Retroviruses integrated at unique locations in the host genome can be expressed at different levels. We have analyzed the preintegration sites of three transcriptionally competent avian endogenous proviruses (evs) to determine whether the various levels of provirus expression correlate with their location in active or inactive regions of chromatin. Our results show that in three of four cell types, the chromatin conformation (as defined by relative nuclease sensitivity) of virus preintegration sites correlates with the level of expression of the resident provirus in ev+ cells: two inactive proviruses (ev-1 and ev-2) reside in nuclease-resistant chromatin domains and one active provirus (ev-3) resides in a nuclease-sensitive domain. Nuclear runoff transcription assays reveal that the preintegration sites of the active and inactive viruses are not transcribed. However, in erythrocytes of 15-day-old chicken embryos (15d RBCs), the structure and activity of the ev-3 provirus is independent of the conformation of its preintegration site. In this cell type, the ev-3 preintegration site is organized in a nuclease-resistant conformation, while the ev-3 provirus is in a nuclease-sensitive conformation and is transcribed. In addition, the nuclease sensitivity of host sequences adjacent to ev-3 is altered in ev-3+ 15dRBCs relative to that found in 15d RBCs that lack ev-3. These data suggest that the relationship between preintegration site structure and retrovirus expression is more complex than previously described.Avian and murine retroviruses can be expressed at different levels after integration into the host cell genome (2,14,21,26,29). In some cases, this variation is not due to genetic differences between the proviruses but instead is dependent on their site of integration (26,29). Analyses of two mouse mammary tumor virus proviruses acquired by exogenous infection in cultured cells indicated that the differential activity of these proviruses is dependent on their location in nuclease-sensitive or nuclease-resistant regions of the host cell genorne (14). An analogous relationship is not evident, however, for murine viruses introduced into the mouse germ line (Mov proviruses;27,28). In the latter case, inherited proviruses are inactive, even when located in transcriptionally active regions of chromatin (4,20). In contrast to Mov proviruses, some of the naturally occurring avian endogenous viruses (evs) are active in their inherited chromosomal location (2, 21). We were therefore interested in the relationship between provirus expression and the structure and activity of virus preintegration sites in this system.The avian endogenous viruses are highly related and stable genetic elements that were introduced into the germ line of chickens during evolution (1,7,24,25,33). Of the three viruses analyzed in this report, ev-1 and ev-2 are normally inactive in their inherited locations (producing less than 1 copy of stable RNA per cell; 2, 21), while ev-3 is active (producing 50 to 100 copies of stable mRNAs per cell; 2, 21...