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Contribution of V(H) replacement products in mouse antibody repertoire.

Huang L, Lange MD, Yu Y, Li S, Su K, Zhang Z - PLoS ONE (2013)

Bottom Line: The frequencies of VH replacement products are significantly elevated in IgH genes derived from several strains of autoimmune prone mice and in IgH genes encoding autoantibodies.Moreover, the identified VH replacement footprints in IgH genes from autoimmune prone mice or IgH genes encoding autoantibodies preferentially encode positively charged amino acids.These results revealed a significant contribution of VH replacement products to the diversification of antibody repertoire and potentially, to the generation of autoantibodies in mice.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.

ABSTRACT
VH replacement occurs through RAG-mediated recombination between the cryptic recombination signal sequence (cRSS) near the 3' end of a rearranged VH gene and the 23-bp RSS from an upstream unrearranged VH gene. Due to the location of the cRSS, VH replacement leaves a short stretch of nucleotides from the previously rearranged VH gene at the newly formed V-D junction, which can be used as a marker to identify VH replacement products. To determine the contribution of VH replacement products to mouse antibody repertoire, we developed a Java-based VH Replacement Footprint Analyzer (VHRFA) program and analyzed 17,179 mouse IgH gene sequences from the NCBI database to identify VH replacement products. The overall frequency of VH replacement products in these IgH genes is 5.29% based on the identification of pentameric VH replacement footprints at their V-D junctions. The identified VH replacement products are distributed similarly in IgH genes using most families of VH genes, although different families of VH genes are used differentially. The frequencies of VH replacement products are significantly elevated in IgH genes derived from several strains of autoimmune prone mice and in IgH genes encoding autoantibodies. Moreover, the identified VH replacement footprints in IgH genes from autoimmune prone mice or IgH genes encoding autoantibodies preferentially encode positively charged amino acids. These results revealed a significant contribution of VH replacement products to the diversification of antibody repertoire and potentially, to the generation of autoantibodies in mice.

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The enriched VH replacement products identified in different strains of autoimmune prone mice or IgH genes encoding autoantibodies have been positively selected during autoimmune responses.(A) Analysis of the frequencies of positively charged versus negatively charged amino acids encoded by the 3′ end VH genes and the identified VH replacement footprints from different strains of mice or IgH genes encoding autoantibodies. Statistical significance was determined using a two-tailed Chi square test with Yate’s correction. p<0.05 (*) is considered significant. (B) Comparison of the amino acids encoded by the identified VH replacement footprints in MRL/lpr mice. n, numbers of amino acids encoded by the identified VH replacement footprints. (C) Mutation status analysis of identified VH replacement products and non-VH replacement products from different subgroups of IgH genes.
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pone-0057877-g005: The enriched VH replacement products identified in different strains of autoimmune prone mice or IgH genes encoding autoantibodies have been positively selected during autoimmune responses.(A) Analysis of the frequencies of positively charged versus negatively charged amino acids encoded by the 3′ end VH genes and the identified VH replacement footprints from different strains of mice or IgH genes encoding autoantibodies. Statistical significance was determined using a two-tailed Chi square test with Yate’s correction. p<0.05 (*) is considered significant. (B) Comparison of the amino acids encoded by the identified VH replacement footprints in MRL/lpr mice. n, numbers of amino acids encoded by the identified VH replacement footprints. (C) Mutation status analysis of identified VH replacement products and non-VH replacement products from different subgroups of IgH genes.

Mentions: The preferential contribution of charged amino acids by VH replacement footprints is likely predetermined by the 3′ end sequences of VH germline genes. Based on the 3′ end sequences of VH germline genes, VH replacement footprints can contribute almost equal numbers of positively or negatively charged residues (Fig. 5A). Indeed, in the identified VH replacement products from IgH genes derived from BALB/c or C57BL/6 mice, the frequencies of positively and negatively charged amino acids encoded by the VH replacement products are similar (Fig. 5A). However, in the identified VH replacement products in IgH genes from autoimmune prone mice, including MRL/lpr and Sle1/Sle3 mice, the frequencies of positively charged residues encoded by the VH replacement footprints are significantly higher than that in the control mice. Meantime, the frequencies of negatively charged residues encoded by the VH replacement footprints are significantly lower than that in the control mice (Fig. 5A). The frequencies of negatively charged residues encoded by the identified VH replacement footprints are significantly lower in IgH genes derived from C56BL/6/lpr mice and in IgH genes encoding anti-DNA or ANA antibodies (Fig. 5A). Detailed analysis of the functional versus non-functional IgH genes derived from MRL/lpr mice showed that the frequencies of positively charged residues encoded by the identified VH replacement footprints were elevated in functional but not in non-functional IgH genes (Fig. 5B). These results indicate that the positively charged residues encoded by VH replacement products were positively selected in these autoimmune prone mice.


Contribution of V(H) replacement products in mouse antibody repertoire.

Huang L, Lange MD, Yu Y, Li S, Su K, Zhang Z - PLoS ONE (2013)

The enriched VH replacement products identified in different strains of autoimmune prone mice or IgH genes encoding autoantibodies have been positively selected during autoimmune responses.(A) Analysis of the frequencies of positively charged versus negatively charged amino acids encoded by the 3′ end VH genes and the identified VH replacement footprints from different strains of mice or IgH genes encoding autoantibodies. Statistical significance was determined using a two-tailed Chi square test with Yate’s correction. p<0.05 (*) is considered significant. (B) Comparison of the amino acids encoded by the identified VH replacement footprints in MRL/lpr mice. n, numbers of amino acids encoded by the identified VH replacement footprints. (C) Mutation status analysis of identified VH replacement products and non-VH replacement products from different subgroups of IgH genes.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3585286&req=5

pone-0057877-g005: The enriched VH replacement products identified in different strains of autoimmune prone mice or IgH genes encoding autoantibodies have been positively selected during autoimmune responses.(A) Analysis of the frequencies of positively charged versus negatively charged amino acids encoded by the 3′ end VH genes and the identified VH replacement footprints from different strains of mice or IgH genes encoding autoantibodies. Statistical significance was determined using a two-tailed Chi square test with Yate’s correction. p<0.05 (*) is considered significant. (B) Comparison of the amino acids encoded by the identified VH replacement footprints in MRL/lpr mice. n, numbers of amino acids encoded by the identified VH replacement footprints. (C) Mutation status analysis of identified VH replacement products and non-VH replacement products from different subgroups of IgH genes.
Mentions: The preferential contribution of charged amino acids by VH replacement footprints is likely predetermined by the 3′ end sequences of VH germline genes. Based on the 3′ end sequences of VH germline genes, VH replacement footprints can contribute almost equal numbers of positively or negatively charged residues (Fig. 5A). Indeed, in the identified VH replacement products from IgH genes derived from BALB/c or C57BL/6 mice, the frequencies of positively and negatively charged amino acids encoded by the VH replacement products are similar (Fig. 5A). However, in the identified VH replacement products in IgH genes from autoimmune prone mice, including MRL/lpr and Sle1/Sle3 mice, the frequencies of positively charged residues encoded by the VH replacement footprints are significantly higher than that in the control mice. Meantime, the frequencies of negatively charged residues encoded by the VH replacement footprints are significantly lower than that in the control mice (Fig. 5A). The frequencies of negatively charged residues encoded by the identified VH replacement footprints are significantly lower in IgH genes derived from C56BL/6/lpr mice and in IgH genes encoding anti-DNA or ANA antibodies (Fig. 5A). Detailed analysis of the functional versus non-functional IgH genes derived from MRL/lpr mice showed that the frequencies of positively charged residues encoded by the identified VH replacement footprints were elevated in functional but not in non-functional IgH genes (Fig. 5B). These results indicate that the positively charged residues encoded by VH replacement products were positively selected in these autoimmune prone mice.

Bottom Line: The frequencies of VH replacement products are significantly elevated in IgH genes derived from several strains of autoimmune prone mice and in IgH genes encoding autoantibodies.Moreover, the identified VH replacement footprints in IgH genes from autoimmune prone mice or IgH genes encoding autoantibodies preferentially encode positively charged amino acids.These results revealed a significant contribution of VH replacement products to the diversification of antibody repertoire and potentially, to the generation of autoantibodies in mice.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.

ABSTRACT
VH replacement occurs through RAG-mediated recombination between the cryptic recombination signal sequence (cRSS) near the 3' end of a rearranged VH gene and the 23-bp RSS from an upstream unrearranged VH gene. Due to the location of the cRSS, VH replacement leaves a short stretch of nucleotides from the previously rearranged VH gene at the newly formed V-D junction, which can be used as a marker to identify VH replacement products. To determine the contribution of VH replacement products to mouse antibody repertoire, we developed a Java-based VH Replacement Footprint Analyzer (VHRFA) program and analyzed 17,179 mouse IgH gene sequences from the NCBI database to identify VH replacement products. The overall frequency of VH replacement products in these IgH genes is 5.29% based on the identification of pentameric VH replacement footprints at their V-D junctions. The identified VH replacement products are distributed similarly in IgH genes using most families of VH genes, although different families of VH genes are used differentially. The frequencies of VH replacement products are significantly elevated in IgH genes derived from several strains of autoimmune prone mice and in IgH genes encoding autoantibodies. Moreover, the identified VH replacement footprints in IgH genes from autoimmune prone mice or IgH genes encoding autoantibodies preferentially encode positively charged amino acids. These results revealed a significant contribution of VH replacement products to the diversification of antibody repertoire and potentially, to the generation of autoantibodies in mice.

Show MeSH
Related in: MedlinePlus