The organization of the heavy-chain locus is more complex than that of the κ light-chain locus. The heavy-chain locus contains not only a large tandem array of V segments (each equipped with its own promoter) and multiple J segments, but also multiple D (diversity) segments (see Figure 23-15b). Somatic recombination of a V, a D, and a J segment generates a rearranged sequence encoding the heavy-chain variable region (V_H).

At the 3′ end of each V segment in heavy-chain DNA, there are conserved heptamer and nonamer sequences separated by spacer DNA, similar to the recombination signal sequences (RSSs) in light-chain DNA. These RSSs are also found in complementary and antiparallel configuration at the 5′ end and the 3′ end of each D segment (see Figure 23-16a). The J segments are similarly equipped at their 5′ end with the requisite RSS. The spacer lengths in these RSSs are such that D segments can join to J segments, and V segments to already rearranged DJ segments. However, neither direct V-to-J nor D-to-D joining is allowed, in compliance with the 12/23-bp spacer rule. Heavy-chain rearrangements proceed via the same mechanisms described above for light-chain rearrangements.

In the course of B-cell development, the heavy-chain locus is always rearranged first, starting with D-J rearrangement. D-J rearrangement is followed by V-D-J rearrangement. In the course of the D-J and V-D-J rearrangements, an enzyme called terminal deoxynucleotidyltransferase (TdT) may add nucleotides to free 3′ OH ends of DNA in a template-independent fashion. Up to a dozen or so nucleotides, called the N-region or N-nucleotides, may be added, generating additional sequence diversity at the junctions whenever D-J and V-D-J rearrangements occur (see Figure 23-16c, step 7). Only one in three rearrangements yields the proper reading frame for the rearranged VDJ sequence. If the rearrangement yields a sequence encoding a functional protein, it is called productive. Although the heavy-chain locus is present on each of two homologous chromosomes, only one productive rearrangement is permitted, as we will see below.

An enhancer located downstream of the cluster of J segments and upstream of the constant-region segment activates transcription from the promoter at the 5′ end of the rearranged VDJ sequence (see Figure 23-15). Splicing of the primary transcript produced from the rearranged heavy-chain gene generates a functional mRNA encoding the µ heavy chain. For both heavy-chain and light-chain genes, somatic recombination places the promoters upstream of the V segments within functional reach of the enhancers necessary to allow transcription, so that only rearranged VJ and VDJ sequences, and not the V segments that remain in the germ-line configuration, are transcribed.