Thesis
Analysis of the process of N-region addition in V(D)J recombination through diversity identification of the CDR3 region of B and T cells
Master of Science (M.S.), Drexel University
May 2013
DOI:
https://doi.org/10.17918/etd-4241
Abstract
A diverse and adaptable population of antigen receptors is an essential characteristic of a strong immune system. One way of generating this diversity is through V(D)J recombination which occurs in the third complimentary determining region (CDR3) of heavy chain antibodies presented by B and T cells. This process of diversification combines both germline encoded diversity through the recombination of 123 V genes, 27 D genes, 6 J genes, and non-germline encoded diversity. The later type of diversity is the result of terminal deoxynucleotidyl transferase (TdT) adding non-templated N-nucleotides. In this study I have created a set of computational tools to annotate the CDR3 for the most likely source of each nucleotide. After building these tools to identify palindromic (P) nucleotides and germline encoded elements, I sought to characterize the patterns of N-nucleotides in unique CDR3 sequences featuring a specific combinations of V, D, and J genes to determine the extent of non-templated diversity constraints. To do this, I quantified the amino acid distribution in both the V-D junction and the D-J junction and compared them against uniform distributions in B cells, in T cells, and in the out-of-frame distributions in B cells. This analysis revealed a significantly non-uniform distribution in all junction types. Comparisons between in frame and out-of-frame sequences also showed a significant difference in amino acid distribution. A pattern analysis of the N-regions lengths showed reading frame frequency peaks that conserve the D reading frame as recombinative joining is carried out. All of this suggests the non template regions are not fully randomized sources of diversity, rather they are used to generate a specific type of diversity while maintaining the amino acids of germline encoded elements. Further analysis of N-regions and their distributions under different environmental stresses, like illness, may give insight into the dynamic role of TdT and non templated V gene regions in a rapidly evolving environment.
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Details
- Title
- Analysis of the process of N-region addition in V(D)J recombination through diversity identification of the CDR3 region of B and T cells
- Creators
- Renae Judy - DU
- Contributors
- Uri Hershberg (Advisor) - Drexel University (1970-)
- Awarding Institution
- Drexel University
- Degree Awarded
- Master of Science (M.S.)
- Publisher
- Drexel University; Philadelphia, Pennsylvania
- Resource Type
- Thesis
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems (1997-2026); Drexel University
- Other Identifier
- 4241; 991014632444504721