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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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Immunoglobulin VH, DH, and JH gene usages in the mouse IgH sequence repertoire.The mouse IgH gene sequence data set containing 17,179 entries was downloaded from NCBI databases. The potential VH, DH, and JH germline gene assignments were performed using the IMGT/V-QUEST program by sending batches of sequences by the VHRFA program. Clonally redundant IgH sequences were removed if they contain identical CDR3 regions. The usages of different families of VH germline genes (A), DH genes (B), and JH (C) genes in the functional or non-functional unique IgH genes were analyzed.
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pone-0057877-g001: Immunoglobulin VH, DH, and JH gene usages in the mouse IgH sequence repertoire.The mouse IgH gene sequence data set containing 17,179 entries was downloaded from NCBI databases. The potential VH, DH, and JH germline gene assignments were performed using the IMGT/V-QUEST program by sending batches of sequences by the VHRFA program. Clonally redundant IgH sequences were removed if they contain identical CDR3 regions. The usages of different families of VH germline genes (A), DH genes (B), and JH (C) genes in the functional or non-functional unique IgH genes were analyzed.

Mentions: To analyze a large number of IgH gene sequences and to identify potential VH replacement products, we developed a Java based VH Replacement Footprint Analyzer (VHRFA) program. Using the VHRFA program, we analyzed 17,179 mouse IgH gene sequences from the NCBI databases to identify VH replacement products. First, the potential VH, DH, and JH germline gene usage were assigned using the IMGT/V-QUEST program by sending batches of sequences using the VHRFA program (shown in Table S1). Based on the IgH CDR3 region sequences, clonally identical sequences were stripped out. There are 11309 unique IgH gene sequences; 10159 of them have clearly identifiable VH, DH, and JH genes; 9774 of them are productive and 373 of them are non-productive IgH rearrangements. In these IgH genes, different families of VH genes are used differentially (Fig. 1). There are 63683 (65%) functional IgH genes using the IGHV1/VHJ558 family of VH genes; 911 (or 9.3%) functional IgH genes using the IGHV5/VH7183 family of VH genes. The other families of VH genes, including IGHV4/X-24, IGHV11/CP3, IGHV12/CH27, IGHV13/3609N, and IGHV15/VH15A, are used at much lower frequencies (Fig. 1A). Among the non-functional IgH rearrangements, the usages of most VH gene families are similar to those in functional IgH genes, but the usages of the IGHV5/VH7183 and IGHV3/36–60 gene families are increased (Fig. 1A). Among different DH genes, the IGHD1-1 gene is used the most frequent in almost 39% of the IgH sequences (Fig. 1B). For the JH genes, the IGHJ2 gene is used the most frequent in 43% of IgH genes (Fig. 1C). It should be noted that these 17179 mouse IgH sequences were derived from about 861 published reports (Table S2), presumably from more than 861 experiments with different mice. This analysis represents a comprehensive view of the IgH repertoire of the current available mouse IgH gene sequences in the NCBI database.


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)

Immunoglobulin VH, DH, and JH gene usages in the mouse IgH sequence repertoire.The mouse IgH gene sequence data set containing 17,179 entries was downloaded from NCBI databases. The potential VH, DH, and JH germline gene assignments were performed using the IMGT/V-QUEST program by sending batches of sequences by the VHRFA program. Clonally redundant IgH sequences were removed if they contain identical CDR3 regions. The usages of different families of VH germline genes (A), DH genes (B), and JH (C) genes in the functional or non-functional unique IgH genes were analyzed.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585286&req=5

pone-0057877-g001: Immunoglobulin VH, DH, and JH gene usages in the mouse IgH sequence repertoire.The mouse IgH gene sequence data set containing 17,179 entries was downloaded from NCBI databases. The potential VH, DH, and JH germline gene assignments were performed using the IMGT/V-QUEST program by sending batches of sequences by the VHRFA program. Clonally redundant IgH sequences were removed if they contain identical CDR3 regions. The usages of different families of VH germline genes (A), DH genes (B), and JH (C) genes in the functional or non-functional unique IgH genes were analyzed.
Mentions: To analyze a large number of IgH gene sequences and to identify potential VH replacement products, we developed a Java based VH Replacement Footprint Analyzer (VHRFA) program. Using the VHRFA program, we analyzed 17,179 mouse IgH gene sequences from the NCBI databases to identify VH replacement products. First, the potential VH, DH, and JH germline gene usage were assigned using the IMGT/V-QUEST program by sending batches of sequences using the VHRFA program (shown in Table S1). Based on the IgH CDR3 region sequences, clonally identical sequences were stripped out. There are 11309 unique IgH gene sequences; 10159 of them have clearly identifiable VH, DH, and JH genes; 9774 of them are productive and 373 of them are non-productive IgH rearrangements. In these IgH genes, different families of VH genes are used differentially (Fig. 1). There are 63683 (65%) functional IgH genes using the IGHV1/VHJ558 family of VH genes; 911 (or 9.3%) functional IgH genes using the IGHV5/VH7183 family of VH genes. The other families of VH genes, including IGHV4/X-24, IGHV11/CP3, IGHV12/CH27, IGHV13/3609N, and IGHV15/VH15A, are used at much lower frequencies (Fig. 1A). Among the non-functional IgH rearrangements, the usages of most VH gene families are similar to those in functional IgH genes, but the usages of the IGHV5/VH7183 and IGHV3/36–60 gene families are increased (Fig. 1A). Among different DH genes, the IGHD1-1 gene is used the most frequent in almost 39% of the IgH sequences (Fig. 1B). For the JH genes, the IGHJ2 gene is used the most frequent in 43% of IgH genes (Fig. 1C). It should be noted that these 17179 mouse IgH sequences were derived from about 861 published reports (Table S2), presumably from more than 861 experiments with different mice. This analysis represents a comprehensive view of the IgH repertoire of the current available mouse IgH gene sequences in the NCBI database.

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