Genetics of the Antibody Loci

Chapter 23

(pp. 712-715, augmented)

There are two pairs of two different chains in an antibody, the Light Chain and the Heavy chain. Both come from different loci on different chromosomes that are highly processed both as DNA and as hnRNA to yield a fantastic number of antibodies, estimated to be over 10¹⁰ in humans! This might be considered to be some kind of "ultimate" coding of multiple polypeptides in a couple of cistrons! The light chain has two loci of somewhat different forms, the l-chain on chromosome 22 and the k-chain on chromosome 2. The gene for the heavy chain is on chromosome 14. Let's take a look at how they are organized, and how they are processed at each of these levels.

The chains for a Y-shaped tetramer, with the light chains paralleling the NH₂ ends of the heavy chain. The forks of the Y react with the different antigens. The base of the Y determines the vehicle from which the antibodies function - the classes of antibodies. There are several such classes of antibodies, and the cells producing the antibodies have considerable flexibility to change the class over time. Some of the classes of antibodies and their properties are in the following table:

The molecular organization of the genes for the chains varies among species, but the general arrangement is as follows:

The k-light chain locus is approximately 1,228.5kb long. This requires about 6,140 nucleosomes to coil this DNA. The eventual "hookup" of the parts combines only one of each type of exon, one L, one V, one J and one C. Different combinations give different antigenic specificity. The V-region in humans codes for 95 amino acids of the final polypeptide. It is the "variable" part that reacts with a specific antigen. It is coded into 150 exons each coding for 95 amino acids, but have a diversity of particular amino acids in the composition. Different species have different numbers of V-regions. Each V-region is preceded by a short exon, the L-region, that codes for 17-20 amino acids that help position the polypeptide in the endoplasmic reticulum, and then they are cleaved from the polypeptide. The J-region codes for 13 amino acids, and has a small number of variations (half a dozen or so, depending on the species) among the exons, all of which can join the V-region to the C-region (which is constant - only one per light chain locus). Below you will see how the actual formation of the connection between a V-region and a J-region also generates further diversity.

Upon proper stimulation, a cell with the full set of exons begins to remove all but one of the L-V's by attaching one to a J-region from the DNA. This is analogous of the processing of hnRNA, but involves the double stranded DNA strand. Once modified in the DNA, future cells produced by mitosis form a clone of cells that can only produce the kinds of antibodies limited by this genetic specialization.

In order to accomplish this genetic excision of most of the antibody locus, and the associated potential for diversity in antibody production, the single strand individually folds on itself, and a long stretch is removed very precisely. A mistake of only one nucleotide would cause a frame shift mutation, and inactivate the locus. Indeed, this happens, and, unless repaired, the affected locus has no possible antibody formation function. However, as a diploid cell, it has two chances each for the light chain and the heavy chain. If the first locus is successfully modified to produce a functional antibody, the second locus is left unchanged. If the first fails, and the second succeeds, only the antibody from the second locus is produced. The restriction to one, and only one, of each of the two antibody alleles to function at each of the two loci (heavy chain locus and light chain locus) is called allelic exclusion. As a result, the process of differentiation in an antibody locus by discarding a large amount of it's DNA produces clones of cells that can reliably, for the life of the clone, produce one or a very limited array of antibodies. This is the source of the very important molecular tools, "monoclonal antibodies."

The heavy chain locus is on another chromosome, and even larger than the light chain. This chain has a greater potential for antibody diversity in two ways: by having another class of exons, D-exons (for "diversity"), and by having multiple forms of the C-class of exons (one for each class of antibodies including those shown in the table above). The selection of a particular combination of V, D, and J exons are made by DNA processing. Only some of the exon switching for the C-exons is done at the DNA level, leaving the remainder to occur in the processing of the hnRNA transcript.

Notice that the size of the C-region for the heavy chain is about three times that of the C-region of the light chain. If we examine the sequences, we find that the heavy chain C-region is a triplication of one nucleotide sequence, and each of the three copies if very similar to the C-region of the light chain. Apparently these coding regions arose from a common coding region. This represents a dispersed family of genes between the light and heavy antibody loci, but with part of the family being a tandem repeated unit within the heavy chain. Of course, the multiple copies of each of the exon groups, V's, J, and D's (in the heavy chain) also form families of exons. We see that the idea of multiple copies that are diverged from a common original sequence is not restricted to a full cistron, but exons and sets of exons within a cistron.

Although there is some variability in the architecture of the long chain locus among species, the general organization is as follows:

Not only does this locus have additional D-exons, but it has a special switch region for poly-A tail selection. Newly differentiated B-cells generally produce IgM by using the C_m exon, which is nearest the differentiated VDJ region. However, cells can either switch C-exons by either hnRNA processing, or by further gene modification removing some of the C-exons. This allows additional physiological diversity by switching among classes of antibodies having the same antigenic specificity as a clone grows.

In the case of the switching by modification of the hnRNA, it is unclear whether it is by a change in termination site for transcription, polyadenylation, or alternative splicing. It may be a combination of any or all of these mechanisms.

If the DNA is modified, as in previous modifications the intervening region between the J-exon and the C-exon of "choice" is removed, producing a permanent and irreversible reduction in possible classes of antibodies that cell and it's descendants can produce. Each of the C-exons, with the exception of C_d-exon, is preceded by a switch region of a few base pairs of multiply repeated and complimentary, thereby forming signal sequences for recombination.

These DNA manipulations occur over huge nucleotide distances. However, the physical distance may be greatly reduced by precise coiling and folding of the chromosome.

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Last updated 09/01/97