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BACKGROUND Immunoglobulin (IG) complementarity determining region (CDR) includes VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3. Of these, VH CDR3 plays a dominant role in recognizing and binding antigens. Three major mechanisms are involved in the formation of the VH repertoire: germline gene rearrangement, junctional diversity and somatic hypermutation. Features of the generation mechanisms of VH repertoire in humans and mice share similarities while VH CDR3 amino acid (AA) composition differs. Previous studies have mainly focused on germline gene rearrangement and the composition and structure of the CDR3 AA in humans and mice. However the number of AA changes due to somatic hypermutation and analysis of the junctional mechanism have been ignored. METHODS Here we analyzed 9,340 human and 6,657 murine unique productive sequences of immunoglobulin (IG) variable heavy (VH) domains derived from IMGT/LIGM-DB database to understand how VH CDR3 AA compositions significantly differed between human and mouse. These sequences were identified and analyzed by IMGT/HighV-QUEST (http://www.imgt.org), including gene usage, number of AA changes due to somatic hypermutation, AA length distribution of VH CDR3, AA composition, and junctional diversity. RESULTS Analyses of human and murine IG repertoires showed significant differences. A higher number of AA changes due to somatic hypermutation and more abundant N-region addition were found in human compared to mouse, which might be an important factor leading to differences in VH CDR3 amino acid composition. CONCLUSIONS These findings are a benchmark for understanding VH repertoires and can be used to characterize the VH repertoire during immune responses. The study will allow standardized comparison for high throughput results obtained by IMGT/HighV-QUEST, the reference portal for NGS repertoire.
Bin Shi, and
Long Ma, and
Xiaoyan He, and
Xiaomei Wang, and
Peng Wang, and
Li Zhou, and
Xinsheng Yao
January 2006,
Nucleic acids research,
Bin Shi, and
Long Ma, and
Xiaoyan He, and
Xiaomei Wang, and
Peng Wang, and
Li Zhou, and
Xinsheng Yao
June 2017,
BMC immunology,
Bin Shi, and
Long Ma, and
Xiaoyan He, and
Xiaomei Wang, and
Peng Wang, and
Li Zhou, and
Xinsheng Yao
January 2012,
Methods in molecular biology (Clifton, N.J.),
Bin Shi, and
Long Ma, and
Xiaoyan He, and
Xiaomei Wang, and
Peng Wang, and
Li Zhou, and
Xinsheng Yao
January 2016,
Frontiers in immunology,
Bin Shi, and
Long Ma, and
Xiaoyan He, and
Xiaomei Wang, and
Peng Wang, and
Li Zhou, and
Xinsheng Yao
January 2013,
Nature communications,
Bin Shi, and
Long Ma, and
Xiaoyan He, and
Xiaomei Wang, and
Peng Wang, and
Li Zhou, and
Xinsheng Yao
January 2017,
Frontiers in immunology,
Bin Shi, and
Long Ma, and
Xiaoyan He, and
Xiaomei Wang, and
Peng Wang, and
Li Zhou, and
Xinsheng Yao
January 1998,
Proceedings. International Conference on Intelligent Systems for Molecular Biology,
Bin Shi, and
Long Ma, and
Xiaoyan He, and
Xiaomei Wang, and
Peng Wang, and
Li Zhou, and
Xinsheng Yao
September 1995,
Annals of the New York Academy of Sciences,
Bin Shi, and
Long Ma, and
Xiaoyan He, and
Xiaomei Wang, and
Peng Wang, and
Li Zhou, and
Xinsheng Yao
January 2005,
Nucleic acids research,
Bin Shi, and
Long Ma, and
Xiaoyan He, and
Xiaomei Wang, and
Peng Wang, and
Li Zhou, and
Xinsheng Yao
February 1993,
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme,
