Diversity of Antibodies

The expression of antibodies is produced by somatic gene rearrangements that provide the extraordinarily diverse specificities of B lymphocytes. The Gene rearrangement process irreversibly changes the lymphocyte’s DNA, and all its progeny inherits the same receptor specificity. Different germline gene segments coding for the variable Ig heavy and light chains are joined by somatic V(D)J gene rearrangement to generate Immunoglobulin (Ig) diversity. Moreover, the addition or removal of nucleotides during recombination at the junctions and somatic hypermutation in the complementary-determining regions (CDR) of the V_L and V_H genes results in a high diversity of the Ig repertoire.

The Rearrangement of Antibodies

Ig heavy (H) and light (L) chains are each encoded by a separate multigene family, and the individual V and C domains are each encoded by independent elements: variable (V), diversity (D), and joining (J) gene segments for the V domain and individual exons for the C domains. For the L chain, the joining of a V_L and a J_L gene segment creates an exon that encodes the whole V_L region. The J_L gene segment of the rearranged V_L region is separated from a C_L-region sequence only by a short intron. To make a complete Ig L-chain messenger RNA, the V-region exon is joined to the C-region sequence by RNA splicing after transcription. For the H-chain, there is one additional complication, D_H, which lies between the V_H and J_H gene segments. First, a D_H segment is joined to a J_H segment. And then a V_H segment rearranges to DJ_H to form a V_H-region exon. Finally, the V-region sequence is joined to the neighboring C-region gene by RNA splicing.

Fig1 The rearrangement of antibodies. (Feederle, 2017)

The H- and L-chain Loci in the Human Genome.

There are three sets of Ig chains: the H-chain, and two equivalent types of L-chains, the κ and λ chains.

• The λ locus, which is located on chromosome 22q11.2. The λ L-chain has 29-33 functional V_λ gene segments and four or five pairs of functional J_λ gene segments and C_λ genes. The functional C_λ exon is associated with its own J_λ. The k locus is located on chromosome 2p11.2.
• The κ domain contains 5 J_κ and 75 V_κ gene segments upstream of C_κ. One third of the V_κ gene segments contain frameshift mutations or stop codons that preclude them from forming the functional protein. The remaining sequences, about 38 functional V_κ gene segments, have been found in functional Igs.
• The H-chain locus, which is located on chromosome 14q32.33. There are approximately 40 functional V_H gene segments and a cluster of around 23 D_H segments lying between these V_H gene segments and 6 J_H gene segments.

Fig2 The germline organization of the Ig H- and L-chain loci in the human genome. (Harry, 2010)

RAGs and NHEJ

The recombination of V, D, and J coding genes of antibodies is performed by enzymes collectively called ‘VDJ recombinase’. The products of two genes known as Recombination Activating Gene (RAG)-1 and RAG-2 form this recombinase. RAGs are almost exclusively expressed in developing lymphocytes. RAG1 and RAG2 introduce a DNA double-strand break between the terminus of the rearranging gene segment and its adjacent recombination signal sequence (RSS). These breaks are then repaired by ubiquitously expressed components of a DNA repair process, which is known as nonhomologous end-joining (NHEJ), that are common to all cells of the body. The NHEJ process creates precise joins between the RSS ends and imprecise joins of the coding ends. Terminal deoxynucleotidyl transferase (TdT), which is expressed only in lymphocytes, can variably add non-germline-encoded nucleotides to the coding ends of the recombination product.

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References

1. Feederle, R.; Schepers, A. Antibodies specific for nucleic acid modifications. Rna Biology. 2017:1089-1098.
2. Harry, W.; et al. Structure and function of immunoglobulins - ScienceDirect. Journal of Allergy and Clinical Immunology. 2010, 125 (Supplement 2): S348.