BACKGROUND
endogenous retroviruses  are known to make up approximately  <dig> % of the mouse genome  <cit> .
the available data suggest that the majority of the erv population in the genome of c57bl/6j harbor sequences similar to murine leukemia viruses .
limited copies of endogenous mouse mammary tumor viruses  are identified in the genome of almost all laboratory mouse strains, including c57bl/6j with three genomic loci of mtv- <dig>  mtv- <dig>  and mtv- <dig>  <cit> .
although only three loci of endogenous mmtvs  are confirmed in the national center for biotechnology information  database, identification of the mtv- <dig> superantigen  sequence from c57bl/6j mice has been reported  <cit> .
certain endogenous mmtvs, such as mtv- <dig>  are known to be capable of producing infectious virus particles, predominantly in the mammary gland, which are transmitted to the pups through the milk  <cit> .
both endogenous and exogenous mmtvs encode sags from an open reading frame residing on the 3' long terminal repeat   <cit> .
mmtv sags, which are type ii membrane proteins presented in a major histocompatibility complex class ii restricted manner, are capable of activating a large fraction of t cells via interaction with specific vβ region of t cell receptors   <cit> .
individual mmtv sag isoforms display differential tcr vβ specificities.
during thymic t cell development, endogenous mmtv sags are recognized as self-antigens resulting in the clonal deletion of specific tcr vβ t cell subsets  <cit> .
in addition, presentation of mmtv sags in the peripheral immune system leads to the activation of tcr vβ-specific t cell subsets followed by anergy and cell death  <cit> .
presumably, sags from exogenous mmtvs participate in the peripheral modulation of the t cell repertoire in a tcr vβ-specific manner.
however, it may be reasonable to speculate that altered forms of sags originating from endogenous mmtvs will acquire different binding affinities for the same vβ chain and/or new tcr vβ specificity.
as a result, they may contribute to the dynamic shaping of the peripheral t cell repertoire by tolerance induction throughout the lifespan of the animal.
in addition, various types of stress signals  are likely to increase the rate of mmtv sag somatic mutation in mice leading to an altered post-stress peripheral t cell profile, which may then contribute to phenotypic variations in inbred laboratory animals.
in this study, we tested the hypothesis that a set of de novo somatic mutations in the endogenous mmtv sag genes contribute to the dynamic shaping of the peripheral t cell repertoire by examining the presence of divergent sag isoform profiles at the genome and expression levels.
RESULTS
de novo somatic mutations in endogenous mmtv sag coding sequences
to examine the spectrum of de novo somatic mutation events in the endogenous mmtv sag coding sequences in c57bl/6j mice, sag sequences were pcr amplified and cloned from the genomic dnas isolated from the liver, lungs, and bone marrow of normal mice.
liver and lungs were selected to represent differentiated tissues while bone marrow consists of both immature and mature  immune cells  <cit> .
alignment analyses of the sag clones identified a number of unique sag coding sequences within each tissue sample  .
some sag coding sequences  were shared by more than one tissue and a total of  <dig> unique sequences were identified.
a range of point mutations were observed in random loci throughout the sag coding region.
in some cases, mutations in sag isoforms introduced a premature stop codon.
phylogenetic evaluation of the unique sag coding sequences from all three tissues with the reference sag sequences from mtv- <dig>  mtv- <dig>  mtv- <dig>  and mtv- <dig> revealed a tree with a number of branching units.
as expected, three branching units with the sag reference sequences from mtv- <dig>  mtv- <dig>  and mtv- <dig>  which are the three endogenous mmtvs of c57bl/6j mice, had more sag isoforms than the other branching units.
interestingly, the sag isoforms in one branching unit were phylogenetically closer to the mtv- <dig> sag reference rather than to the sags from mtv- <dig>  mtv- <dig>  and mtv- <dig>  furthermore, a substantial number of sag clones formed unique branching units separate from any of the reference sags.
a different, but somewhat similar branching pattern was observed within the phylogenetic tree of the in silico translated sequences  of the sag isoforms .
the results presented in figure  <dig> demonstrate that there are a high number of mmtv sag isoforms in the genome of c57bl/6j mice, which had been previously reported to harbor only three endogenous mmtv loci   <cit> .
the presence of numerous mmtv sag isoforms might represent a heterogeneous mixture  of mutated sags, derived from both endogenous and/or exogenous mmtv genomes in conjunction with a relatively high number of mutation events during the viral replication process  <cit> .
although mtv- <dig>  mtv- <dig>  and mtv- <dig> are presumed to be inactive in replication, it is possible that biologically active viruses can be derived from recombination with replicating exogenous mmtvs in conjunction with the generation of numerous mutations in the sag coding sequences  <cit> .
for instance, a replication-competent recombinant mmtv provirus  has been reported in gr mice  <cit> .
it has been described that exogenous mmtvs are able to infect and develop mammary tumors in c57bl/6j mice  <cit> .
mutations from the reverse transcription process of the retroviral rna genome is reported to incur at an estimated rate of  <dig> - <dig> mutation/genome/cycle.
these de novo mutations from replicating mmtvs may occur constantly throughout the lifespan of the host.
these findings provide some evidence suggesting that mmtvs replicate and mutate in c57bl/6j mice.
although the origins  of the proviral copies identified in this study are unknown, we noticed that three main branching units were formed along with the sag references from mtv- <dig>  mtv- <dig>  and mtv- <dig>  furthermore, the successful isolation and cloning of a number of sag isoforms from genomic dna suggests the integration of proviral copies of these mmtv isoforms into the genome of certain host cells.
expression of divergent mmtv sag isoforms in various tissues
the identification of a number of mmtv sag isoforms at the genomic level led us to investigate whether such a variability of sag isoforms is present at the expression/transcription level and whether their mutation rates and profiles are associated with differences in tissue type.
the sag sequences were pcr cloned from cdnas prepared from  <dig> different tissues from normal c57bl/6j mice  and subjected to alignment analyses to identify unique sag coding sequences within each tissue.
subsequently, phylogenetic analyses of the sag sequences from all  <dig> tissues  were performed to examine the distribution and similarities of the sag cdna isoforms .
six sag cdna sequences were shared by more than one tissue type and a total of  <dig> unique sag isoforms were identified from this study.
the total number of unique sag cdna coding sequences  was similar to the number of unique genomic sag coding sequences .
however, a direct comparison of the number of unique sag isoforms between these two groups  may not be feasible since the cloning process was not normalized.
phylogenetic evaluation of the sag cdna isoforms with the same references used for the analysis of genomic sag sequences revealed a unique tree pattern with a number of branching units that was substantially different from the genomic sag tree .
a smaller number of sag cdna isoforms were present in the branching unit with the mtv- <dig> sag reference compared to the genomic sag tree.
in contrast, the branching unit with the mtv- <dig> sag reference had a larger number of sag cdna isoforms than the mtv- <dig> branching unit in the genomic sag tree.
similar to the genomic sag tree, a few unique branching units, which are distant from the reference sags , were formed in the sag cdna tree.
one interesting finding is that none of the sag cdna isoforms isolated from the bone marrow were present in the branching units formed with the reference sag of mtv- <dig> or mtv- <dig>  the branching pattern of the sag tree using in silico translated amino acid sequences resembled its nucleotide  sequence tree .
fifty eight unique sag isoforms  were identified in different tissues and a number of sag cdna isoforms share amino acid sequences that are identical to the reference mtv- <dig>  - <dig> and - <dig> sags.
the unique branching pattern of the sag cdna isoforms  compared to the pattern from the genomic sag isoforms  indicate that the expression of certain sag isoforms is tissue type specific in conjunction with a range of internal as well as external stress signals.
no significant differences in mutation rates were observed between the hypervariable and non-hypervariable regions of the sags at both the genomic dna and cdna levels.
examination of putative tcr vβ specificity of sag cdna isoforms isolated from various tissues
in this study, to determine whether changes in the hypervariable c-terminus regions of the sag isoforms, which are known to determine the tcr vβ specificity, affect their superantigenic function, we examined the putative tcr vβ specificity of the sag cdna isoforms isolated from various tissues.
initially, unique c-terminus sequences  of individual sag cdna isoforms were selected within each tissue, and a total of  <dig> sequences were identified from all  <dig> tissues .
a phylogenetic analysis of the  <dig> c-terminus sequences identified  <dig> unique hypervariable region sequences .
then, the  <dig> sag c-terminus sequences were subjected to alignment analyses to identify the regions responsible for determining their putative tcr vβ specificities .
the matching c-terminus sequences of the mtv- <dig>  mtv- <dig>  mtv- <dig>  and mtv- <dig> sags and their reported tcr vβ specificities were used as references  <cit> .
among the  <dig> unique c-terminus sequences, only four of them were  <dig> % homologous to the mtv- <dig>  mtv- <dig>  mtv- <dig>  or mtv- <dig> sag .
the c-terminal ~ <dig> amino acid region has been used as a reference for the classification of mmtv sags into seven families in regard to their tcr vβ specificities  <cit> .
these c-terminus regions from different mmtv sags are highly polymorphic.
a region within the c-terminus  was determined to be important for tcr vβ specificity, including binding affinity  <cit> .
among the  <dig> unique sag isoforms,  <dig> sags had non-synonymous point mutations in this region in comparison to the reference sags.
however, little is known about the precise amino acid position and/or composition responsible for tcr vβ specificity in the c-terminal region.
the mmtv sags, whose sequences are almost identical, often display slightly different tcr vβ specificities due to differences in binding affinity and/or differences in expression levels  <cit> .
the results from this study indicate that the majority of the sag isoforms identified in this study display unique c-terminus region sequences and are different from the reference endogenous mmtv sags.
this finding may suggest that the tcr vβ specificity and binding affinity of some of these sag isoforms may be altered, in part or full, due to changes in the interactions of the hypervariable c-terminus domain with the tcr vβ region.
on the other hand, changes in certain amino acids in the sag c-terminus region may not affect tcr vβ specificity at all  <cit> .
it may be necessary to determine the tcr vβ specificity of each mmtv sag isoform by an in vitro t-cell activation study.
mtv- <dig> locus within the variable region of immunoglobulin κ chain on chromosome 6
in this study, three mmtv proviral loci  were mapped on the c57bl/6j genome based on the ncbi database.
detailed maps of the genes and other genetic elements surrounding the loci of mtv- <dig>  mtv- <dig>  and mtv- <dig>  were established by surveying sequences upstream  and downstream  of each locus and are presented in figure  <dig>  as expected, there were only three endogenous mmtv loci  in the genome of c57bl/6j mice and the mtv- <dig> provirus was integrated into the variable region of immunoglobulin κ  chain .
it needs to be noted that mtv- <dig> has previously been mapped to this specific genomic region  <cit> .
a very limited number of annotated genes/genetic elements were found in the region surrounding the mtv- <dig> locus on chromosome  <dig> .
annotated genes/genetic elements near the mtv- <dig> locus on chromosome  <dig> of c57bl/6j genome are listed in table  <dig>
the igκ variable gene segments located within  <dig> mb upstream and  <dig> mb downstream of mtv- <dig> locus are indicated in bold.
the coordinates of the entire igκ chain cluster are indicated .
it is documented that dna sequences under the control of immunoglobulin gene promoters/enhancers are subjected to somatic hypermutation, which is frequently observed in the immunoglobulin variable gene segments after antigenic stimulation for a positive and/or a negative selection of developed b cells  <cit> .
based on the mtv-8's location in the variable region of igκ gene cluster, we can speculate that the mtv- <dig> proviral sequence is subjected to somatic hypermutations following antigenic stimulation of b cells, which is reflected in certain mtv-8-derived sag isoforms identified in this study.
it will be interesting to investigate whether the mtv- <dig> loci in other mouse strains, such as balb/c and c3h, undergo similar somatic hypermutation events in comparison to the other mtv loci, which are not embedded near the immunoglobulin clusters.
in addition, the finding that the mtv- <dig> provirus is integrated into the igκ variable region suggests that it may be deleted from the genome depending on the structure of the variable regions of the individual chains during igκ gene rearrangement in developing b cells.
thus, certain mature b cells may not be able to express the mtv- <dig> sag and/or its isoforms.
CONCLUSIONS
it has been reported that a peripheral selection event involving dynamic and persistent induction of t cell tolerance configures the peripheral t cell repertoire  <cit> .
a range of factors, including an individual's genetic profile and pathophysiologic status, may contribute to the process of shaping the peripheral t cell repertoire.
the existence of a substantially diverse population of mmtv sag coding sequences  may be directly linked to the differential as well as dynamic shaping of the peripheral t cell repertoire in mice.
on the other hand, incomplete or failed induction of tolerance against the freshly formed endogenous sag isoforms may lead to local as well as systemic accumulation of autoreactive t cell populations.

 endogenous retroviruses are known to make up approximately % of the mouse genome. the available data suggest that the majority of the erv population in the genome of c57bl/6j harbor sequences similar to murine leukemia viruses. limited copies of endogenous mouse mammary tumor viruses are identified in the genome of almost all laboratory mouse strains, including c57bl/6j with three genomic loci of mtv- mtv- and mtv-. although only three loci of endogenous mmtvs are confirmed in the national center for biotechnology information database, identification of the mtv- superantigen sequence from c57bl/6j mice has been reported. certain endogenous mmtvs, such as mtv- are known to be capable of producing infectious virus particles, predominantly in the mammary gland, which are transmitted to the pups through the milk. both endogenous and exogenous mmtvs encode sags from an open reading frame residing on the 3' long terminal repeat. mmtv sags, which are type ii membrane proteins presented in a major histocompatibility complex class ii restricted manner, are capable of activating a large fraction of t cells via interaction with specific vβ region of t cell receptors. individual mmtv sag isoforms display differential tcr vβ specificities. during thymic t cell development, endogenous mmtv sags are recognized as self-antigens resulting in the clonal deletion of specific tcr vβ t cell subsets. in addition, presentation of mmtv sags in the peripheral immune system leads to the activation of tcr vβ-specific t cell subsets followed by anergy and cell death. presumably, sags from exogenous mmtvs participate in the peripheral modulation of the t cell repertoire in a tcr vβ-specific manner. however, it may be reasonable to speculate that altered forms of sags originating from endogenous mmtvs will acquire different binding affinities for the same vβ chain and/or new tcr vβ specificity. as a result, they may contribute to the dynamic shaping of the peripheral t cell repertoire by tolerance induction throughout the lifespan of the animal. in addition, various types of stress signals are likely to increase the rate of mmtv sag somatic mutation in mice leading to an altered post-stress peripheral t cell profile, which may then contribute to phenotypic variations in inbred laboratory animals. in this study, we tested the hypothesis that a set of de novo somatic mutations in the endogenous mmtv sag genes contribute to the dynamic shaping of the peripheral t cell repertoire by examining the presence of divergent sag isoform profiles at the genome and expression levels.  de novo somatic mutations in endogenous mmtv sag coding sequences to examine the spectrum of de novo somatic mutation events in the endogenous mmtv sag coding sequences in c57bl/6j mice, sag sequences were pcr amplified and cloned from the genomic dnas isolated from the liver, lungs, and bone marrow of normal mice. liver and lungs were selected to represent differentiated tissues while bone marrow consists of both immature and mature immune cells. alignment analyses of the sag clones identified a number of unique sag coding sequences within each tissue sample. some sag coding sequences were shared by more than one tissue and a total of unique sequences were identified. a range of point mutations were observed in random loci throughout the sag coding region. in some cases, mutations in sag isoforms introduced a premature stop codon. phylogenetic evaluation of the unique sag coding sequences from all three tissues with the reference sag sequences from mtv- mtv- mtv- and mtv- revealed a tree with a number of branching units. as expected, three branching units with the sag reference sequences from mtv- mtv- and mtv- which are the three endogenous mmtvs of c57bl/6j mice, had more sag isoforms than the other branching units. interestingly, the sag isoforms in one branching unit were phylogenetically closer to the mtv- sag reference rather than to the sags from mtv- mtv- and mtv- furthermore, a substantial number of sag clones formed unique branching units separate from any of the reference sags. a different, but somewhat similar branching pattern was observed within the phylogenetic tree of the in silico translated sequences of the sag isoforms. the results presented in figure demonstrate that there are a high number of mmtv sag isoforms in the genome of c57bl/6j mice, which had been previously reported to harbor only three endogenous mmtv loci. the presence of numerous mmtv sag isoforms might represent a heterogeneous mixture of mutated sags, derived from both endogenous and/or exogenous mmtv genomes in conjunction with a relatively high number of mutation events during the viral replication process. although mtv- mtv- and mtv- are presumed to be inactive in replication, it is possible that biologically active viruses can be derived from recombination with replicating exogenous mmtvs in conjunction with the generation of numerous mutations in the sag coding sequences. for instance, a replication-competent recombinant mmtv provirus has been reported in gr mice. it has been described that exogenous mmtvs are able to infect and develop mammary tumors in c57bl/6j mice. mutations from the reverse transcription process of the retroviral rna genome is reported to incur at an estimated rate of - mutation/genome/cycle. these de novo mutations from replicating mmtvs may occur constantly throughout the lifespan of the host. these findings provide some evidence suggesting that mmtvs replicate and mutate in c57bl/6j mice. although the origins of the proviral copies identified in this study are unknown, we noticed that three main branching units were formed along with the sag references from mtv- mtv- and mtv- furthermore, the successful isolation and cloning of a number of sag isoforms from genomic dna suggests the integration of proviral copies of these mmtv isoforms into the genome of certain host cells. expression of divergent mmtv sag isoforms in various tissues the identification of a number of mmtv sag isoforms at the genomic level led us to investigate whether such a variability of sag isoforms is present at the expression/transcription level and whether their mutation rates and profiles are associated with differences in tissue type. the sag sequences were pcr cloned from cdnas prepared from different tissues from normal c57bl/6j mice and subjected to alignment analyses to identify unique sag coding sequences within each tissue. subsequently, phylogenetic analyses of the sag sequences from all tissues were performed to examine the distribution and similarities of the sag cdna isoforms. six sag cdna sequences were shared by more than one tissue type and a total of unique sag isoforms were identified from this study. the total number of unique sag cdna coding sequences was similar to the number of unique genomic sag coding sequences. however, a direct comparison of the number of unique sag isoforms between these two groups may not be feasible since the cloning process was not normalized. phylogenetic evaluation of the sag cdna isoforms with the same references used for the analysis of genomic sag sequences revealed a unique tree pattern with a number of branching units that was substantially different from the genomic sag tree. a smaller number of sag cdna isoforms were present in the branching unit with the mtv- sag reference compared to the genomic sag tree. in contrast, the branching unit with the mtv- sag reference had a larger number of sag cdna isoforms than the mtv- branching unit in the genomic sag tree. similar to the genomic sag tree, a few unique branching units, which are distant from the reference sags, were formed in the sag cdna tree. one interesting finding is that none of the sag cdna isoforms isolated from the bone marrow were present in the branching units formed with the reference sag of mtv- or mtv- the branching pattern of the sag tree using in silico translated amino acid sequences resembled its nucleotide sequence tree. fifty eight unique sag isoforms were identified in different tissues and a number of sag cdna isoforms share amino acid sequences that are identical to the reference mtv- - and - sags. the unique branching pattern of the sag cdna isoforms compared to the pattern from the genomic sag isoforms indicate that the expression of certain sag isoforms is tissue type specific in conjunction with a range of internal as well as external stress signals. no significant differences in mutation rates were observed between the hypervariable and non-hypervariable regions of the sags at both the genomic dna and cdna levels. examination of putative tcr vβ specificity of sag cdna isoforms isolated from various tissues in this study, to determine whether changes in the hypervariable c-terminus regions of the sag isoforms, which are known to determine the tcr vβ specificity, affect their superantigenic function, we examined the putative tcr vβ specificity of the sag cdna isoforms isolated from various tissues. initially, unique c-terminus sequences of individual sag cdna isoforms were selected within each tissue, and a total of sequences were identified from all tissues. a phylogenetic analysis of the c-terminus sequences identified unique hypervariable region sequences. then, the sag c-terminus sequences were subjected to alignment analyses to identify the regions responsible for determining their putative tcr vβ specificities. the matching c-terminus sequences of the mtv- mtv- mtv- and mtv- sags and their reported tcr vβ specificities were used as references. among the unique c-terminus sequences, only four of them were % homologous to the mtv- mtv- mtv- or mtv- sag. the c-terminal ~ amino acid region has been used as a reference for the classification of mmtv sags into seven families in regard to their tcr vβ specificities. these c-terminus regions from different mmtv sags are highly polymorphic. a region within the c-terminus was determined to be important for tcr vβ specificity, including binding affinity. among the unique sag isoforms, sags had non-synonymous point mutations in this region in comparison to the reference sags. however, little is known about the precise amino acid position and/or composition responsible for tcr vβ specificity in the c-terminal region. the mmtv sags, whose sequences are almost identical, often display slightly different tcr vβ specificities due to differences in binding affinity and/or differences in expression levels. the results from this study indicate that the majority of the sag isoforms identified in this study display unique c-terminus region sequences and are different from the reference endogenous mmtv sags. this finding may suggest that the tcr vβ specificity and binding affinity of some of these sag isoforms may be altered, in part or full, due to changes in the interactions of the hypervariable c-terminus domain with the tcr vβ region. on the other hand, changes in certain amino acids in the sag c-terminus region may not affect tcr vβ specificity at all. it may be necessary to determine the tcr vβ specificity of each mmtv sag isoform by an in vitro t-cell activation study. mtv- locus within the variable region of immunoglobulin κ chain on chromosome 6 in this study, three mmtv proviral loci were mapped on the c57bl/6j genome based on the ncbi database. detailed maps of the genes and other genetic elements surrounding the loci of mtv- mtv- and mtv- were established by surveying sequences upstream and downstream of each locus and are presented in figure as expected, there were only three endogenous mmtv loci in the genome of c57bl/6j mice and the mtv- provirus was integrated into the variable region of immunoglobulin κ chain. it needs to be noted that mtv- has previously been mapped to this specific genomic region. a very limited number of annotated genes/genetic elements were found in the region surrounding the mtv- locus on chromosome. annotated genes/genetic elements near the mtv- locus on chromosome of c57bl/6j genome are listed in table the igκ variable gene segments located within mb upstream and mb downstream of mtv- locus are indicated in bold. the coordinates of the entire igκ chain cluster are indicated. it is documented that dna sequences under the control of immunoglobulin gene promoters/enhancers are subjected to somatic hypermutation, which is frequently observed in the immunoglobulin variable gene segments after antigenic stimulation for a positive and/or a negative selection of developed b cells. based on the mtv-8's location in the variable region of igκ gene cluster, we can speculate that the mtv- proviral sequence is subjected to somatic hypermutations following antigenic stimulation of b cells, which is reflected in certain mtv-8-derived sag isoforms identified in this study. it will be interesting to investigate whether the mtv- loci in other mouse strains, such as balb/c and c3h, undergo similar somatic hypermutation events in comparison to the other mtv loci, which are not embedded near the immunoglobulin clusters. in addition, the finding that the mtv- provirus is integrated into the igκ variable region suggests that it may be deleted from the genome depending on the structure of the variable regions of the individual chains during igκ gene rearrangement in developing b cells. thus, certain mature b cells may not be able to express the mtv- sag and/or its isoforms.  it has been reported that a peripheral selection event involving dynamic and persistent induction of t cell tolerance configures the peripheral t cell repertoire. a range of factors, including an individual's genetic profile and pathophysiologic status, may contribute to the process of shaping the peripheral t cell repertoire. the existence of a substantially diverse population of mmtv sag coding sequences may be directly linked to the differential as well as dynamic shaping of the peripheral t cell repertoire in mice. on the other hand, incomplete or failed induction of tolerance against the freshly formed endogenous sag isoforms may lead to local as well as systemic accumulation of autoreactive t cell populations. 
similarly, unique sag sequences were cloned from the cdnas of different tissues. sag coding sequences were cloned from the genomic dnas and/or cdnas of various tissues of female c57bl/6j mice. a total of unique sag sequences were identified from the genomic dnas of liver, lungs, and bone marrow, which are presumed to harbor only three endogenous mmtv loci. the peripheral t cell repertoire is dynamically shaped by the steady induction of t cell tolerance against self antigens throughout the lifespan. we hypothesize that de novo somatic mutation of endogenous mmtv sags contributes to the modulation of the peripheral t cell repertoire. the pool of diverse sag isoforms, generated by de novo somatic mutation, may play a role in the shaping of the peripheral t cell repertoire including the autoimmune t cell population. examination of putative tcr vβ specificity suggested that some of the sag isoforms identified in this study have vβ specificities different from the reference sags of mtv- mtv- or mtv- 
 superantigens of mouse mammary tumor viruses play a crucial role in t cell selection in the thymus in a t cell receptor vβ-specific manner and sags presented by b cells activate t cells in the periphery. the peripheral t cell repertoire is dynamically shaped by the steady induction of t cell tolerance against self antigens throughout the lifespan. we hypothesize that de novo somatic mutation of endogenous mmtv sags contributes to the modulation of the peripheral t cell repertoire.  sag coding sequences were cloned from the genomic dnas and/or cdnas of various tissues of female c57bl/6j mice. a total of unique sag sequences were identified from the genomic dnas of liver, lungs, and bone marrow, which are presumed to harbor only three endogenous mmtv loci. similarly, unique sag sequences were cloned from the cdnas of different tissues. examination of putative tcr vβ specificity suggested that some of the sag isoforms identified in this study have vβ specificities different from the reference sags of mtv- mtv- or mtv-  the pool of diverse sag isoforms, generated by de novo somatic mutation, may play a role in the shaping of the peripheral t cell repertoire including the autoimmune t cell population. 