Unlike most genes, the complete DNA sequence of the variable-region exon is not present in the germline of the individual, but is originally encoded by two separate DNA segments, as illustrated in Fig. 5.2. These two DNA segments are spliced together to form the complete exon 2 as the B cell develops in the bone marrow. The first 95–101 amino acids of the variable region, encoding βsheets A–F and the first two complete hypervariable regions, originate from a
Fig. 5.2 The CDR3 region originates from two or more individual gene segments that are joined during lymphocyte development. Panel a: a complete light-chain variable region encoding the CDR1, CDR2, and CDR3 loops resides in a single exon. Panel b: the complete variable region is derived from distinct germline DNA sequences. A V gene segment encodes the CDR1 and CDR2 loops, and the CDR3 loop is formed by sequences from the end of the V gene segment and the beginning of the J gene segment, and by nucleotides added or lost when these gene segments are joined during lymphocyte development. The exon for the CDR3 loop of the heavy chain is formed by the joining of sequences from V, D, and J gene segments (not shown).
variable or V gene segment (see Fig. 5.2). This segment also contributes part of the third hypervariable region. Other parts of the third hypervariable region, and the remainder of the variable region including β sheet G (up to 13 amino acids), originate from a joining or J gene segment. By convention, we will refer to the exon encoding the complete variable region formed by the splicing together of these gene segments as the V-region gene.
In nonlymphoid cells, the V-region gene segments remain in their original germline configuration, and are a considerable distance away from the sequence encoding the C region. In mature B lymphocytes, however, the assembled V-region sequence lies much closer to the C region, as a consequence of a splicing event of the gene’s DNA. Rearrangement within the immunoglobulin genes was originally discovered almost 40 years ago, when the techniques of restriction enzyme analysis first made it possible to study the organization of the immunoglobulin genes in both B cells and nonlymphoid cells. Such experiments showed that segments of genomic DNA within the immunoglobulin genes are rearranged in cells of the B-lymphocyte lineage, but not in other cells. This process of rearrangement is known as ‘somatic’ DNA recombination to distinguish it from the meiotic recombination that takes place during the production of gametes.
5-2 Complete genes that encode a variable region are generated by the somatic recombination of separate gene segments.
The rearrangements that produce the complete immunoglobulin light-chain and heavy-chain genes are shown in Fig. 5.3. For the light chain, the joining of a VL and a JL gene segment creates an exon that encodes the whole light-chain VL region. In the unrearranged DNA, the VL gene segments are located relatively far away from the exons encoding the constant region of the light chain (CL region). The JL gene segments are located close to the CL region, however, and the joining of a VL gene segment to a JL gene segment also brings the VL gene segment close to a CL-region sequence. The JL gene segment of the rearranged VL region is separated from a CL-region sequence only by a short intron. To make a complete immunoglobulin light-chain messenger RNA, the V-region exon is joined to the C-region sequence by RNA splicing after transcription.