Mutation in a reporter gene depends on proximity to and transcription of immunoglobulin variable transgenes

Cooperation between non-essential DNA polymerases contributes to genome stability in Saccharomyces cerevisiae

DNA polymerases influence genome stability through their involvement in DNA replication, response to DNA damage, and DNA repair processes. Saccharomyces cerevisiae possess four non-essential DNA polymerases, Pol λ, Pol η, Pol ζ, and Rev1, which have varying roles in genome stability. In order to assess the contribution of the non-essential DNA polymerases in genome stability, we analyzed the pol4Δ rev1Δ rev3Δ rad30Δ quadruple mutant in microhomology mediated repair, due to recent studies linking some of these DNA polymerases to this repair pathway. Our results suggest that the length and quality of microhomology influence both the overall efficiency of repair and the involvement of DNA polymerases. Furthermore, the non-essential DNA polymerases demonstrate overlapping and redundant functions when repairing double-strand breaks using short microhomologies containing mismatches. Then, we examined genome-wide mutation accumulation in the pol4Δ rev1Δ rev3Δ rad30Δ quadruple mutant compared to wild type cells. We found a significant decrease in the overall rate of mutation accumulation in the quadruple mutant cells compared to wildtype, but an increase in frameshift mutations and a shift towards transversion base-substitution with a preference for G:C to T:A or C:G. Thus, the non-essential DNA polymerases have an impact on the nature of the mutational spectrum. The sequence and functional homology shared between human and S. cerevisiae non-essential DNA polymerases suggest these DNA polymerases may have a similar role in human cells.

Somatic translocation and differential expression of Ig mu transgene copies implicate a role for the Igh locus in memory B cell development

Memory B cells of mice with Ig mu transgenes often carry transgene copies that have moved into the Igh locus via somatic translocation. This phenomenon has been attributed to a selection pressure for somatic hypermutations, which generally are observed at much higher frequencies in translocated copies than in ectopic copies. We tested this idea by immunizing Ig-mu transgenic mice in a manner designed to select B cells that required only one V(H) mutation for a switch in antigenic specificity and recruitment into the memory pool. Despite the minimal mutation requirement, hybridomas carrying somatic translocations to the Igh locus were obtained. Importantly, this occurred despite the fact that translocated and untranslocated mu-transgenes were mutated comparably. Evidently, a strong selection advantage was conferred upon B cells by the somatic translocations. Among the hybridomas, translocated mu-transgenes were active, while ectopic mu-transgenes were uniformly silent. The translocated copy that had conferred an affinity-based selection advantage was expressed at the highest level. Moreover, translocated copies were differentially expressed among hybridoma members, which belonged to a common post-mutational lineage. This suggests that adjustments in transgene expression levels had occurred during memory cell development. These results indicate that, apart from their potential influences on somatic hypermutagenesis and class switch recombination, elements in the Igh locus promote the selection of memory B cells in another way, possibly by regulating the level of Ig expression at various stages of antigen-driven differentiation.

The PU.1 and NF-EM5 binding motifs in the Igkappa 3' enhancer are responsible for directing somatic hypermutations to the intrinsic hotspots in the transgenic Vkappa gene

Somatic hypermutation is a key mechanism in generating Ig with higher affinities to antigen, a process known as affinity maturation. Using Igkappa transgenes, the 3' enhancer (kappaE3') has been shown to play an important role in introducing hypermutations. In order to identify the cis-acting elements that regulate hypermutagenesis, we have generated transgenic substrates containing mutations/deletions in the kappaE3' region. Here, we report that base substitutions in the kappaE3', either in the PU.1 or in the NF-EM5 binding motif, not only reduce the mutation rate but also disrupt the directed mutagenesis in the intrinsic hotspots of the Igkappa transgene.

The reverse transcriptase model of somatic hypermutation

The evidence supporting the reverse transcriptase model of somatic hypermutation is critically reviewed. The model provides a coherent explanation for many apparently unrelated findings. We also show that the somatic hypermutation pattern in the human BCL-6 gene can be interpreted in terms of the reverse transcriptase model and the notion of feedback of somatically mutated sequences to the germline over evolutionary time.

A unifying hypothesis for the molecular mechanism of somatic mutation and gene conversion in rearranged immunoglobulin variable genes

We have reviewed available data concerning the mechanism of somatic hypermutation in rearranged variable genes of Ig in B lymphocytes of mice and the gene conversion process which generates diversity in these genes in the B lymphocytes of chickens. In our view, these data are consistent with a unifying hypothesis of diversity generating mechanisms involving reverse transcription to produce cDNA from RNA transcripts followed by homologous recombination into chromosomal DNA. Thus, seemingly different processes in the mouse and chicken may have a common molecular basis.

Analysis of the targeting of the hypermutational machinery and the impact of subsequent selection on the distribution of nucleotide changes in human VHDJH rearrangements

B cells are unique in that they generate and tolerate a high rate of mutations in their antigen receptor genes and employ these mutations as a basis of avidity maturation. The precise role of the mutational machinery versus subsequent selection in determining the frequency and distribution of mutations has not been fully analyzed. To address these issues, the influence of the intrinsic mutational machinery and subsequent selection on the frequency and distribution of mutations in the expressed human immunoglobulin repertoire was analyzed. Analysis of non-productively rearranged VH genes from individual human B cells provided an opportunity to examine the immediate impact of somatic hypermutation without superimposed selective influences. Comparison with the frequency and distribution of mutations in the productively rearranged human VH genes permitted an estimate of the influences of subsequent selection.

The signature of somatic hypermutation appears to be written into the germline IgV segment repertoire

We present here a unifying hypothesis for the molecular mechanism of somatic hypermutation and somatic gene conversion in IgV genes involving reverse transcription using RNA templates from the V-gene loci to produce cDNA which undergoes homologous recombination with chromosomal V(D)J DNA. Experimental evidence produced over the last 20 years is essentially consistent with this hypothesis. We also review evidence suggesting that somatically generated IgV sequences from B lymphocytes have been fed back to germline DNA over evolutionary time.

Immunoglobulin hypermutation in cultured cells

Studies of endogenous and engineered Ig genes in mice have begun to reveal some of the cis-acting regions that are involved in the somatic hypermutation of variable regions in vivo. These studies suggest that the initiation of transcription plays a role in this process. However, it will be difficult to identify and manipulate the individual genetic elements and the trans-acting proteins that regulate and target the mutational events using solely in vivo assays. These studies would be greatly facilitated if constructs containing the genetic elements that are essential for V-region mutation could be transfected into cultured cells and undergo high rates of V-region mutation in vitro, and if permissive and non-permissive cell lines could be identified. Such in vitro systems would also allow a detailed molecular and biochemical analysis of this process. Here, we discuss some of the in vitro systems that have been developed and use data from our own studies in cultured cells to illustrate the potential benefits of studying V-region hypermutation in model in vitro systems.

Immunoglobulin gene hypermutation in germinal centers is independent of the RAG-1 V(D)J recombinase

Antigen-driven somatic hypermutation in immunoglobulin genes coupled with stringent selection leads to affinity maturation in the B-lymphocyte populations present in germinal centers. To date, no gene(s) has been identified that drives the hypermutation process. The site-specific recombination of antigen-receptor gene segments in T and B lymphocytes is dependent on the expression of two recombination activating genes, RAG-1 and RAG-2. The RAG-1 and RAG-2 proteins are essential for the cleavage of DNA at highly conserved recombination signals to make double-strand breaks and their expression is sufficient to confer V(D)J recombination activity to non-lymphoid cells. Until very recently, expression of the V(D)J recombinase in adults was believed to be restricted to sites of primary lymphogenesis. However, several laboratories have now demonstrated expression of RAG-1 and RAG-2 and active V-to-(D)J recombination in germinal center B cells. This observation of active recombinase in germinal centers raises the issue of RAG-mediated nuclease activity as a component of V(D)J hypermutation. Here, we show that a transgenic kappa-light chain gene in a RAG-1-/- genetic background can acquire high frequencies of mutations. Thus, the RAG-1 protein is not essential for the machinery of immunoglobulin hypermutation. The genetic approaches to identifying the genes necessary for somatic hypermutation will require further studies on DNA-repair and immunodeficient models.

Mechanism of antigen-driven somatic hypermutation of rearranged immunoglobulin V(D)J genes in the mouse

Available data relevant to the mechanism of somatic hypermutation have been critically evaluated in the context of alternative models: (i) error-generating reverse transcription (RT) followed by homologous recombination; and (ii) error-prone DNA replication/repair. A set of basic principles concerning somatic hypermutation has also been formulated and a revised and expanded "RT-Mutatorsome" concept (analogous to telomerase) is presented which is consistent with these principles and all data on the distribution of somatic mutations in normal and Ig transgenic mice carrying particular V(D)J and flanking region constructs. It is predicted that in the mouse VH and Vk loci. the J-C intronic Enhancer-Nuclear Matrix Attachment Region (Ei/MAR) contains a unique sequence motif or secondary structure which ensures that only V(D)J sequences mutate whilst other regions of the genome are not mutated.

Somatic hypermutation of immunoglobulin genes

The relationship between somatic hypermutation and affinity maturation in the mouse is delineated. Recent work on the anatomical and cellular site of this process is surveyed. The molecular characteristics of somatic hypermutation are described in terms of the region mutated and the distinctive patterns of nucleotide changes that are observed. The results of experiments utilizing transgenic mice to find out the minimum cis-acting sequences required to recruit hypermutation are summarized. The hypothesis that V gene sequences have evolved in order to target mutation to certain sites but not others is discussed. The use that different species make of somatic hypermutation to generate either the primary or secondary B cell repertoire is considered. Possible molecular mechanisms for the hypermutation process and future goals of research are outlined.

Tissue specificity of spontaneous point mutations in lambda supF transgenic mice

Transgenic mice carrying multiple copies of a recoverable lambda phage shuttle vector carrying the supF mutation reporter gene (lambda supF) were constructed for the purpose of studying mutagenesis in a whole animal. Spontaneous mutations in rescued supF target genes from mouse liver and skin were analyzed. The mutation frequency was similar in both tissues (in the range of 2 x 10(-5)), but the spectrum of point mutations was distinct, with transitions common in the skin and transversions more prominent in the liver (P = 0.01). These results may help to elucidate pathways of endogenous mutagenesis in vivo, and they illustrate potentially important tissue-specific differences in genetic instability.

Reciprocal homologous recombination in or near antibody VDJ genes

To determine if rearranged heavy chain variable (VDJ) genes can recombine with each other by crossing over of DNA strands, we constructed a transgene that contained a promoter, VDJ gene, reporter gene to detect crossover events, intron enhancer, matrix attachment region, and constant gene for IgM (C mu). Following immunization of transgenic mice, hybrid molecules were isolated from B cell DNA which contained the transgene recombined with the endogenous IgH locus. Reciprocal products of crossovers were detected by plasmid rescue and PCR amplification, and they were sequenced. Recombination occurred somewhere within 147 bp of homology that contained the JH4 gene segment and 3' flanking DNA. The recombined transgenes had a 20-fold increase in mutation in the VDJ region compared to nonrecombined transgenes, which indicates that DNA sequences 3' of the C mu gene in the endogenous IgH locus are necessary for full activity of the mutator mechanism. The recovery of recombinants between VDJ transgenes and endogenous VDJ genes raises the possibility that reciprocal recombination may somatically diversify rearranged genes between maternal and paternal alleles.

Targeting of non-Ig sequences in place of the V segment by somatic hypermutation

Affinity maturation of antibodies is characterized by localized hypermutation of the DNA around the V segment. Here we show, using mice containing single or multiple transgene constructs, that an immunoglobulin V kappa segment can be replaced by human beta-globin or prokaryotic neo or gpt genes without affecting the rate of hypermutation; the V gene itself is not necessary for recruiting hypermutation. The ability to target hypermutation to heterologous genes in vivo could find more general applications in biology.

Somatic hypermutation

For the generation of secondary response antibodies, immunoglobulin genes are subjected to hypermutation. Cells expressing antibodies with higher affinity are then selected by antigen. Recent clues to the mechanism of hypermutation come from experiments using transgenic mice enabling analysis of the controlling cis-acting elements and the intrinsic features of the hypermutation, dissociated from the effects of antigenic selection.

In situ studies of the primary immune response to (4-hydroxy-3-nitrophenyl)acetyl. III. The kinetics of V region mutation and selection in germinal center B cells

In the murine spleen, germinal centers are the anatomic sites for antigen-driven hypermutation and selection of immunoglobulin (Ig) genes. To detail the kinetics of Ig mutation and selection, 178 VDJ sequences from 16 antigen-induced germinal centers were analyzed. Although germinal centers appeared by day 4, mutation was not observed in germinal center B cells until day 8 postimmunization; thereafter, point mutations favoring asymmetrical transversions accumulated until day 14. During this period, strong phenotypic selection on the mutant B lymphocytes was inferred from progressively biased distributions of mutations within the Ig variable region, the loss of crippling mutations, decreased relative clonal diversity, and increasingly restricted use of canonical gene segments. The period of most intense selection on germinal center B cell populations preceded significant levels of mutation and may represent a physiologically determined restriction on B cells permitted to enter the memory pathway. Noncanonical Ig genes recovered from germinal centers were mostly unmutated although they probably came from antigen-reactive cells. Together, these observations demonstrate that the germinal center microenvironment is rich and temporally complex but may not be constitutive for somatic hypermutation.

Extensive and selective mutation of a rearranged VH5 gene in human B cell chronic lymphocytic leukemia

B cell chronic lymphocytic leukemia (CLL) is the malignant, monoclonal equivalent of a human CD5+ B cell. Previous studies have shown that the VH and VL genes rearranged and/or expressed in CLL have few and apparently random mutations. However, in this study, we have found that the rearranged VH251 gene, one of the three-membered VH5 family, has extensive and selective mutations in B-CLL cells. Somatic mutation at the nucleotide level is 6.03% in B-CLLs whereas the somatic mutation levels are much lower in CD5+ and CD5- cord B cells, adult peripheral blood B cells, and Epstein-Barr virus-transformed CD5+ B cell lines (0.45, 0.93, and 1.92%, respectively). Complementary determining region 1 (CDR1) mutation in CLLs is particularly prevalent, and interchanges in CDRs often lead to acquisition of charge. Analysis of somatic mutations and mutations to charged residues demonstrated that the mutations in CLLs are highly selected.

Analysis of VH251 gene mutation in chronic lymphocytic leukemia (CLL) and normal B-cell subsets

B-cell chronic lymphocytic leukemia (CLL) is the malignant, monoclonal equivalent of a human CD5+ B cell. Previous studies have shown that the VH and VL genes rearranged and/or expressed in CLL have low and random mutations. In this study, however, we have found that the rearranged VH251 gene, one of the three-membered VH5 family, has extensive and selective mutations in B-CLL cells. Somatic mutation at the nucleotide level is 6.03%, and there is a high ratio of replacement to silent mutation in CDRs relative to FWRs. CDR1 mutation is particularly prevalent, and interchanges often lead to acquisition of charge. In VH251 rearranged in CD5+ and CD5- cord-blood B cells, adult peripheral-blood B cells and EBV-transformed CD5+ B-cell lines, the somatic mutation levels are much lower (0.45%, 0.93%, and 1.92%, respectively) with concomitantly lower replacement to silent ratios in CDRs relative to FWRs. The extensive and highly selective somatic mutation of VH251 used in CD5+ CLL cells strongly suggests that part of CLL is generated under the influence of antigen selection and stimulation.