HIV-1 LTR C/EBP binding site sequence congurations preferentially encountered in brain lead to enhanced C/EBP factor binding and increased LTR-specic activity

Recent studies have shown that two CAAT/enhancer binding protein (C/EBP) sitesare critically important for efŽcient human immunodeŽciencyvirus (HIV) type 1 (HIV-1) replication within cells of the monocyte/macrophage lineage, a primary cell type infected by HIV-1 and a potentially important vehicle for transport of virus to the central nervous system (CNS). Given the relevance of HIV-1 LTR sequence variation with respect to HIV-1 replication within monocyte populations and the important role that monocyte tropism likely plays in HIV-1 infection of the brain, C/EBP site sequence variation was examined within peripheral bloodand brain-derived LTR populations. Brain-derived LTRs commonly possessed a C/EBP site I conŽguration (6G, comprised of a thymidine to guanosine substitution with respect to the clade B consensus sequence at position 6 of C/EBP site I) that leads to enhanced binding of C/EBP proteins over that observed with the HIV-1 clade B consensus sequence at this site. In contrast, the 6G C/EBP site I conŽguration appeared infrequentlywithin sequenced peripheral blood-derived LTRs. In addition, C/EBP site II was even more highly conserved in brain-derivedHIV-1 LTR populations than site I. This was not the case with peripheral blood-derived LTR C/EBP site II sequences. The high degree of C/EBP site II conservation in brain-derived LTRs was likely important in LTR regulation since the clade B consensus sequence conserved at C/EBP site II recruited high amounts of C/EBP family members. Transient transfection analyses indicated that conservation of the strong C/EBP site II in brain-derived LTRs was likely due to important interactions with Tat. Overall, brain-derived HIV-1 LTRs preferentially contained two highly reactive C/EBP binding sites, which may suggest that these sites play important roles in LTRdirected transcriptionduring invasion andmaintenance of HIV-1 in the central nervous system. Journal of NeuroVirology (2001) 7, 235–249.