Basis of HTLV type 1 target site selection

Sequencing integration sites from greater than or equal to 200 proviruses i solated from infected individuals revealed that HTLV-1 integration is not r andom at the level of the nucleotide sequence. The virus was found to integ rate in A/T-rich regions with a weak consensus sequence at positions within and without the hexameric repeat generated during integration. These featu res were not associated with a preference for integration near active regio ns or repeat elements of the host chromosomes. However, about 6% of HTLV-1 proviruses were found to be integrated into transcription units, suggesting that in some cells, HTLV-1 integration may alter gene expression in vivo. Therefore, the target choice in vivo seems to be determined by local featur es rather than by the accessibility of specific regions. This led us subseq uently to analyze the role of the DNA structure in HTLV-1 integration in vi tro. Double-strand HTLV-1 or HIV-1 3' LTR extremities were used as substrat es for in vitro strand transfer reactions using highly purified HTLV-1 and HIV-1 integrases (INs) expressed in Escherichia coil, and two synthetic nak ed 50-bp double-strand DNA molecules harboring different structures were us ed as targets. A fluorometric quantitative analysis of integration products was designed to assess the reaction efficiency for both target sequences. As suggested for HTLV-1 in vivo (present results), and, as previously descr ibed for other retroviruses in vitro, the structure of the target was found to greatly influence the site and the efficiency of integration. Both HIV- 1 and HTLV-1 INs underwent the same target structural constraint, i.e., a s trong preference for curved DNA. Altogether these results indicate that if most or all the regions of the genome appear to be accessible to HTLV-1 int egration, local DNA curvature seems to confer a kinetic advantage for both in vitro and in vivo HTLV-1 integration.