LENGTH POLYMORPHISM OF THE HUMAN-COMPLEMENT COMPONENT C4 GENE IS DUE TO AN ANCIENT RETROVIRAL INTEGRATION

The fourth component of the complement system, C4, is encoded by two h ighly homologous MHC-linked genes expressing the two isotypes C4A and C4B. A gene size polymorphism (either 22.5 or 16 kb) has been describe d which depends on the presence or absence of a 6.5-kb insertion in in tron 9 of the C4 gene. By sequencing a C4A-specific lambda clone from a human genomic library containing the long intron 9 as well as PCR-am plified DNA containing the short intron, the DNA sequences of both int rons were determined. The long and short introns have lengths of 6,787 bp and 415 bp, respectively. The sequence of the short intron is almo st identical (96%) to the corresponding parts of the long intron. At p osition 282 of the short intron, a 6,372-bp insertion is present in th e long intron which has all characteristics of a full-length endogenou s retrovirus. The proviral DNA is flanked by two 6-bp target site repe ats. The orientation of the proviral sequence is opposite to that of t he C4 coding strand. Long terminal repeats (LTRs) of 548 bp were found at both ends of the provirus. A TATA box and an SV40 enhancer core as well as a polyadenylation signal are present in the LTR. A 5' primer binding site for lysine tRNA was identified. The strongest sequence ho mologies were found in comparison to human endogenous retrovirus (HERV -K): between 65-88% for gag, pol and env genes. However, a search for open reading frames in these regions indicated the presence of multipl e stop codons in all three reading frames. Thus it can be concluded th at the retroviral genes are dysfunctional due to these mutations. It c an be assumed that the integration of the retroviral sequence occurred prior to the separation of human and primate species, which can be da ted to a period between 23 and 10 million years ago.