The nonpathogenic human virus adeno-associated virus type 2 (AAV) has evolved the potentially unique strategy to establish latency by site-specifically integrating its genome into human chromosome 19 (19q13.3-qter) at a locus designated AAVS1. This nonhomologous, site-specific recombination of viral DNA with the human genome provides a basis for developing targeted gene therapy vectors. To assess whether the region surrounding AAVS1 might have contributed to the selection of the specific integration site, we have investigated this locus. Here, we show that AAVS1 is closely linked to the slow skeletal troponin T gene, TNNT1, which has been mapped previously to 19q13.4. In support of this idea, we demonstrate that site-specific AAV DNA integration can result in the formation of TNNT1-AAV junctions. The question now arises whether muscle represents a natural target tissue for latent AAV infection. This possibility is of additional interest in view of recent observations that muscle tissue is particularly well suited for AAV-mediated gene transfer. The question also occurs whether latent infection by AAV can lead to phenotypic changes of the multinucleated muscle fiber cells.T he human parvovirus adeno-associated virus type 2 (AAV) has adopted the strategy of alternate life styles to ensure a successful relationship with its host (1). This nonpathogenic virus productively replicates only in the presence of helper virus co-or superinfection (2). In the absence of such helper conditions, AAV has evolved a strategy potentially unique among eukaryotic viruses. On infection of the non-coinfected host cell, AAV establishes latency by integrating its genome sitespecifically into a region on the q arm of human chromosome 19 (19q13.3-qter) (3, 4), designated AAVS1.The 4.7-kb linear single-stranded genome contains two ORFs and is flanked by inverted terminal repeats (ITRs) (5). The right ORF encodes three capsid proteins, and the left ORF encodes the four nonstructural proteins (Rep proteins) that are involved in regulating all aspects of the viral life style (2).The 145-nt ITRs are the only viral sequences required in cis for DNA replication, packaging of the viral genome into the capsid, and site-specific DNA integration. Within the ITRs, a Rep binding site (RBS) allows for specific recruitment of the large Rep proteins (i.e., Rep68 and Rep78) to the origin of replication (6-8). A Rep-specific endonuclease site (terminal resolution site, TRS) is separated from the RBS by a 13-nt spacer (9-11). Together, RBS and TRS can act as a minimal origin for Rep-mediated DNA replication (12).To dissect the requirements for site specificity in targeted AAV DNA integration, an 8.2-kb fragment of AAVS1 has been isolated from embryonic lung fibroblast (WI38) DNA, and a 4-kb sequence was determined (13). It was shown by using an episomal model system that site specificity is determined by cellular sequences (14) and that a 33-nt sequence is necessary and sufficient for this targeted nonhomologous recombination event to occur (15). This 33-n...