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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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Comparison of the amino acids encoded by VH replacement footprints and the IgH CDR3 lengths of VH replacement products.(A) The usages of different amino acids encoded by VH replacement footprints with 5, 4, or 3 nucleotides were compared. n, number of amino acid residues encoded by the identified VH replacement footprints with different lengths. Statistical significance was determined using a two-tailed Chi square test with Yate’s correction. p<0.05 (*) is considered significant and p<0.0001 (**) is considered extremely significant. (B) Comparison of the IgH CDR3 lengths of VH replacement products containing the 5-mer or the 3-mer VH replacement products with the CDR3 length of the total functional IgH genes. n, number of IgH sequences or VH replacement products with 3- or 5-mer VH replacement footprints. Statistical significance was determined using unpaired t test. p<0.05 (*) is considered significant and p<0.0001 (**) is considered extremely significant.
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pone-0057877-g004: Comparison of the amino acids encoded by VH replacement footprints and the IgH CDR3 lengths of VH replacement products.(A) The usages of different amino acids encoded by VH replacement footprints with 5, 4, or 3 nucleotides were compared. n, number of amino acid residues encoded by the identified VH replacement footprints with different lengths. Statistical significance was determined using a two-tailed Chi square test with Yate’s correction. p<0.05 (*) is considered significant and p<0.0001 (**) is considered extremely significant. (B) Comparison of the IgH CDR3 lengths of VH replacement products containing the 5-mer or the 3-mer VH replacement products with the CDR3 length of the total functional IgH genes. n, number of IgH sequences or VH replacement products with 3- or 5-mer VH replacement footprints. Statistical significance was determined using unpaired t test. p<0.05 (*) is considered significant and p<0.0001 (**) is considered extremely significant.

Mentions: VH replacement was considered as a receptor editing process to change non-functional IgH rearrangements or IgH genes encoding autoantibodies [29], [41]. Finding that the 5-mer VH replacement footprints preferentially encoded charged amino acids, especially R and K residues, is contrast to the original goal of VH replacement to eliminate autoreactive IgH genes. Because charged residues within the IgH CDR3 might contribute to autoreactivity. Interestingly, when we analyzed the amino acids encoded by the identified 3-mer VH replacement footprints, the usages of charged residues, including R, K, and E, are significantly reduced; meantime, the usages of several neutral residues, including H, L, and Y, are significantly increased (Fig. 4A). These results showed that shorter VH replacement footprints are less likely to encode charged residues.


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)

Comparison of the amino acids encoded by VH replacement footprints and the IgH CDR3 lengths of VH replacement products.(A) The usages of different amino acids encoded by VH replacement footprints with 5, 4, or 3 nucleotides were compared. n, number of amino acid residues encoded by the identified VH replacement footprints with different lengths. Statistical significance was determined using a two-tailed Chi square test with Yate’s correction. p<0.05 (*) is considered significant and p<0.0001 (**) is considered extremely significant. (B) Comparison of the IgH CDR3 lengths of VH replacement products containing the 5-mer or the 3-mer VH replacement products with the CDR3 length of the total functional IgH genes. n, number of IgH sequences or VH replacement products with 3- or 5-mer VH replacement footprints. Statistical significance was determined using unpaired t test. p<0.05 (*) is considered significant and p<0.0001 (**) is considered extremely significant.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3585286&req=5

pone-0057877-g004: Comparison of the amino acids encoded by VH replacement footprints and the IgH CDR3 lengths of VH replacement products.(A) The usages of different amino acids encoded by VH replacement footprints with 5, 4, or 3 nucleotides were compared. n, number of amino acid residues encoded by the identified VH replacement footprints with different lengths. Statistical significance was determined using a two-tailed Chi square test with Yate’s correction. p<0.05 (*) is considered significant and p<0.0001 (**) is considered extremely significant. (B) Comparison of the IgH CDR3 lengths of VH replacement products containing the 5-mer or the 3-mer VH replacement products with the CDR3 length of the total functional IgH genes. n, number of IgH sequences or VH replacement products with 3- or 5-mer VH replacement footprints. Statistical significance was determined using unpaired t test. p<0.05 (*) is considered significant and p<0.0001 (**) is considered extremely significant.
Mentions: VH replacement was considered as a receptor editing process to change non-functional IgH rearrangements or IgH genes encoding autoantibodies [29], [41]. Finding that the 5-mer VH replacement footprints preferentially encoded charged amino acids, especially R and K residues, is contrast to the original goal of VH replacement to eliminate autoreactive IgH genes. Because charged residues within the IgH CDR3 might contribute to autoreactivity. Interestingly, when we analyzed the amino acids encoded by the identified 3-mer VH replacement footprints, the usages of charged residues, including R, K, and E, are significantly reduced; meantime, the usages of several neutral residues, including H, L, and Y, are significantly increased (Fig. 4A). These results showed that shorter VH replacement footprints are less likely to encode charged residues.

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