Excision products of immunoglobulin gene rearrangements

Impaired V(D)J recombination and lymphocyte development in core RAG1-expressing mice

RAG1 and RAG2 are the lymphocyte-specific components of the V(D)J recombinase. In vitro analyses of RAG function have relied on soluble, highly truncated “core” RAG proteins. To identify potential functions for noncore regions and assess functionality of core RAG1 in vivo, we generated core RAG1 knockin (RAG1^c/c) mice. Significant B and T cell numbers are generated in RAG1^c/c mice, showing that core RAG1, despite missing ∼40% of the RAG1 sequence, retains significant in vivo function. However, lymphocyte development and the overall level of V(D)J recombination are impaired at the progenitor stage in RAG1^c/c mice. Correspondingly, there are reduced numbers of peripheral RAG1^c/c B and T lymphocytes. Whereas normal B lymphocytes undergo rearrangement of both J_H loci, substantial levels of germline J_H loci persist in mature B cells of RAG1^c/c mice, demonstrating that DJ_H rearrangement on both IgH alleles is not required for developmental progression to the stage of V_H to DJ_H recombination. Whereas V_H to DJ_H rearrangements occur, albeit at reduced levels, on the nonselected alleles of RAG1^c/c B cells that have undergone D to J_H rearrangements, we do not detect V_H to D_H rearrangements in RAG1^c/c B cells that retain germline J_H alleles. We discuss the potential implications of these findings for noncore RAG1 functions and for the ordered assembly of V_H, D_H, and J_H segments.

The molecular mechanism underlying formation of deletions in Fanconi anemia cells may involve a site-specific recombination

Spontaneous and induced chromosomal breakage is an important cellular feature of Fanconi anemia (FA), an inherited DNA repair disorder characterized by progressive bone marrow failure, developmental abnormalities, and predisposition to leukemia. We have previously reported that in comparison to normal cells, there is a substantial increase in frequency of intragenic deletions at an endogenous locus (HPRT) in FA lymphoblasts. Taken together with the increased chromosomal instability, these observations indicated that the wild-type FA gene(s) plays an important role in the maintenance of the genomic integrity. To obtain information on the mechanism(s) underlying the genomic rearrangements in FA, the breakpoint sites of deletions in 11 FA-derived HPRT- mutants were analyzed. The results indicate that a significant proportion of deletions involving a loss of a given exon are identical and that two deletions of different size have the same 3' breakpoint. Interestingly, it appears that in most of the mutants there is a common deletion signal sequence, which suggests that the mutations in the FA gene(s) may lead to an aberrant site-specific cleavage activity that might be responsible for the deletion proneness and the chromosomal instability characteristic of the FA pathology. From the similarity or even identity of the signal sequence at some of the breakpoints with the consensus heptamer which directs cleavage and joining in the assembly of immunoglobulin and T-cell receptor genes, we speculate that steps in common with the V(D)J recombinational process may be illegitimately involved in FA cells.

Polydnavirus-facilitated endoparasite protection against host immune defenses

The polydnavirus of Campoletis sonorensis has evolved with an unusual life cycle in which the virus exists as an obligate symbiont with the parasite insect and causes significant physiological and developmental alterations in the parasite's host. The segmented polydnavirus genome consists of double-stranded superhelical molecules; each segment is apparently integrated into the chromosomal DNA of each male and female wasp. The virus replicates in the nucleus of calyx cells and is secreted into the oviduct. When the virus is transferred to the host insect during oviposition, gene expression induces host immunosuppression and developmental arrest, which ensures successful development of the immature endoparasite. In the host, polydnavirus expression is detected by 2 hr and during endoparasite development. Most of the abundantly expressed viral genes expressed very early after parasitization belong to multigene families. Among these families, the "cysteine-rich" gene family is the most studied, and it may be important in inducing host manifestations resulting in parasite survival. This gene family is characterized by a similar gene structure with introns at comparable positions within the 5' untranslated sequence and just 5' to a specific cysteine codon (*C) within a cysteine motif, C-*C-CC-C-C. Another unusual feature is that the nucleotide sequences of introns 2 in the subfamily WHv1.0/WHv1.6 are more conserved than those of the flanking exons. The structures of these viral genes and possible functions for their encoded protein are considered within the context of their endoparasite and virus strategy for genetic adaptation and successful parasitization.

The regulated expression of B lineage associated genes during B cell differentiation in bone marrow and fetal liver

The expression of B lineage associated genes during early B cell differentiation stages is not firmly established. Using cell surface markers and multiparameter flow cytometry, bone marrow (BM) cells can be resolved into six fractions, representing sequential stages of development; i.e., pre-Pro-B, early Pro-B, late Pro-B/large Pre-B, small Pre-B, immature B, and mature B cells. Here we quantitate the levels of several B lineage associated genes in each of these fractions by RT-PCR, demonstrating different patterns of expression. We find that expression of terminal deoxynucleotidyl transferase (TdT), lambda 5, and VpreB is predominantly restricted to the Pro-B stages. Rag-1 and Rag-2 expression is also tightly regulated, and is found largely in the Pro-B through small Pre-B stages. Mb-1 is present from Pro-B throughout the pathway at high levels. Finally, Bcl-2 is expressed at high levels only at the pre-Pro-B and mature B stages, whereas it is low during all the intermediate stages. We also correlate this expression data with an analysis of the onset of Ig gene rearrangement as assessed by amplifying D-JH, VH-DJH, and VK-JK. Finally, we report differences in gene expression during B lymphopoiesis at two distinct ontogenic timings, in fetal liver and adult BM: both TdT and the precursor lymphocyte regulated myosin-like light chain are expressed at high levels in the Pro-B cell stage in bone marrow, but are absent from the corresponding fraction in fetal liver. In contrast, lambda 5, VpreB, Rag-1, and Rag-2 are expressed at comparable levels.

Increased amount and contour length distribution of small polydisperse circular DNA (spcDNA) in Fanconi anemia

Small polydisperse circular DNA (spcDNA) in Fanconi anemia (FA) was analyzed from cultured fibroblast-like cells by electron microscopy. Application of the mica-press adsorption technique for the semi-quantitative determination of spcDNA amounts to three FA and three normal control skin-derived fibroblast strains revealed 85-fold increased levels of spcDNA in the FA cells. An even higher excess over controls was suggested when the FA fibroblasts were propagated for up to 11 serial in vitro passages, consistent with the short replicative life-span of primary FA cells and their rapid transition into a poorly dividing state, in which spcDNA reportedly further increases. In addition, contour length distributions of gradient-purified spcDNA preparations from five FA fibroblast strains were compared with those from five normal control strains. Mean spcDNA contour lengths were significantly greater in the FA than in the control cells. The reported findings of increased spcDNA amounts and sizes in FA coincide with a similar association of chromosome instability and abnormal spcDNA formation previously observed in cultured cells derived from angiofibromas in tuberous sclerosis. Circumstantial evidence from the present study in the paradigmatic chromosome breakage syndrome FA further supports the suggestion that a common mechanism underlies chromosome instability and the surplus generation of spcDNA. Notably, this apparent mechanism is functional in homonuclear primary cell strains with a distinct inherited basis of their chromosome instability, and is not restricted to heteroploid and neoplastoid cell lines.

DNA looping

DNA-looping mechanisms are part of networks that regulate all aspects of DNA metabolism, including transcription, replication, and recombination. DNA looping is involved in regulation of transcriptional initiation in prokaryotic operons, including ara, gal, lac, and deo, and in phage systems. Similarly, in eukaryotic organisms, the effects of enhancers appear to be mediated at least in part by loop formation, and examples of DNA looping by hormone receptor proteins and developmental regulatory proteins have been found. In addition, instances of looped structures have been found in replication and in recombination in both prokaryotes and eukaryotes. DNA loop formation may have different functions in different cellular contexts; in some cases, the loop itself is requisite for regulation, while in others the increase in the effective local concentration of protein may account for the effects observed. The ability of DNA to form loops is affected by the distance between binding sites; by the DNA sequence, which determines deformability and bendability; and by the presence of other proteins that exert an influence on the conformation of a particular sequence. Alteration of the stability of DNA loops and/or protein-DNA binding by extra- or intracellular signals provides responsivity to changing metabolic or environmental conditions. The fundamental property of site-specific protein binding to DNA can be combined with protein-protein and protein-ligand interaction to generate a broad range of physiological states.

Deletions of immunoglobulin C kappa region characterized by the circular excision products in mouse splenocytes

We have identified circular DNAs containing the kappa light chain constant region (C kappa), as well as the excision products of V kappa-J kappa and V lambda-J lambda joining in adult mouse splenocytes. Analysis of C kappa-positive circular DNA clones revealed two recombination sites (intron recombining sequence [IRS]1 and -2) within the germline J kappa-C kappa intron region and the recombining sequence (RS) located downstream of the C kappa exon. While RS contains a conserved heptamer and nonamer separated by a 23-bp spacer on the 5' side, IRS1 sequence is an isolated heptamer without an obvious nonamer, and IRS2 contains a variant heptamer, CACAAAA. Since IRS1 and IRS2 recombined with both RS (23-bp spacer signal) and V kappa (12-bp spacer signal) with significant frequency, intron recombination sites seem to have dual recombination signals. These findings provide direct evidence that C kappa deletion preceding lambda gene rearrangement can occur by looping out and excision. Increased accessibility of inefficient recombinational loci within the intron may enable recombinase to accept wide signal sequence variation.

The size of small polydisperse circular DNA (spcDNA) in angiofibroma-derived cell cultures from patients with tuberous sclerosis (TSC) differs from that in fibroblasts

Cell cultures were derived from angiofibromas of three patients with tuberous sclerosis (TSC), from the unaffected skin of these patients, and from the skin of five healthy donors. The length distributions of the small polydisperse circular DNA (spcDNA) fraction of these cell cultures were then analyzed. Nearly half the spcDNA molecules from the angiofibroma cultures were longer than 0.4 micron, whereas only about 7% exceeded this threshold in the spcDNA preparations from the skin fibroblast cultures. The percentage of the larger size class of spcDNA showed an increase at higher numbers of in vitro passages in all three types of cultures, but this effect was much more conspicuous in the angiofibroma-derived cultures than in those from the skin fibroblasts. An age-dependent increase in the overall amount of spcDNA was only seen in the angiofibroma-derived cultures. Our earlier finding of elevated amounts of spcDNA in angiofibroma cultures was confirmed in cultures from an additional TSC patient.

Lack of feedback inhibition of V kappa gene rearrangement by productively rearranged alleles

Circular DNAs excised by immunoglobulin kappa chain gene rearrangements were cloned and characterized. 16 of 17 clones examined were double recombination products containing a V kappa-J kappa rearrangement (coding joint) as well as the reciprocal element (signal joint) of another V kappa-J kappa rearrangement. These products suggested multiple recombination, primary inversion, and secondary excision. In primary events, 5 of 16 translational reading frames were in-phase. Thus, V kappa gene rearrangement may not be inhibited by the presence of a productively rearranged allele. An unusually large trinucleotide (P) insertion forming a palindrome of 12 nucleotides was also observed in one of the coding joints.

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.

Extrachromosomal circular DNAs and genomic sequence plasticity in eukaryotic cells

The ability of eukaryotic organisms of the same genotype to vary in developmental pattern or in phenotype according to varying environmental conditions is frequently associated with changes in extrachromosomal circular DNA (eccDNA) sequences. Although variable in size, sequence complexity, and copy number, the best characterized of these eccDNAs contain sequences homologous to chromosomal DNA which indicates that they might arise from genetic rearrangements, such as homologous recombination. The abundance of repetitive sequence families in eccDNAs is consistent with the notion that tandem repeats and dispersed repetitive elements participate in intrachromosomal recombination events. There is also evidence that a fraction of this DNA has characteristics similar to retrotransposons. It has been suggested that eccDNAs could reflect altered patterns of gene expression or an instability of chromosomal sequences during development and aging. This article reviews some of the findings and concepts regarding eccDNAs and sequence plasticity in eukaryotic genomes.

Circular DNA is excised by immunoglobulin class switch recombination

We have purified extrachromosomal circular DNAs from adult mouse spleen cells, and cloned into a phage vector the BamHl fragments hybridizing with C mu and S gamma 1 probes. We obtained 52 S mu+S gamma 1+ clones by screening 1.4 million phage clones derived from spleen cells stimulated with bacterial lipopolysaccharide and interleukin 4. We have identified the breakpoints of six clones that contain S gamma 1 and S mu sequences fused in the 5' to 3' orientation. All these switch recombination sites were assigned to the central repetitive sequences of the S mu and S gamma 1 regions. Since the common S mu-S gamma 1 sequences at the recombination sites are at most 2 bases long, typical homologous recombination cannot account for their joining. These findings provide direct evidence that mu-gamma 1 class switching can occur by the looping out and excision of chromosomal DNA, with formation of a circle.