Linkage of two pseudogenes from V_κ1 and V_κ9 murine immunoglobulin families

As an initial step towards the molecular analysis of the murine V_κ locus, a cosmid library from BALB/cJ mouse liver DNA was screened with probes representing 10 V_κ families. Of eight cosmids that were isolated from the initial screen, five contained a single restriction fragment that hybridized to the probes. Two cosmids contained two fragments that hybridized to the same probe, V_κ4, indicating that some V_κ4 gene segments are linked. One cosmid had two genes that belonged to different families, V_κ1 and V_κ9. The two gene segments were located within 12 kb of each other and lay in the same transcriptional orientation. Linkage of gene segments from the V_κ1 and V_κ9 families is consistent with a genetic map of the locus, and provides physical evidence for the first time that two genes from different families are closely linked in the murine κ locus. Sequence analysis revealed that both genes are pseudogenes: the V_κΨ 1.7 gene segment has eight mutations, including termination codons, insertions, and deletions, and the V_κΨ 9B.8 gene segment has two mutations of an insertion and altered RNA splice site. Both genes have the potential to rearrange based on the sequence of their heptamer-nonamer motifs. The identification of pseudogenes raises the question of how many nonfunctional genes are present in the murine germline repertoire.