Recombination Generates Extensive Diversity

KEY CONCEPTS
- The human IgH locus can generate in excess of 10⁴ V_H DJ_H sequences.
- Imprecision of joining and insertion of unencoded nucleotides further increase V_H DJ_H diversity to 10⁸ sequences.
- A recombined V_H DJ_H -C_H chain can be paired with in excess of 10⁴ different recombined V_K J_K -C_K or V_λ J_λ -C_λ chains.
A census of the available V, D, J, and C gene segments provides a measure of the diversity that can be accommodated by the variety of the coding regions carried in the germline. In both the IgH and L chain loci, many V gene segments are linked to a much smaller number of C gene segments.
The human λ locus (chromosome 22) has seven C_λ genes, each preceded by its own J segment (FIGURE 16.10). The mouse λ locus (chromosome 16) is much less diverse. The main difference is that in a mouse there are only two V gene segments, each of which is linked to two J_λ C_λ regions. One of the C segments is a pseudogene (nonfunctional gene). This configuration suggests that the mouse suffered in its evolutionary history a large deletion of most of its germline V_λ gene segments.

FIGURE 1. The lambda family consists of V_λ gene segments and a small number of J_λ -C_λ gene segments.
Both the human κ locus (chromosome 2) and the mouse κ locus (chromosome 6) have only one C gene segment, preceded by six J gene segments (one of them being a pseudogene) (FIGURE
2). The Vκ gene segments occupy a large cluster on the chromosome, upstream of the Cκ region. The human cluster has two regions. Just upstream of the Cκ gene segment a 600-kb region contains the Jκ segments and 40 Vκ gene segments. A gap of 800 kb separates this region from another cluster of 36 V gene segments.

FIGURE 2. The human and mouse Igκ families consist of V_K gene segments and five functional J_K segments linked to a single C_K gene segment. V_K genes include nonfunctional pseudogenes.

The V_H , V_κ , and V_λ gene segments are segregated into families. A family comprises members that share more than 80% amino acid identity. In humans, the V_H locus comprises six V_H families: V_H 1 through V_H 6. V_H 3 and V_H 4 are the largest families, each with more than 10 functional members; V_H 6 is the smallest family, consisting of one member only. In mice, the Vκ locus comprises about 18 Vκ families, which vary in size from 2 to 100 members. Like other families of related genes, related V gene segments form subclusters, which were generated by duplication and divergence of individual ancestral members. Many of the V segments are pseudogenes. Although nonfunctional, some of these may function as donors of partial V sequences in secondary rearrangements.
A given lymphocyte expresses either a κ or a λ chain to be paired with a V_H DJ_H -C_H chain. In humans, about 60% of B cells express κ chains and about 40% express λ. In the mouse, 95% of B cells express a κ chain, presumably because of the reduced number of λ gene segments available.
The single IgH chain locus (human chromosome 14) consists of multiple discrete segments (FIGURE 16.12). The furthest 3′ member of the V_H cluster is separated by only 20 kb from the first D segment. The D segments (30) are spread over approximately 50 kb, followed by the cluster of 6 J_H segments. Over the next 220 kb lie all the C_H genes. In addition to the nine functional C_H genes, there are two pseudogenes. The human IgH locus organization suggests that a Cγ gene was duplicated to generate the Cγ-Cγ-Cε- Cα subcluster, after which the entire subcluster was then tandemly duplicated. The mouse IgH locus (chromosome 12) has more V_H gene segments, fewer D and J segments, and eight (instead of nine) C_H genes.

FIGURE 3. A single gene cluster in humans contains all the information for the IgH chain. Depicted is a schematic map of the human IgH chain locus.
The human IgH locus alone can produce more than 10⁴ different V_H DJ_H sequences by combining 51 V_H genes, 30 D segments, and 6 J_H segments. This degree of diversity is further compounded by the imprecision in the V_H DJ_H joinings, the insertion of unencoded nucleotide (N) additions, and use of multiple D-D segments. By combining any one of more than 50 V gene segments with any 1 of 5 J_K segments the human κ locus has the potential to produce 300 different V_K J _Ksegments. These, however, are conservative estimates, because more diversity is introduced by insertion of untemplated N nucleotides, albeit at lower frequency than in V_H DJ_H .
Further diversity is produced by pairing of the same V_H DJ_H -C chain with different V_K J_K -C_K or V_λ J_λ -C_λ chains. Finally, diversification in individual genes after V_H DJ_H , V_K J_K , and V_λ J_λ recombination occurs by somatic hypermutation (SHM) .