The surprising amount of TCR repertoire overlap observed by HTS methods may be explained, at least in part, by convergent recombination models, in which certain CDR3 clonotypes are consistently generated at higher efficiencies during V(D)J recombination [52], and therefore more likely to be shared in different individuals. To contend with the broad variety and unpredictability of potential threats, the adaptive immune system relies on somatic diversification processes that generate immense sequence variation in B cell immunoglobulin (herein referred to as B cell receptor, BCR) and T cell receptor (TCR) genes to create massive repertoires of lymphocytes with distinct immune receptors and antigen specificities. Upon recognition of their specific antigens, lymphocytes can undergo clonal expansion with appropriate pathogen-targeted effector and subsequent memory functions. Although functionally distinct, BCRs and TCRs are similarly organized and correspondingly diverse (Figure 1A). Both are composed of two distinct subunit chains, each chain N6,N6-Dimethyladenosine containing a variable domain that contributes to the antigen binding surface of the heterodimeric receptor. Primary diversification of the genes encoding these variable domains proceeds by analogous mechanisms for BCRs and TCRs. On account of these similarities, hereafter we refer to BCRs and TCRs collectively as antigen receptors, with specific distinction where appropriate. During lymphocyte development, variable antigen receptor gene segments (Variable, Joining, Diversity: V, J, D) are rearranged through targeted DNA recombination events (Figure 1B, reviewed in [1]). Substantial sequence complexity is also introduced by the addition or removal of nucleotides at the junctions of these segments. While the entire variable region shapes receptor function, sequence within several complementarity determining regions (CDRs), and CDR3 in particular, contribute most to BCR and TCR specificities [2]. As this recombination process occurs separately for both sub-unit chains, subsequent heterodimeric pairing brings forth still greater combinatorial diversity. Taken together, the diversity established through these molecular mechanisms is staggering, N6,N6-Dimethyladenosine with the theoretical number of distinct BCRs and TCRs estimated N6,N6-Dimethyladenosine to exceed 1013 and 1018 [2], respectively. In addition, upon antigen recognition, mature B lymphocytes may also undergo secondary diversification processes in lymphoid germinal centers. Here, activation-induced cytidine deaminase (AID) and error-prone repair mechanisms introduce somatic hypermutation (SHM) in BCR variable region sequences, enabling selection of lymphocytes with superior BCR properties (a process known as affinity maturation) [3]. BCRs may also undergo class-switch recombination (CSR), in which gene segments encoding immunoglobulin constant regions are recombined to switch the isotype of the expressed antibody, thereby altering its Rabbit polyclonal to PLCXD1 effector properties [4]. Open in a separate window Figure 1 Diversification of antigen receptor repertoires. (A) BCRs and TCRs are similarly organized. Each receptor is composed of two distinct subunit chains (BCR: light chain and heavy chain, TCR: chain and chain). The antigen binding surface is formed by the variable region of each chain, which is encoded by recombined V, J, and D (BCR heavy and TCR) gene segments. (B) Antigen receptor diversification. A schematic of the BCR heavy locus is shown; with the exception of somatic hypermutation and class-switch recombination, analogous mechanisms proceed at the TCR locus (with differences in segment organization). Antigen receptor repertoire diversity is primarily established during lymphocyte development, during which V (orange), D (green), and J (yellow) gene segments are rearranged through the process of V(D)J recombination. Numbers of distinct V, D, and J segments are shown for each antigen receptor locus [2]. During the recombination process, nucleotides may be added or deleted at segment junctions (magenta), contributing to additional sequence diversity. Complementarity determining regions are indicated. BCR-specific secondary diversification may occur following antigen recognition. In somatic hypermutation processes, mutations (red) are introduced throughout the variable region such that modified BCRs may be selected through affinity maturation. In class-switch recombination, gene segments encoding constant regions (blue) are rearranged resulting in the production of antibodies with different isotypes and corresponding effector functions. Abbreviations: BCR, B cell receptor; TCR, T cell receptor; V, J, and D, Variable, Joining, and Diversity gene segments. As the principal sites for antigen recognition, BCRs and TCRs are fundamental in lymphocyte development, effector function, and immune memory. As such, immunologists have developed a variety of techniques in attempts to measure diversity and/or perturbations of antigen receptor.