Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection

Abstract

Retroviruses differ in their preferences for sites for viral DNA integration in the chromosomes of infected cells. Human immunodeficiency virus (HIV) integrates preferentially within active transcription units, whereas murine leukemia virus (MLV) integrates preferentially near transcription start sites and CpG islands. We investigated the viral determinants of integration-site selection using HIV chimeras with MLV genes substituted for their HIV counterparts. We found that transferring the MLV integrase (IN) coding region into HIV (to make HIVmIN) caused the hybrid to integrate with a specificity close to that of MLV. Addition of MLV gag (to make HIVmGagmIN) further increased the similarity of target-site selection to that of MLV. A chimeric virus with MLV Gag only (HIVmGag) displayed targeting preferences different from that of both HIV and MLV, further implicating Gag proteins in targeting as well as IN. We also report a genome-wide analysis indicating that MLV, but not HIV, favors integration near DNase I–hypersensitive sites (i.e., +/− 1 kb), and that HIVmIN and HIVmGagmIN also favored integration near these features. These findings reveal that IN is the principal viral determinant of integration specificity; they also reveal a new role for Gag-derived proteins, and strengthen models for integration targeting based on tethering of viral IN proteins to host proteins. A required step in the replication cycle of retroviruses is the integration of a DNA copy of the viral genome into a host cell chromosome. Recent studies have shown that human immunodeficiency virus (HIV) and murine leukemia virus (MLV) favor integration near different chromosomal features. HIV preferentially targets active genes, while MLV prefers integration near start sites of gene transcription. The authors investigated integration-target site–selection by HIV derivatives substituted with segments of MLV to determine which viral proteins are responsible for integration-targeting preferences. They found that the viral integrase protein is the dominant determinant of integration-site selection, probably through its tethering to cellular proteins bound near preferred genomic regions. In addition, components of the viral structural polyprotein, Gag, appear to be involved in targeting. These findings provide a functional map of the viral proteins involved in directing integration-site selection.