Somatic hypermutation of the JC intron is markedly reduced in unrearranged kappa and H alleles and is unevenly distributed in rearranged alleles.

Somatic hypermutation of the Ig genes occurs in rearranged V(D)J and its flanking sequences after Ag stimulation. Even though C regions and unrearranged V segments have been found to lack mutations, it is not known whether the mutational mechanism can be active in unrearranged J segments and their flanking regions. By polymerase chain reaction and direct sequencing of the 500 bp at the 5' end of the JC intron of hybridoma DNA derived from splenic B cells, we show that the frequency of mutations in unrearranged J regions of kappa and H chain genes is 0/7849 bp (upper 95% confidence interval, less than 0.00038) and 1/3209 bp (upper 95% confidence interval, less than 0.0015), respectively. The frequency (f) for the same region of rearranged kappa and H chain genes was 29/9380 bp (95% confidence, 0.0021 less than f less than 0.0044) and 16/2750 bp (95% confidence, 0.0033 less than f less than 0.0094), respectively. The significantly higher frequency of mutations in the rearranged alleles indicates that rearrangement is needed to effect full activation of the mutational mechanism. The data also show that mutations occur predominantly in the 5'-most 250 bp of the JC kappa intron. Statistical analysis of the distribution of mutations within the 5'-most 521 bp of the JC kappa intron reveals significant deviation (p = 0.000085) from a theoretically determined uniform distribution, indicating that mutations are not evenly distributed within this region.