Systematic Characterization and Comparative Analysis of the Rabbit Immunoglobulin Repertoire
Rabbits have been used extensively as a model system for the elucidation of the mechanism of immunoglobulin diversification and for the production of antibodies. We employed Next Generation Sequencing to analyze Ig germline V and J gene usage, CDR3 length and amino acid composition, and gene convers...
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| Format: | Online |
| Language: | English |
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Public Library of Science
2014
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076286/ |
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pubmed-4076286 |
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pubmed-40762862014-07-02 Systematic Characterization and Comparative Analysis of the Rabbit Immunoglobulin Repertoire Lavinder, Jason J. Hoi, Kam Hon Reddy, Sai T. Wine, Yariv Georgiou, George Research Article Rabbits have been used extensively as a model system for the elucidation of the mechanism of immunoglobulin diversification and for the production of antibodies. We employed Next Generation Sequencing to analyze Ig germline V and J gene usage, CDR3 length and amino acid composition, and gene conversion frequencies within the functional (transcribed) IgG repertoire of the New Zealand white rabbit (Oryctolagus cuniculus). Several previously unannotated rabbit heavy chain variable (VH) and light chain variable (VL) germline elements were deduced bioinformatically using multidimensional scaling and k-means clustering methods. We estimated the gene conversion frequency in the rabbit at 23% of IgG sequences with a mean gene conversion tract length of 59±36 bp. Sequencing and gene conversion analysis of the chicken, human, and mouse repertoires revealed that gene conversion occurs much more extensively in the chicken (frequency 70%, tract length 79±57 bp), was observed to a small, yet statistically significant extent in humans, but was virtually absent in mice. Public Library of Science 2014-06-30 /pmc/articles/PMC4076286/ /pubmed/24978027 http://dx.doi.org/10.1371/journal.pone.0101322 Text en © 2014 Lavinder et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Lavinder, Jason J. Hoi, Kam Hon Reddy, Sai T. Wine, Yariv Georgiou, George |
| spellingShingle |
Lavinder, Jason J. Hoi, Kam Hon Reddy, Sai T. Wine, Yariv Georgiou, George Systematic Characterization and Comparative Analysis of the Rabbit Immunoglobulin Repertoire |
| author_facet |
Lavinder, Jason J. Hoi, Kam Hon Reddy, Sai T. Wine, Yariv Georgiou, George |
| author_sort |
Lavinder, Jason J. |
| title |
Systematic Characterization and Comparative Analysis of the Rabbit Immunoglobulin Repertoire |
| title_short |
Systematic Characterization and Comparative Analysis of the Rabbit Immunoglobulin Repertoire |
| title_full |
Systematic Characterization and Comparative Analysis of the Rabbit Immunoglobulin Repertoire |
| title_fullStr |
Systematic Characterization and Comparative Analysis of the Rabbit Immunoglobulin Repertoire |
| title_full_unstemmed |
Systematic Characterization and Comparative Analysis of the Rabbit Immunoglobulin Repertoire |
| title_sort |
systematic characterization and comparative analysis of the rabbit immunoglobulin repertoire |
| description |
Rabbits have been used extensively as a model system for the elucidation of the mechanism of immunoglobulin diversification and for the production of antibodies. We employed Next Generation Sequencing to analyze Ig germline V and J gene usage, CDR3 length and amino acid composition, and gene conversion frequencies within the functional (transcribed) IgG repertoire of the New Zealand white rabbit (Oryctolagus cuniculus). Several previously unannotated rabbit heavy chain variable (VH) and light chain variable (VL) germline elements were deduced bioinformatically using multidimensional scaling and k-means clustering methods. We estimated the gene conversion frequency in the rabbit at 23% of IgG sequences with a mean gene conversion tract length of 59±36 bp. Sequencing and gene conversion analysis of the chicken, human, and mouse repertoires revealed that gene conversion occurs much more extensively in the chicken (frequency 70%, tract length 79±57 bp), was observed to a small, yet statistically significant extent in humans, but was virtually absent in mice. |
| publisher |
Public Library of Science |
| publishDate |
2014 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076286/ |
| _version_ |
1612108070265028608 |