Somatic hypermutation in 5′ flanking regions of heavy chain antibody variable regions

The aim of this study has been to determine the distribution of somatic mutations in the 5′ flanking regions of rearranged immunoglobulin heavy chain variable region genes (VDJ).We sequenced the 5′ flanking region in 12 secondary immune response antibodies produced in C57BL/6J mice against the hapten (4‐hydroxy‐3‐nitrophenyl)acetyl (NP) coupled to chicken‐Y‐globulin. In these and previously published sequences, almost 97 % of the mutations occurred in the transcribed region of the gene, and only a minority of genes (5/29) contained mutations upstream of the transcription start (cap) site. No potential germ‐line donor was found for a cluster of five base changes previously found in a single heavy chain gene, 3B62. However, the uniqueness of this mutational cluster and its distance from the normally mutated region suggests that the nucleotide changes may not be due to the normal mutator mechanism. Thus, as this was the only instance of somatic mutations that far upstream of the promoter/cap site region, the reverse transcriptase model for somatic hypermutation is still a possibility. The data are consistent with a mutational mechanism that requires transcription of the rearranged target V(D)J gene which appears to result in the generation of a positively skewed asymmetrical distribution of somatic mutations. A single mode is centered near the V(D)J and a long tail extends into the 3′ non‐translated region of the J‐C intron. Two classes of model could explain this mutation distribution pattern: those where transcription products (RNA, cDNA) are the direct mutational substrates, or those that postulate local unfolding of the chromatin around a V(D)J rearrangement directly exposing the DNA of the transcribed region to specific mutational enzymes.