Analysis of in vivo integration patterns has provided no data to support the notion that retroelement integration is random. Rather, the diversity of insertion patterns of retroelements suggests numerous ways in which genomic DNA is identified for preferential targeting. These range from specific to general and include sequence content, removal of chromatin proteins, nuclear localization, distinctive topology, and association with particular trans-acting factors. Many are similar to mechanisms already demonstrated to affect activities of previously described recombinases. Moreover, such proposed targeting mechanisms could act directly or indirectly to influence integration site selection. A variety of observations are consistent with the preferential use of open chromatin for retroelement insertion. The site-specific retroelements insert into transcribed regions. In vitro studies with retroviruses and Ty1 have shown that naked DNA can function, at least under some conditions, as a target. The association of integration sites of retroviruses and regions in which DNase I hypersensitive sites exist and the preferential integration of Ty1 at the 5' ends of some genes might suggest that regions which do not have phased nucleosomes are targets for integration. Is targeting to transcriptionally active regions essentially passive, because they are not densely associated with chromatin proteins, or is targeting active in the sense of being a more specific process? Specific targets could be generated from DNA or protein motifs. Nucleosome-free regions are associated with a variety of nonnucleosome proteins, including topoisomerases, nuclear matrix proteins, transcription factors, or replication proteins. These then are candidates for proteins which target integration directly, by associating with the transposition complex or, indirectly, by inducing changes in the DNA. Polymerase III-transcribed genes, which are relatively defined targets of integration for some retrotransposon systems, probably exemplify several of these mechanisms. Promoter sequences may be directly involved in targeting some elements and positioning of the transcription complex may fix the integration sites of others. The most common sequence feature of characterized in vivo insertion sites is that they are AT-rich. This may reflect specificity of the IN protein, particularly the gypsylike elements, increased nicking of DNA, which is relatively weakly base-paired, as appears to be the case for the FLP recombinase (130), or simply the AT content of accessible regions in chromatin. Some of these questions will be resolved by the characterization of in vitro integration sites that have been recovered by physical means, rather than by biological assay. The insertion patterns of a number of retroposons suggest that retroelements can insert with a high degree of sequence specificity.(ABSTRACT TRUNCATED AT 400 WORDS)