 diversity.


   Materials and Methods
Top
 Abstract
 Introduction
 Materials and Methods
Results
 Discussion
 References
 
Construction and analysis of channel catfish extrachromosomal circular DNA (cir-DNA) library

Cir-DNA was isolated from the anterior kidney of 30 individual 4- to 6-mo-old channel catfish, Ictalurus punctatus (~26 g each) using a modified alkaline lysis procedure (27) with subsequent ATP-dependent DNase treatment (United States Biochemical, Cleveland, OH). Briefly, 108 anterior kidney lymphocytes were lysed in a buffer containing 50 mM NaCl, 2 mM EDTA, and 1% SDS (pH 12.5). The solution was neutralized with the addition of 0.2 volumes of 1 M Tris-HCl (pH 7.0) and RNase treated. After the addition of 0.1 volumes of 5 M NaCl, the solution was proteinase K treated, phenol/chloroform extracted, and precipitated with 2 volumes of ethanol. The solution was then treated at 37°C with 2 U/microgram of ATP-dependent DNase in a buffer containing 6.7 mM glycine (pH 9.4), 30 mM MgCl2, 8.3 mM 2-ME, 0.5 mM ATP, and 10 µg/ml of BSA.

A library was constructed from the enriched cir-DNA by cloning into the EcoRI site of {lambda}ZAP II (Stratagene, La Jolla, CA). The library contained 2.3 x 105 recombinants and was subjected to one round of amplification. Replicate lifts were screened with two different probes. The first, a 1.5-kb EcoRI-ClaI restriction fragment, represented a region immediately 5' of the JH locus. The second, a 4.2-kb XbaI restriction fragment, represented a region downstream of the JH locus and included the Cµ1 and Cµ2 coding region domains. Selected cir-DNA clones were subcloned into pBluescript SK(-).

Cloning and characterization of DH gene segments

A previously constructed {lambda}DASH II genomic library (24) was screened by hybridization using fragments obtained from the cir-DNA clones, and nine overlapping genomic clones were isolated. Southern blot analysis determined which EcoRI fragment contained DH gene segments, and these were subcloned into pBluescript SK(-). Overlapping nested deletion subclones were constructed using exonuclease III as previously described (25) and sequenced using Sequenase 2.0 (United States Biochemical).

RNA isolation, cDNA construction, and PCR approaches

Total RNA was purified by lysing PBL obtained from two adult channel catfish as described earlier (28). mRNA was purified from the total by oligo(dT) column elution (Qiagen, Chatsworth, CA) and double-stranded cDNA was synthesized utilizing Moloney murine leukemia virus (M-MuLV) reverse transcriptase and oligo(dT) priming (Pharmacia Biotech, Piscataway, NJ).

The V regions of the expressed Ig H chains were amplified by PCR using forward primers specific for the FR1 regions of the VH1–VH6 variable gene families and a reverse primer specific for the Cµ1 domain. The sequences of the primers was as follows: VH1-FR1, 5'-ATGGACAGTCCCTGACC-3'; VH2-FR1, 5'-G/TGAACTGACTCAGCCT-3'; VH3-FR1, 5'-TATTCCTGCAGTCAGAC-3'; VH4-FR1, 5'-GGGATGTGCAGTAGAAC-3'; VH5-FR1, 5'-CTGAGCTCATCCAGCCA-3'; VH6-FR1, 5'-GCTGCTGGCAGCCGTAC-3'; and Cµ1–18, 5'-GCCGCACTGCCACACGGG-3'. Thirty cycles of PCR amplification were conducted using the GeneAmp DNA Amplification kit (Perkin-Elmer Cetus, Norwalk, CT), a Twin Block System thermocycler (Ericomp, San Diego, CA), and the following amplification parameters: 1 min at 94°C, 2 min at 50°C, and 3 min at 72°C for a total of 30 cycles. The amplicons were purified and ligated into a T/A plasmid (Invitrogen; Carlsbad, CA). Clones were randomly chosen for sequencing.

Database comparisons of the derived nucleic acid sequences were conducted with BLAST algorithm (29). Selected sequences were also analyzed using the Pustell DNA/Protein analysis program (IBI, New Haven, CT). Assignment of nucleotides to the framework region (FR) and CDR-encoded regions is according to Kabat et al. (30).

Southern blot analysis

Genomic DNA, obtained from the nucleated erythrocytes of an individual adult channel catfish, was restricted and blotted onto a nylon membrane. The blots were hybridized with either a 700-bp StuI-StyI restriction fragment derived from a region located downstream of the DH1 germline gene segment or with a 950-bp SstI fragment derived from a region located downstream of the DH2 germline gene segment. The methods for labeling of genomic restriction fragments as well as conditions for Southern blot hybridization were identical to those described earlier (24).


   Results
Top
 Abstract
 Introduction
 Materials and Methods
 Results
Discussion
 References
 
Characterization of DH-JH recombination signal joints in cir-DNA of the channel catfish

Inspection of H chain sequences derived from earlier cDNA studies indicated that it would be difficult to design specific primers for use in PCR strategies to characterize catfish germline DH segments. However, the catfish JH locus had been sequenced, and we reasoned that it should be possible to make a library derived from cir-DNA and effectively probe this library to identify possible excision products of DH to JH recombination events. A {lambda} library was made using cir-DNA derived from lymphocytes of the anterior kidneys (a major hematopoietic organ in bony fish) of juvenile catfish using a modified alkaline lysis procedure with subsequent ATP-dependent DNase treatment. Replicate lifts of the library were screened with two different probes. The first probe, a 1.5-kb EcoRI-ClaI fragment, begins immediately upstream of the JH locus and extends downstream to include the JH1 segment. The second probe, a 4.2-kb XbaI fragment, begins downstream of the JH locus and extends into the intron located between the Cµ2 and Cµ3 domains. Clones that hybridized under stringent conditions with the EcoRI-ClaI probe, and negatively with the XbaI probe, were considered as candidates representing the excision products of DH to JH rearrangement events.

Representative clones that met the above criteria were sequenced. The partial nucleotide sequence for three of these cir-DNA clones is shown in Fig. 1Go. A signal joint consisting of head-to-head RSS elements was present in each clone. The signal joints consisted of a conserved nonamer, a 23-bp spacer, and heptamer immediately adjacent (or separated by one or two nucleotides) to a heptamer, 12-bp spacer, and a nonamer. The RSS elements in clones Cir-E5, Cir-B1, and Cir-D2 contained 23-bp spacers that were identical to the RSS elements of the germline JH8, JH3, and JH1 gene segments, respectively. Nucleotide identity with the 5' flanking region of the respective JH segment continued further upstream (data not shown), and in each clone, the JH coding and 3'-flanking regions were absent. This indicated that each clone represents an extrachromosomal product of a recombination event between a germline JH gene segment and a putative DH gene segment with an RSS element containing a 12-bp spacer. Initial sequence comparisons of clones Cir-E5 and Cir-B1 indicated that a similar DH segment was used in both rearrangements. The sequences of Cir-E5 and Cir-B1 were extended an additional 2 kb downstream of the DH RSS and only 8-bp differences were identified (data not shown). These analyses suggest that different alleles of the same DH segment were involved in these recombination events or that a family of DH segments whose flanking regions are highly conserved exists. The DH segment utilized in Cir-D2 was different from that found in the other two clones. The sequence of clone Cir-D2 was extended about 500 bp into the DH flanking region, and there was no significant homology with the DH flanking regions found in Cir-E5 or Cir-B1 (data not shown). The signal joint identified in clone Cir-B1 was precise. However, nucleotide insertions were observed between the abutted signal heptamers in the other two clones; Cir-E5 had a 1-bp insertion and Cir-D2 had a 2-bp insertion. These insertions are likely N-region additions to the DH-JH signal joint (see Discussion).



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  		FIGURE 1. Nucleotide sequences of the recombination signal joint identified in three cir-DNA clones aligned with the sequence of the germline JH and DH segments that were utilized in the recombination event. Clones Cir-E5, Cir-B1, and Cir-D2 were derived from cir-DNA obtained from anterior kidney lymphocytes of channel catfish and cloned in {lambda} libraries. The nonamer (9-mer) and heptamer (7-mer) sequences of the RSS in JH and DH segments are boxed. Nucleotide identities with the cir-DNA sequence are indicated by dots. The nonamer and heptamer sequences in the 5' RSS of the DH segments are underlined.

 
Mapping, genomic organization, and structure of catfish germline DH gene segments

To locate the germline DH gene segments utilized in these cir-DNA clones, a channel catfish {lambda} genomic library was initially screened with a 700-bp StuI-StyI probe derived from the DH flanking region of Cir-E5 (designated 3'-DH1). Restriction mapping and hybridization analysis showed that four genomic clones (13-4, 13-6.1, 2-2, and 13-7) overlapped each other and overlapped a previously isolated clone, C7 (25), which contained the JH locus and the Cµ (Fig. 2Go). The cumulative distance spanned by these overlapping clones is ~30 kb. Each clone hybridized with the 3'-DH1 probe, but only clones 2-2 and 13-7 hybridized with a 4.1-kb BamHI-EcoRI probe derived from the DH flanking region of clone Cir-D2 (designated 3'-DH2). It was concluded that the 4.3-kb and the 6.3-kb EcoRI fragments contained the regions that hybridized with the 3'-DH1 and the 3'-DH2 probes, respectively. The 4.3-kb EcoRI fragment was partially sequenced and a single germline DH gene segment, designated DH1, was identified. The 3'-RSS DH1 sequence was identical to the 3'-DH-RSS sequence found in clones Cir-E5 and Cir-D2 (Fig. 1Go). Restriction sites within the 3'-DH2 flanking region placed the DH2 segment in a 2.2-kb EcoRI-XbaI fragment located at the 5' end of the 6.3-kb EcoRI fragment. This fragment was sequenced, and two DH segments were identified. The DH2 segment contained the identical DH-3'-RSS sequence that was identified in Cir-D2 (Fig. 1Go). Further upstream (~0.8 kb) another DH segment, designated DH3, was identified whose sequence was distinct from DH1 and DH2.



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  		FIGURE 2. Partial restriction map and genomic location of DH, JH, and Cµ gene segments in the channel catfish. The restriction enzymes used to map the locus are indicated by single letter designations: E, EcoRI; H, HindIII; B, BamHI; S, SstI; and Bs, BstEII. The location of the four Cµ domains (stippled boxes) and the JH and DH gene segments (solid boxes) are indicated. The positions of the overlapping genomic clones (13-7, 2-2, 13-6.1, 13-4, and C7) that span the locus are shown beneath the restriction map. The sizes of the internal EcoRI restriction fragments within these clones are shown in italics. The stippled bars shown above the restriction map indicate the relative locations of the 950-bp SstI and the 700-bp StuI-StyI restriction fragments that were used in Southern blot analyses.

 
The nucleotide sequence of the three germline DH gene segments is shown in Fig. 3GoA. Each DH gene segment has a 5'- and 3'-RSS with a 12-bp spacer. All three DH gene segments are in the same transcriptional orientation relative to each other as well as to the downstream JH segments. The DH1 and DH2 gene segments have conserved heptamers (CACT/AGTG) 5' and 3' of the coding region; however, the 5' and 3' heptamers of the DH3 gene segment differ from the consensus by 3 bp and 2 bp, respectively. The 5' nonamer of each DH gene segment is T-rich, whereas the 3' nonamers are A-rich. In comparison to the DH1 gene segment, DH2 and DH3 have 8- and 7-bp identities in the 5' RSS spacer regions respectively, whereas the 3' RSS elements of DH2 and DH3 have 4- and 3-bp identities. Sequence comparisons showed that there was little, if any, sequence similarity in the 5' and 3' flanking regions of the three DH segments (Fig. 3GoB).



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  		FIGURE 3. Nucleotide sequence comparison of the catfish DH1, DH2, and DH3 segments. A, The nonamer (9-mer) and heptamer (7-mer) sequences of the 5' and 3' RSS elements are boxed. The predicted amino acids encoded by the three reading frames within the DH coding region are indicated. The reading frames that principally encode hydrophilic/polar, hydrophobic, or stop codon(s) are indicated. B, Partial sequence of the immediate 5' and 3' flanking regions of the DH1, DH2, and DH3 segments. Only the nonamer sequences within the DH 5' and 3' RSS are shown.

 
The potential coding regions of the DH segments are 11–19 bp in length. Corbett et al. (6) in their study on human DH segments proposed that coding regions of DH segments could be characterized by the coding character of their amino acids rather than by defining the reading frames relative to the RSS as done by Ichihara et al. (31). Inspection indicates that catfish DH coding regions could be grouped into this same character pattern: one reading frame generally encodes polar/hydrophilic amino acids, a second generally encodes hydrophobic amino acids, and a third features a stop codon(s) (Fig. 3GoA).

Genomic Southern analyses indicate that catfish DH1 and DH2 represent single member gene families

The germline DH gene segments in murine and human H chain loci are grouped as families as initially demonstrated by genomic hybridization experiments (32, 33). Subsequent sequence analysis showed that members of the same family share nucleotide homology in the coding regions, RSS elements, and flanking regions (6). To determine whether families of DH gene segments are present in the catfish, probes were derived from the 3' flanking regions of the DH1 and the DH2 segments and used in genomic Southern blots. If multiple DH family members exist in catfish, then Southern blot analysis should reveal the presence of different hybridizing fragments. However, these studies showed that only a single band (or two bands which were readily interpreted by the genomic map and sequence) were defined when the Southern blots were hybridized with these probes (Fig. 4Go).



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  		FIGURE 4. Southern blots of restricted genomic DNA hybridized with DH flanking region probes. The DNA was restricted with the following enzymes: E, EcoRI; H, HindIII; B, BstEII; P, PstI; S, SstI; or X, XbaI. A, The restricted DNA was hybridized with a 700-bp StuI-StyI fragment derived from the 3' flanking region of the catfish DH1 segment. B, The restricted DNA was hybridized with a 950-bp SstI restriction fragment derived from the 3' flanking region of the catfish DH2 segment.

 
Expression of DH1–3 segments and analysis of the CDR3 region of catfish H chain cDNA

Based on genomic sequence data, each of the three DH gene segments appears functional. The functionality of these segments would be supported if each could be identified in an expressed VDJ rearrangement. Toward this end, cDNA was constructed from mRNA obtained from the PBL of two adult channel catfish. Following cDNA synthesis, forward primers corresponding to the FR1 region of six different catfish VH families were used in conjunction with a reverse primer for the Cµ1 in PCR studies. The PCR products were cloned, and representative clones from these families were sequenced. Members of the VH7 family were not analyzed because it is a small family representing less than 10 members (22). The encoded V region was compared with germline sequences, and the utilized coding regions of the VH, DH, and JH segments were assigned. Representative sequences that used longer DH encoded regions and provided information regarding the mechanisms of VDJ joining are presented in Table IGo. The sequences that utilized the DH1, DH2, or DH3 segments showed that there was extensive coding-end processing consisting of both the removal and addition of various numbers of nucleotides from the VH, DH, and JH segments. Only one cDNA sequence was identified that utilized the full-length DH1, DH2, or DH3 coding region. Nucleotide deletions from the DH coding regions were found at the 5' and the 3' ends, or from both the 5' and 3' ends. P-nucleotide additions were also identified in sequences that utilized the full-length 5' or 3' ends of the DH coding region. Most of the P-region additions, one or two nucleotides in length, were located at the 3' end of the DH coding region, although one sequence (5.rh8) had a P-nucleotide added to the 5' end of the DH3 coding region. The expressed reading frame of the DH segments also exhibited variation. Examples of sequences that utilized the polar/hydrophilic, hydrophobic, or stop DH1 reading frame are shown in Table IGo. The stop reading frame of DH2, as well as the hydrophobic reading frame of DH3 was not utilized in any of the cDNA clones that were sequenced.


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  		Table I. Assignment of nucleotides within the CDR3 encoded region of different channel catfish Ig heavy chain cDNA clones to germline VH, DH, and JH segments

 
JH-encoded sequences were readily assigned to segments JH1–JH9, except for clone 6.rh11 that may have used JH3, JH4, or JH5. In all but two of these sequences, nucleotides were deleted from the 5' end of the JH coding region. The number of bases deleted from these JH segments averaged 4.4 and ranged in length from 3–7 bases. In two sequences that expressed the full-length JH coding region (1.rh17 and 4.rh18), P-region additions of 4 and 5 nt, respectively, were added at the 5' end of the JH coding region.

Based on limited information on catfish VH germline sequences, the CDR3-encoded region of germline VH segments representing these different families is generally 4 nt in length (Ref. 23 and our unpublished data). Nucleotides that are identical to those present within characterized germline members of these six VH families are indicated in Table IGo. These analyses indicate that nucleotides can be deleted from the germline CDR3 encoded VH region. In one example, in clone 3.rh14 where the full-length VH region was likely expressed, a single P-region nucleotide was represented.

These analyses also provided information on nontemplated or N-region additions. N-region additions were located between V-D junctions as well as between D-J junctions. Because it is difficult to strictly assign N-region nucleotides to VD junctions, more informative data were derived from the D-J junctions. N-region additions in the DJ junctions of these clones averaged 4.7 bp and ranged in length from 1 to 11 bp. The majority of these nucleotides were pyrimidines, principally C. Base stacking of pyrimidine or purine nucleotides was a common feature of these N-region additions. There did not appear to be a strong correlation between the length of the DH- and JH-encoded regions and the number of N-nucleotides between these junctions. There was also evidence of point mutations within the utilized DH and JH segments. Whether these represent somatic or perhaps allelic differences will have to await additional studies. Thus cDNA analyses indicate that DH1, DH2, and DH3 are functional DH segments that can undergo productive VDJ rearrangements.


   Discussion
Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
References
 
These results allow several conclusions to be made regarding the structure, genomic organization, and diversity patterns of Ig DH segments in early vertebrate phylogeny. The analysis of cir-DNA derived from anterior kidney lymphocytes of juvenile channel catfish defined the excision products of D-J recombination events. The sequenced clones contained recombination signal joints represented by head to head joining of DH and JH RSS elements. Sequence comparisons indicated that the flanking as well as the RSS elements with 23-bp spacers were identical to previously characterized germline JH gene segments. The RSS elements with 12-bp spacer were identical to subsequently characterized DH segments. Hybridization studies indicated that the DH1 and DH2 segments were represented in the cir-DNA library in approximately equal numbers. A cir-DNA library, derived from anterior kidney lymphocytes of two adult catfish, was also constructed, and no positive clones were identified using the identical screening approach even though this library was nearly twice as large. These data suggest that the frequency of DH to JH recombination is higher in anterior kidney lymphocytes of juvenile rather than adult catfish, although it also possible that deletion circles from adult fish may more difficult to isolate if additional DH segments reside further upstream. Nonetheless, these results establish that the gene recombination mechanisms that result in the excision of DH-JH signal joints evolved early in vertebrate phylogeny.

The signal joints of clones Cir-E5 and Cir-D2 had nucleotide insertions between the DH and JH RSS. During excision of the RSS, recombination activating gene-1 (RAG-1) and RAG-2 have been shown to associate with all four ends of the mammalian recombination products. Coding joint processing appears to result in a hairpin structure, whereas processing of the signal joints results in an open-ended or blunt-end structure (reviewed in Refs. 4, 34). Because RAG and TdT are present in fish (35, 36, 37, 38), the additional nucleotides between the DH and JH RSS are probably N-region additions attributable to TdT following RAG-mediated cleavage. The analyses of mammalian recombination signal joints indicate that N-region additions are found in high frequency in TCR recombination events (39), but less commonly observed in Ig recombination events. Murine pre-B cell transfection studies with recombination substrates indicated that N-region additions are present in an average of 14% of the signal joints formed. These nucleotides are mostly G and C and their presence correlated with TdT activity (40).

Sequence comparison of the DH1 and DH2 flanking regions in the cir-DNA clones indicated little structural similarity. As a result, DH1- and DH2-specific probes were derived and used to isolate and characterize a set of overlapping genomic {lambda} clones. Based upon mapping and sequencing studies, the DH1 segment is JH proximal and located about 8.8 kb upstream from the JH1 segment. The DH2 segment is located about 6.8 kb upstream from DH1. The DH3 segment, which was identified by sequencing, is located about 0.8 kb upstream from DH2. These DH segments span a region of about 7.6 kb and, as shown by genomic Southern blot studies, the DH1 and DH2 segments represent single member families. Thus unlike the DH segments of mouse and humans that can be grouped into families based upon similarities in their coding as well as flanking region sequences (6, 32, 33), the flanking regions of catfish DH segments are apparently unrelated. These results suggest that these catfish DH segments did not evolve through recent gene duplication events. These results also suggest a phylogenetic primitiveness, and importantly, indicate that evolutionary pressures exerted during early phylogeny may have been confined to the sequence of the DH gene segment itself (the RSS, spacer, and coding region) and not upon potential sequences located within the immediate flanking regions.

The coding regions of catfish DH1, DH2, and DH3 segments (19, 13, and 11 bp in length, respectively) are shorter than many of the DH segments known in mammals. In humans, for example, there are seven DH families and the segments within a family generally exhibit a similar range in the length of their coding region. These coding regions range in size from the smallest family (DHQ52) that is 11 bp to the DH4 family, which is 31–37 bp in length (6). In each of these DH families, one reading frame encodes one or more stop codons, a second tends to encode glycine residues in conjunction with polar/hydrophilic residues, and a third is hydrophobic in character. Corbett et al. (6) used this approach to classify reading frame usage rather than referencing the reading frame relative to the RSS. Reynaud et al. (7) in their earlier study had observed this DH coding character with the reading frames of avian DH segments. The reading frames of the catfish DH segments were readily assigned by this classification approach with similar amino acids represented.

This pattern of reading frames is not apparent in shark DH segments. In the horned shark (Heterodontus) there are ~200 genomic gene clusters, and in about half of these clusters there is germline "joining" of V-D or V-D-J. In the other half of these clusters the DH1 and DH2 segments, although distinct from one another, appear to vary by no more than a single nucleotide when compared with homologous segments in other clusters. Recombination events appear to be restricted to segments within a cluster, and both D1 and D2 appear to be utilized even though the 12/23 rule would allow only the D2 segment to be selected (12, 13). None of the shark DH sequences we examined had a reading frame that encoded a stop codon. The reading frames generally encode both hydrophobic as well as hydrophilic/polar amino acids. If, as suggested, an early role for DH gene segments is a medium for junctional diversity and somatic mutation (13), these studies indicate that bony fish are the first vertebrates to evolve structurally distinct DH gene segments.

DH1 is the only one of these gene segments that contains a start codon and a contiguous open reading frame that extends through the coding region. This start codon is located within the spacer region of the 5' RSS, and A/T rich regions are located upstream that may serve as promoter and transcription initiation sites. Transcriptional enhancer elements have been mapped 3' of the TM2 exon of catfish µ gene (41); hence a DH1-J recombination product might be transcribed and translated. It seems, however, that if a mechanism existed to regulate DH reading frame usage, similar to the well-characterized counter-selection mechanism of the Dµ protein in murine systems (5), each of the catfish DH elements would share these structural features. This is not the case. In addition, the DH1 segment is used in all three reading frames (Table IGo), which also suggests that a mechanism to regulate DH reading frame usage by the production of a Dµ protein may not exist.

The genomic clones that contained the DH segments were hybridized with family-specific VH probes and none of the probes hybridized under relaxed or stringent conditions (data not shown). This indicates that VH segments do not appear to be present within the examined region of the catfish DH locus. An earlier study with the coelacanth Latemeria had suggested that VH and DH segments were interspersed; putative DH segments were located immediately downstream of the VH gene segments (42). Although this study did not show that the gene segments were utilized nor were the location of JH segments identified, this study did suggest an alternate pattern of Ig V region gene organization. The distance separating the DH and JH loci of humans and mice (excluding the DHQ52 segment) is ~20 kb (6, 43, 44). The relatively short distance separating the DH and JH loci in channel catfish parallels the relatively short distance separating the JH locus and the Cµ (1.8 kb). In addition, earlier results showed that members of the different VH families are closely linked (average distance between segments of about 3 kb) and interspersed with each other (23). Pulsed field studies have also determined that catfish VH segments are linked to JH and Cµ on the same large genomic fragments (T. Ventura-Holman and C. J. Lobb, manuscript in preparation). It appears that the structure and characteristic organizational pattern of Ig H chain V region gene segments of higher vertebrates evolved in a compact locus early in vertebrate phylogeny. Bony fish, as represented by studies in the channel catfish, appear to have been the earliest vertebrates to evolve multiple VH gene families upstream of different DH gene segments located in a defined regional arrangement and closely linked to the JH locus.

The analysis of H chain cDNA to define the junctional mechanisms of CDR3 diversity showed that there is extensive processing of the coding ends of the catfish VH, DH, and JH segments during recombination. Representative cDNA sequences showed that the DH1–DH3 segments are functional and that these segments are used in different reading frames. Although the full-length coding region of the DH segments was expressed in some cDNA clones, deletion of nucleotides from the 5' end, the 3' end, or both ends of the DH coding region was generally observed. Deletion of nucleotides from the CDR3 encoded region of germline VH and JH coding region was also observed. Of particular importance in these studies is that there is further junctional modification of the coding region ends by the addition of N- and P-region nucleotides. These analyses are the first studies in bony fish that have the necessary germline information to indicate these processes. These patterns parallel those known from mammalian studies and imply that the mechanisms that provide for junctional diversity of Ig V region genes evolved early in phylogeny and are present at the level of the bony fish.

Approximately 50% of the 50 H chain cDNA clones analyzed in this study utilized DH1, DH2, or DH3 in CDR3. The DH segments utilized in 25% of the remaining clones could not be determined because the length of the CDR3 was generally less than 8 nt when VH and JH contributed nucleotides were identified, and the majority of these nucleotides appeared to represent N-region additions. In the other 25% of the clones, sequence comparisons of the CDR3 indicate that there may be one additional germline DH segment represented among these sequences. Thus it is possible that there are a few other, as yet uncharacterized germline DH sequences, but present cDNA analyses do not indicate an extensive repertoire of germline DH segments in the catfish.

Only about 5% of these cDNA sequences utilized DH3 and inspection of the germline DH3 sequence indicates that the RSS heptamers sequences vary, although the consensus nonamers are conserved. Changes from consensus in the three heptamer nucleotides adjacent to the coding region have been shown to be the most deleterious for recombination (34). Although these heptamer nucleotides are conserved in each of the three characterized DH segments (Fig. 3Go), changes in other positions are known to effect recombination frequencies in mammalian systems and may account for the decreased usage of catfish DH3 in these analyses.

Inspection of the catfish DH segments indicates conservation of internal coding region sequence motifs. This led us to determine whether any of the sequence motifs present in the coding region of the catfish DH segments were conserved in the DH segments of other vertebrates. Comparative studies of the DH segments in humans, mice, rabbits, and the primitive insectivore, Suncus murinus, have shown that the DHQ52 segment is conserved in both its structure and its location within mammalian IgH loci (45, 46, 47, 48). It represents a single member gene family and is the only DH segment conserved in these diverse lineages of mammals. In each species, the DHQ52 segment is JH proximal and located less than 1 kb from the JH region. These studies suggest that this DH segment is monophyletic and that it may have emerged before the radiation of mammals. The multiple alignment of the DHQ52 segment in these species indicates that the 10–11 bp coding sequence is conserved around the core internal sequence TAACTGGG (Fig. 5GoA). The alignment of catfish DH1–3 indicates that the internal coding motifs TAACT and CTGGG are represented in the catfish DH segments as well as in shark DH segments. The DH1 and DH2 coding regions also share the common internal sequence TATAGC. The sequence databases were searched with the nucleotide sequences of the catfish DH1–DH3 segments using the BLAST algorithm (29). These analyses showed that the sequence of the catfish DH1 was conserved in DH segments of other vertebrates. The alignment with the DH2-2 segment of humans is shown in Fig. 5GoB. As indicated, the catfish DH1 coding region is identical in 13 of the 14 positions with the reverse complement of the DH2-2 coding strand. Although this phylogenetic relationship might indicate conserved Ag recognition motifs, its importance may be in its relationship with the binding of enzymes within the recombinase complex.



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  		FIGURE 5. Nucleotide sequence comparison of catfish DH1–3 segments with DH segments of other vertebrates. A, The sequences of the DHQ52 segments identified in mammals of different lineages are aligned with DH segments from the catfish, Xenopus (10 ), and shark (12 ). Conserved sequence motifs within these segments are underlined. B, The sequence of the human DH2-2 segment (shown double-stranded, Ref. 6 ) aligned with the catfish DH1 segment. The sequence of catfish DH1 segment is shown in the 3'-5' direction. Identical nucleotides in both sequences are shown in capital letters. The conserved coding region sequence located in both human DH2-2 and catfish DH1 is underlined.

 
Notable conservation of sequence motifs also occurs within the coding and the RSS regions of catfish VH, DH, and JH segments. In catfish VH segments the conserved FR3 sequence 5'-GTGTATTACTGTG partially encodes the YYC sequence, a structural hallmark of VH genes, and contains an embedded heptamer, which in mammalian systems is known to be involved in secondary VH recombination events (49, 50). This VH consensus sequence is conserved within the 5' RSS of catfish DH segments. The terminal nine nucleotides of the VH consensus sequence are repeated downstream of the RSS of the catfish JH segments where the sequence 5'-AYTACTGGG (where Y is T or C) is located. This sequence contains the codon for the FR4 tryptophan that is a structural hallmark of JH segments. There is considerable evidence, much of it attained from experiments with extrachromosomal recombination substrates, which show that flanking nucleotides within the coding region influence recombination frequencies. Gerstein and Lieber (51) demonstrated that terminal coding region nucleotides adjacent to the heptamer influenced recombination efficiencies over at least a 260-fold range. A or T nucleotides adjacent to the heptamer reduce recombination frequencies, but these effects are mediated by nucleotides in coding positions 6–8 nt away from the RSS (52, 53). It is reasonable to postulate that these phylogenetically conserved sequence motifs might serve additional functions perhaps related to the association of the recombinase complex.

These phylogenetically conserved VH, DH, and JH sequence motifs might also reflect recognition sites for primitive rearranging gene segments. Recent studies have shown that there appears to be a common evolutionary origin for the RAG proteins and transposases suggesting that transposons played an active role in the evolution of the immune system (54, 55). We recently identified transposons of the Tc1/mariner family located within the H chain locus of the channel catfish and these studies also suggest that transposons may have contributed to the structure and organization of the catfish IgH locus (56). Sakano et al. (57) in their early studies of L chain gene recombination postulated that the heptamer and nonamer of V{kappa} and J{kappa} segments resembled the inverted repeated ends of transposons. The sequence of catfish DH segments phylogenetically supports this hypothesis. Alignment of the catfish DH segments shows that the 5' RSS and the 3' RSS can be considered as inverted terminal repeats that flanks the DH coding region. Five to seven nucleotides within the spacer region of the different DH in addition to the heptamer and the nonamer form this structure.

In conclusion, these studies have shown that the structure and genomic organization of DH segments in a bony fish parallels that known in higher vertebrates. Different DH segments, which contain 12-bp RSS on both the 5' and 3' ends with phylogenetically conserved heptamers, nonamers, and coding region sequence motifs, are located in a defined regional arrangement immediately upstream from the JH locus. Germline recombination of DH to JH segments can lead to the excision of extrachromosomal cir-DNA that contains the DH-JH recombination signal joint, and these signal joints may be modified by the addition of N-region nucleotides. cDNA studies indicate that the same DH segment can be expressed with different JH segments and members of different VH families and thus there is combinatorial diversity of H chain V region gene segments. These studies also have shown that there is extensive junctional modification of the VH, DH, and JH coding region ends during recombination. These modification processes include nucleotide deletion, N- and P-region nucleotide additions, and alternate DH reading frame usage. These combined studies indicate that the structure, genomic organization, and general patterns of DH gene recombination that are typically associated with higher vertebrates evolved early in phylogeny at the level of the bony fish.


   Footnotes
 
1 This work was supported by Grant AI23052 from the National Institutes of Health. Back

2 The sequences discussed in this paper have been entered into the GenBank database under the accession numbers AF161271–AF161289. Back

3 Address correspondence and reprint requests to Dr. Craig J. Lobb, Department of Microbiology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39211. E-mail address: Back

4 Abbreviations used in this paper: RSS, recombination signal sequence; CDR, complementarity determining region; cir-DNA, extrachromosomal circular DNA; FR, framework region; H, heavy chain of Ig; RAG, recombination activating gene. Back

Received for publication June 29, 1999. Accepted for publication December 3, 1999.


   References
Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 

  1. Tonegawa, S.. 1983. Somatic diversification of antibody diversity. Nature 302:575.[Medline]
  2. Yancopoulos, G., F. Alt. 1986. Regulation of the assembly and expression of variable region genes. Annu. Rev. Immunol. 4:339.[Medline]
  3. Early, P., H. Huang, M. Davis, K. Calame, L. Hood. 1980. An immunoglobulin heavy chain variable region gene is generated from three segments of DNA: VH, D and JH. Cell 19:981.[Medline]
  4. Max, E. E.. 1999. Immunoglobulins: molecular genetics. ed. Fundamental Immunology 111. Lippincott-Raven, Philadelphia, PA.
  5. Gu, H., D. Kitamura, K. Rajewsky. 1991. B cell development regulated by gene rearrangement: arrest of maturation by membrane-bound D µ protein and selection of DH element reading frames. Cell 65:47.[Medline]
  6. Corbett, S. J., I. M. Tomlinson, E. L. L. Sonnhammer, D. Buck, G. Winter. 1997. Sequence of the human immunoglobulin diversity (D) segment locus: a systematic analysis provides no evidence for the use of DIR segments, inverted D segments, "minor" D segments or D-D recombination. J. Mol. Biol. 270:587.[Medline]
  7. Reynaud, C.-A., A. Dahan, V. Anguez, J.-C. Weill. 1989. Somatic hyperconversion diversifies the single VH gene of the chicken with a high incidence in the D region. Cell 59:171.[Medline]
  8. McCormack, W. T., L. W. Tjoelker, C. B. Thompson. 1991. Avian B-cell development: generation of an immunoglobulin repertoire by gene conversion. Annu. Rev. Immunol. 9:219.[Medline]
  9. Reynaud, C.-A., V. Anquex, J.-C. Weill. 1991. The chicken D locus and its contribution to the immunoglobulin heavy chain repertoire. Eur. J. Immunol. 21:2661.[Medline]
  10. Schwager, J, N. Bürckert, M. Courtet, L. Du Pasquier. 1991. The ontogeny of diversification at the immunoglobulin heavy chain locus in Xenopus. EMBO J. 10:2461.[Medline]
  11. Mussmann, R., M. Courtet, L. Du Pasquier. 1998. Development of the early B cell population in Xenopus. Eur. J. Immunol. 28:2947.[Medline]
  12. Kokubu, F., R. Litman, M. J. Shamblott, R. Hinds, G. W. Litman. 1988. Diverse organization of immunoglobulin VH gene loci in a primitive vertebrate. EMBO J. 7:3413.[Medline]
  13. Hinds-Frey, K. R., H. Nishikata, R. T. Litman, G. W. Litman. 1993. Somatic variation precedes extensive diversification of germline sequences and combinatorial joining in the evolution of immunoglobulin heavy chain diversity. J. Exp. Med. 178:815.[Abstract/Free Full Text]
  14. Lobb, C. J., L. W. Clem. 1983. Distinctive subpopulations of catfish serum antibody and immunoglobulin. Mol. Immunol. 20:811.[Medline]
  15. Lobb, C. J.. 1985. Covalent structure and affinity of channel catfish anti-dinitrophenyl antibodies. Mol. Immunol. 22:993.[Medline]
  16. Ghaffari, S. H., C. J. Lobb. 1989. Cloning and sequence analysis of channel catfish heavy chain cDNA indicate phylogenetic diversity within the IgM immunoglobulin family. J. Immunol. 142:1356.[Abstract]
  17. Ghaffari, S. H., C. J. Lobb. 1989. Nucleotide sequence of channel catfish heavy chain cDNA and genomic blot analyses: implications for the phylogeny of Ig heavy chains. J. Immunol. 143:2730.[Abstract]
  18. Amemiya, C. T., G. W. Litman. 1990. Complete nucleotide sequence of an immunoglobulin heavy-chain gene and analysis of immunoglobulin gene organization in a primitive teleost species. Proc. Natl. Acad. Sci. USA 87:811.[Abstract/Free Full Text]
  19. Bengten, E., T. Leanderson, L. Pilstrom. 1991. Immunoglobulin heavy chain cDNA from the teleost Atlantic cod (Gadus morhau L.): nucleotide sequences of secretory and membrane form show an unusual splicing pattern. Eur J. Immunol. 21:3027.[Medline]
  20. Hordvik, I., A. M. Voie, J. Glette, R. Male, C. Endresen. 1992. Cloning and sequence analysis of two isotypic IgM heavy chain genes from Atlantic salmon, Salmo salar L. Eur. J. Immunol. 22:2957.[Medline]
  21. Anderson, E., T. Matsunaga. 1993. Complete cDNA sequence of a rainbow trout IgM gene and evolution of vertebrate IgM constant domains. Immunogenetics 38:243.[Medline]
  22. Ventura-Holman, T., S. H. Ghaffari, C. J. Lobb. 1996. Characterization of a seventh family of immunoglobulin heavy chain VH gene segments in the channel catfish, Ictalurus punctatus. Eur. J. Immunogenet. 23:7.[Medline]
  23. Ventura-Holman, T., J. C. Jones, S. H. Ghaffari, C. J. Lobb. 1994. Structure and genomic organization of VH gene segments in the channel catfish: members of different VH gene families are interspersed and closely linked. Mol. Immunol. 31:823.[Medline]
  24. Ghaffari, S. H., C. J. Lobb. 1992. Organization of immunoglobulin heavy chain constant and joining region genes in the channel catfish. Mol. Immunol. 29:151.[Medline]
  25. Hayman, J. R., S. H. Ghaffari, C. J. Lobb. 1993. Heavy chain joining region segments of the channel catfish: genomic organization and phylogenetic implications. J. Immunol. 151:3587.[Abstract]
  26. Ghaffari, S. H., C. J. Lobb. 1991. Heavy chain variable region gene families evolved early in phylogeny: Ig complexity in fish. J. Immunol. 146:1037.[Abstract]
  27. Yamagishi, H. T., T. S. Fujimoto, M. Toda, Y. Maekawa, M. Umeno, M. Anai. 1983. Purification of small polydisperse circular DNA of eukaryotic cells by use of ATP-dependent deoxynuclease. Gene 26:317.[Medline]
  28. Chomczynski, P., N. Sacchi. 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162:156.[Medline]
  29. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389.[Abstract/Free Full Text]
  30. Kabat, E. A., T. T. Wu, H. M. Perry, K. S. Gottesman, C. Foeller. 1991. Sequences of Proteins of Immunological Interest National Institutes of Health, Bethesda, MD.
  31. Ichihara, Y., H. Matsuoka, Y. Kurosawa. 1988. Organization of human immunoglobulin heavy chain diversity gene loci. EMBO J. 7:4141.[Medline]
  32. Kurosawa, Y., S. Tonegawa. 1982. Organization, structure, and assembly of immunoglobulin heavy chain diversity DNA segments. J. Exp. Med. 155:201.[Abstract/Free Full Text]
  33. Siebenlist, U., J. V. Ravetch, S. Korsmeyer, T. Waldmann, P. Leder. 1981. Human immunoglobulin D segments encoded in tandem multigenic families. Nature 294:631.[Medline]
  34. Gellert, M.. 1997. Recent advances in understanding V(D)J recombination. Adv .Immunol. 64:39.[Medline]
  35. Hansen, J. D., S. L. Kaattari. 1996. The recombination activating gene 2 (RAG2) of the rainbow trout Oncorhynchus mykiss. Immunogenetics 44:203.[Medline]
  36. Hansen, J. D.. 1997. Characterization of rainbow trout terminal deoxynucleotidyl transferase structure and expression. TdT and RAG1 co-expression define the trout primary lymphoid tissues. Immunogenetics 46:367.[Medline]
  37. Willett, C. E., J. J. Cherry, L. A. Steiner. 1997. Characterization and expression of the recombination activating genes (rag1 and rag2) of zebrafish. Immunogenetics 45:394.[Medline]
  38. Bernstein, R. M., S. F. Schluter, H. Bernstein, J. J. Marchalonis. 1996. Primordial emergence of the recombination activating gene 1 (RAG1): sequence of the complete shark gene indicates homology to microbial integrases. Proc. Natl. Acad. Sci. USA 93:9454.[Abstract/Free Full Text]
  39. Kanari, Y., R. Nakagawa, H. Arakawa, H. Yamagishi. 1998. Variable gene segment-specific N-insertions at the signal joint of T-cell receptor Vß-Dß recombinations. Immunol. Lett. 61:151.[Medline]
  40. Lieber, M. R., J. E. Hesse, K. Mizuuchi, M. Gellert. 1988. Lymphoid V(D)J recombination: nucleotide insertion at signal joints as well as coding joints. Proc. Natl. Acad. Sci. USA 85:8588.[Abstract/Free Full Text]
  41. Magor, B. G, M. R. Wilson, N. W. Miller, L. W. Clem, D. L. Middleton, G.W. Warr. 1994. An Ig heavy chain enhancer of the channel catfish Ictalurus punctatus: evolutionary conservation of function but not structure. J. Immunol. 153:5556.[Abstract]
  42. Amemiya, C. T., Y. Ohta, R. T. Litman, J. P. Rast, R. N. Haire, G. W. Litman. 1993. VH gene organization in a relict species, the coelacanth Latimeria chalumnae: evolutionary implications. Proc. Natl. Acad. Sci. USA 90:6661.[Abstract/Free Full Text]
  43. Buluwela, L., D. G. Albertson, P. Sherrington, P. H. Rabbitts, N. Spurr, T. H. Rabbitts. 1988. The use of chromosomal translocations to study human immunoglobulin gene organization: mapping DH segments within 35 kb of the Cµ gene and identification of a new DH locus. EMBO J. 7:2003.[Medline]
  44. Wood, C., S. Tonegawa. 1983. Diversity and joining segments of mouse immunoglobulin heavy chain genes are closely linked and in the same orientation: implications for the joining mechanism. Proc. Natl. Acad. Sci. USA 80:3030.[Abstract/Free Full Text]
  45. Ravetch, J.V., U. Siebenlist, S. Korsmeyer, T. Waldmann, P. Leder. 1981. Structure of the human immunoglobulin µ locus: characterization of embryonic and rearranged J and D genes. Cell 27:583.[Medline]
  46. Sakano, H., Y. Kurosawa, M. Weigert, S. Tonegawa. 1981. Identification and nucleotide sequence of a diversity DNA segment (D) of immunoglobulin heavy-chain genes. Nature 290:562.[Medline]
  47. Chen, H. T., C. B. Alexander, F. F. Chen, R. G. Mage. 1996. Rabbit DHQ52 and DH gene expression in early B-cell development. Mol. Immunol. 33:1313.[Medline]
  48. Okamura, K., H. Ishiguro, Y. Ichihara, Y. Kurosawa. 1993. Comparison of nucleotide sequences from upstream of the DQ52 gene to the Sµ region of immunoglobulin heavy-chain gene loci between Suncus murinus, mouse, and human. Mol. Immunol. 30:461.[Medline]
  49. Kleinfield, R., R. R. Hardy, D. Tarlinton, J. Dangl, L. A. Herzenberg, M. Weigert. 1986. Recombination between an expressed immunoglobulin heavy-chain gene segment in a Ly1+ B-cell lymphoma. Nature 322:843.[Medline]
  50. Reth, M. G., S. Jackson, F. W. Alt. 1986. VHDJH formation and DJH replacement during pre-B differentiation: non-random usage of gene segments. EMBO J. 5:2131.[Medline]
  51. Gerstein, R. M., M. R. Lieber. 1993. Coding end sequence can markedly affect the initiation of V(D)J recombination. Genes Dev. 7:1459.[Abstract/Free Full Text]
  52. Ezekiel, U., T. Sun, G. Bozek, U. Storb. 1997. The composition of coding joints formed in V(D)J recombination is strongly affected by the nucleotide sequence of the coding ends and their relationship to the recombination signal sequences. Mol. Cell. Biol. 17:4191.[Abstract]
  53. Nadel, B., A. Tang, G. Escuro, G. Lugo, A. J. Feeney. 1998. Sequence of the spacer in the recombination signal sequence affects V(D)J rearrangement frequency and correlates with nonrandom V{kappa} usage in vivo. J. Exp. Med. 187:1495.[Abstract/Free Full Text]
  54. Agrawal, A., Q. M. Eastman, D. G. Schatz. 1998. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394:744.[Medline]
  55. Hiom, K., M. Melek, M. Gellert. 1998. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94:463.[Medline]
  56. Ghaffari, S. H., C. J. Lobb. 1999. Structure and organization of a second cluster of immunoglobulin heavy chain gene segments in the channel catfish. J. Immunol. 162:1519.[Abstract/Free Full Text]
  57. Sakano, H., K. Hüppi, G. Heinrich, S. Tonegawa. 1979. Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature 280:288.[Medline]



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