At varying distances 3' of the V genes are several J segments that are closely linked to downstream constant region exons. J segments are typically 30 to 50 base pairs long and are separated by noncoding sequences. Between the V and J segments in the Ig H locus, there are additional segments known as D segments. As for V genes, the numbers of J and D genes vary in different Ig loci and different species.

Each Ig locus has a distinct arrangement and number of C region genes. In humans, the Ig k light chain locus has a single C gene (Ck) and the X light chain locus has four functional C genes (CX). The Ig heavy chain locus has nine C genes (CH), arranged in a tandem array, that encode the C regions of the nine different Ig isotypes and subtypes (see Chapter 5). The Ck and CX genes are each composed of a single exon that encodes the entire C domain of the light chains. In contrast, each CH gene is composed of five or six exons. Three or four exons (each similar in size to a V gene segment) each encode a CH domain of the Ig heavy chain, and two smaller exons code for the carboxyl-terminal ends of the membrane form of each Ig heavy chain, including the transmembrane and cytoplasmic domains of the heavy chains (see Fig. 8-6A).

In an Ig light chain protein (k or X), the V domain is encoded by the V and J gene segments; in the Ig heavy chain protein, the V domain is encoded by the V, D, and

J gene segments (see Fig. 8-6A). All junctional residues between the rearranged V and D segments and the D and J segments as well as the sequences of the D and J segments themselves make up the third hypervariable region (also known as complementarity-determining region 3 or CDR3) in the case of the Ig H and TCR P V domains. The junctional sequences between the rearranged V and J segments as well as the J segment itself make up the third hypervariable region of Ig light chains. CDR1 and CDR2 are encoded in the germline V gene segment itself. The V and C domains of Ig molecules share structural features, including a tertiary structure called the Ig fold. As we discussed in Chapter 5, proteins that include this structure are members of the Ig superfamily.

Noncoding sequences in the Ig loci play important roles in recombination and gene expression. As we shall see later, sequences that dictate recombination of different gene segments are found adjacent to each coding segment in Ig genes. Also present are V gene promoters and other cfs-acting regulatory elements, such as locus control regions, enhancers, and silencers, that regulate gene expression at the level of transcription.

Organization of TCR Gene Loci

The genes encoding the TCR a chain, the TCR P chain, and the TCR y chain map to three separate loci on three different chromosomes, and the TCR 8 chain locus is

Human TCR p chain locus (620 kb; chromosome 7)

L Vp1

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