CHROMOSOME STRUCTURE AND HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 CDNA INTEGRATION - CENTROMERIC ALPHOID REPEATS ARE A DISFAVORED TARGET

Integration of retroviral cDNA into host chromosomal DNA. is an essent ial and distinctive step in viral replication. Despite considerable st udy, the host determinants of sites for integration have not been full y clarified. To investigate integration site selection in vivo, we use d two approaches. (i) We have analyzed the host sequences flanking 61 human immunodeficiency virus type 1 (HIV-1) integration sites made by experimental infection and compared them to a library of 104 control s equences. (ii) We have also analyzed HIV-1 integration frequencies nea r several human repeated-sequence DNA families, using a repeat-specifi c PCR-based assay. At odds with previous reports from smaller-scale st udies, we found no strong biases either for or against integration nea r repetitive sequences such as Alu or LINE-1 elements. We also did not find a clear bias for integration in transcription units as proposed previously, although transcription units were found somewhat more freq uently near integration sites than near controls. However, we did find that centromeric alphoid repeats were selectively absent at integrati on sites, The repeat-specific PCR-based assay also indicated that alph oid repeats were disfavored for integration in vivo but not as naked D NA in vitro. Evidently the distinctive DNA organization at centromeres disfavors cDNA integration. We also found a weak consensus sequence f or host DNA at integration sites, and assays of integration in vitro i ndicated that this sequence is favored as naked DNA, revealing in addi tion an influence of target primary sequence.