Three separate loci encode, respectively, all of the Ig heavy chains, the Ig κ light chain, and the Ig λ light chain. Each locus is on a different chromosome. The organization of human Ig genes is illustrated in Fig. 1. Ig genes are organized in essentially the same way in all mammals, although their chromosomal locations and the number and order of different gene segments in each locus may vary.
Fig1. Germline organization of human Ig loci. The human heavy chain, κ light chain, and λ light-chain loci are shown. Only functional gene segments are shown; pseudogenes have been omitted for simplicity. Exons and introns are not drawn to scale. Each CH gene is shown as a single box but is composed of several exons, as illustrated for Cµ. Gene segments are indicated as follows: L, Leader (often called signal sequence); V, variable; D, diversity; J, joining; C, constant; enh, enhancer. In this and in subsequent figures, the tubular structures depict double-stranded segments of chromosomes, with the 5′ and 3′ ends referring to the coding strands.
At the 5′ end of each Ig locus, there is a cluster of V (variable) gene segments, each about 300 base pairs long. The numbers of functional V gene segments vary considerably among the different Ig loci and among different species. For example, in humans there are about 45 functional V gene segments in the heavy-chain locus, 35 in the κ light-chain locus, and about 30 in the λ locus; whereas in mice there are about 250 functional V gene segments in the heavy-chain locus, 30 in the κ locus, and only 2 in the λ light-chain locus. In both species, V gene segments for each locus are spaced over large stretches of DNA, up to 2000 kilobases in length. Located 5′ of each V gene segment is an exon that encodes the first 20 to 30 N-terminal residues of the translated protein. These moderately hydrophobic N-terminal stretches are called the leader peptide (or the signal peptide). Similar leader peptides are found in all newly synthesized secreted and transmembrane proteins and are involved in guiding nascent polypeptides into the lumen of the endoplasmic reticulum. Here the leader pep tides are rapidly cleaved as the protein enters the endoplasmic reticulum even before it starts to fold, and these leader peptides are not present in the mature proteins. Upstream of each leader exon is a V gene segment promoter at which transcription can be initiated, but as discussed later, this occurs most efficiently after rearrangement.
At varying distances 3′ of the V gene segments are several J (joining) segments that are typically 30 to 50 base pairs long and are separated by noncoding sequences. Between the V and J segments in the IgH locus there are additional segments known as D (diversity) segments. D segments are not found in Ig light chain loci. Like V gene segments, the numbers of D and J segments vary in different Ig loci and different species.
The constant (C) region genes are located 3′ of the J segments. Each Ig locus has a distinct arrangement and number of C region genes. In humans, the Ig κ light-chain locus has a single C gene (Cκ), and the λ light-chain locus has four functional C genes (Cλ). The Cκ and Cλ genes are each composed of a single exon that encodes the entire C domain of the light chains. 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 classes and subclasses. In contrast to the light chain C genes, 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 carboxy-terminal ends of the membrane form of each Ig heavy chain, including the transmembrane domains and cytoplasmic tails of the heavy chains (Fig. 2A).
Fig2. Domains of immunoglobulin (Ig) and TCR proteins. The domains of Ig heavy and light chains are shown in (A) and the domains of TCR α and β chains are shown in (B). The relationships between the Ig and TCR gene segments and the domain structure of the antigen receptor polypeptide chains are indicated. The V and C regions of each polypeptide are encoded by different gene segments. The locations of intrachain and interchain disulfide bonds (S-S) are approximate. Areas in the dashed boxes are the hypervariable (complementarity-determining) regions. In the Ig µ chain and the TCR α and β chains, transmembrane (TM) and cytoplasmic (CYT) domains are encoded by separate exons. N and C refer to amino and carboxy termini, respectively. C, Constant; D, diversity, J, joining; V, variable.
The V, J, and (if present) D gene segments are brought together to create the coding sequence for the variable domains of antibody chains (see Fig.2A). In an Ig light-chain protein (κ or λ), the V domain is encoded by the rearranged V and J gene segments; in the Ig heavy-chain protein, the V domain is encoded by the recombined V, D, and J gene segments. In the case of Ig heavy-chain V domains, a few residues from the C-terminal end of the V segment, the nongermline junctional residues between the rearranged V and D segments and the D and J segments, as well as the germline sequences of the D and J segments themselves, make up the third hypervariable region, also known as complementarity-determining region 3 (CDR3). A few terminal residues from the V segment, and the junctional sequences between the rearranged V and J segments as well as the J segment itself make up the third hyper variable region of Ig light chains. CDR1 and CDR2 are encoded in the V gene segment only.
A complete Ig light-chain or heavy-chain protein contains a V domain encoded by a rearranged VJ or VDJ exon, respectively, fused to a C domain or domains. The apposition of coding sequences for Ig V and C domains does not occur at the level of DNA rearrangement but by RNA splicing of the rearranged Ig gene transcript.
Noncoding sequences in the Ig loci play important roles in recombination and gene expression. As we will see later, sequences that dictate a recombination of different gene segments are found adjacent to each coding segment in Ig genes. Also present are V gene promoters and other cis-acting regulatory elements, such as locus control regions, enhancers, and silencers, which regulate gene expression at the level of transcription.
