Of previously reported HIV-1 T cell genome integration sites found in Genbank revealed that in human genes most integration sites are located in noncoding regions and that integration into coding regions is rare. We found that CD27 is one of the few genes in which HIV-1 integrates into the coding region. The CD27 gene is involved in T cell activation; therefore, integration into this gene may influence differentiation of host T cells by altering expression of this gene. Schroeder et al. reported that HIV-1 prefers to integrate into transcriptional activation genes [1]. We hypothesized that HIV-1 integration into the T cell genome occurs during transcriptional activation of the CD27 gene. By characterizing the features of the integration sequence, we may enhance understanding of the integration process. Because we found that the CD27 sequence segment into which HIV-1 integrates includes a palindromic feature, which was anticipated in a previous report, we utilized a biophysical technique, the quartz crystal order Sudan I microbalance (QCM) assay, to examine the affinity of integrase for this sequence segment. Integration into the CD27 segment target sequence was assessed using an in vitro integration assay.Target Sequence of HIV-1 IntegrationMaterials and Methods Identification of the Integration Site in CD27 LocusHIV-1 integration sites were meta-analyzed using previously reported sites in the DNA of HIV-1 nfected cells. Analysis of Homo sapiens PAC clone RP11-102E24 revealed that HIV-1 integrates into the CD27 locus in the genome of HIV-1 nfected clone SupS1 human lymphoma T cells [Genbank Accession No. AF038363] [6,8]. The 1480666 integration site was identified in the first intron located between the first and second exons of CD27. df {2f0 2 dm= (r1=2 mA) ?The left side of the equation (df) represents the change in the frequency, where f0 represents the resonant frequency; r represents the density of the crystal; represents the shear stress; dm represents the change 1676428 in the mass associated with integrase binding; and A represents the active area of the electrode. Therefore, the amount of integrase bound to the target DNA segment could be compared to that bound to the Dimethylenastron site modified target DNA by determining the change in oscillation frequency.In vitro IntegrationIn vitro integration was assessed essentially according to a previously reported protocol [9]. Briefly, 150 ng of U39-R-U59U39-R-U59 tandem LTR HIV-1 cDNA was added to 50 ng of recombinant HIV-1 integrase in 10 mL of binding buffer and incubated for 1 h at 30uC. The binding buffer consisted of 10.1 mM MgCl2, 80 mM potassium glutamate, 10 mM mercaptoethanol, 10 DMSO, and 35 mM MOPS (pH 7.2). The target human CD27 DNA was ligated into circular pCR2.1 TOPO vector plasmid DNA (Invitrogen, Carlsbad, CA), and 500 ng of the ligation product DNA was used as the target DNA for the assay. Truncated target DNA or target DNA with deleted nucleotides was also ligated into circular pCR2.1 TOPO vector plasmid DNA. HIV-1 integrase was kindly provided by Dr. Tomokazu Yoshinaga [10]. The pCR2.1 plasmid containing integrated HIV-1 proviral DNA was used to transform E. coli cells, from which the plasmid DNA was subsequently extracted and sequenced. The sequence of the target DNA was modified in several ways for the in vitro integration assay. Nucleotides within the target segment and nucleotides in the presumed DNA stem were replaced. The details of target sequence and the replacement nucleotides were represented in text.Of previously reported HIV-1 T cell genome integration sites found in Genbank revealed that in human genes most integration sites are located in noncoding regions and that integration into coding regions is rare. We found that CD27 is one of the few genes in which HIV-1 integrates into the coding region. The CD27 gene is involved in T cell activation; therefore, integration into this gene may influence differentiation of host T cells by altering expression of this gene. Schroeder et al. reported that HIV-1 prefers to integrate into transcriptional activation genes [1]. We hypothesized that HIV-1 integration into the T cell genome occurs during transcriptional activation of the CD27 gene. By characterizing the features of the integration sequence, we may enhance understanding of the integration process. Because we found that the CD27 sequence segment into which HIV-1 integrates includes a palindromic feature, which was anticipated in a previous report, we utilized a biophysical technique, the quartz crystal microbalance (QCM) assay, to examine the affinity of integrase for this sequence segment. Integration into the CD27 segment target sequence was assessed using an in vitro integration assay.Target Sequence of HIV-1 IntegrationMaterials and Methods Identification of the Integration Site in CD27 LocusHIV-1 integration sites were meta-analyzed using previously reported sites in the DNA of HIV-1 nfected cells. Analysis of Homo sapiens PAC clone RP11-102E24 revealed that HIV-1 integrates into the CD27 locus in the genome of HIV-1 nfected clone SupS1 human lymphoma T cells [Genbank Accession No. AF038363] [6,8]. The 1480666 integration site was identified in the first intron located between the first and second exons of CD27. df {2f0 2 dm= (r1=2 mA) ?The left side of the equation (df) represents the change in the frequency, where f0 represents the resonant frequency; r represents the density of the crystal; represents the shear stress; dm represents the change 1676428 in the mass associated with integrase binding; and A represents the active area of the electrode. Therefore, the amount of integrase bound to the target DNA segment could be compared to that bound to the modified target DNA by determining the change in oscillation frequency.In vitro IntegrationIn vitro integration was assessed essentially according to a previously reported protocol [9]. Briefly, 150 ng of U39-R-U59U39-R-U59 tandem LTR HIV-1 cDNA was added to 50 ng of recombinant HIV-1 integrase in 10 mL of binding buffer and incubated for 1 h at 30uC. The binding buffer consisted of 10.1 mM MgCl2, 80 mM potassium glutamate, 10 mM mercaptoethanol, 10 DMSO, and 35 mM MOPS (pH 7.2). The target human CD27 DNA was ligated into circular pCR2.1 TOPO vector plasmid DNA (Invitrogen, Carlsbad, CA), and 500 ng of the ligation product DNA was used as the target DNA for the assay. Truncated target DNA or target DNA with deleted nucleotides was also ligated into circular pCR2.1 TOPO vector plasmid DNA. HIV-1 integrase was kindly provided by Dr. Tomokazu Yoshinaga [10]. The pCR2.1 plasmid containing integrated HIV-1 proviral DNA was used to transform E. coli cells, from which the plasmid DNA was subsequently extracted and sequenced. The sequence of the target DNA was modified in several ways for the in vitro integration assay. Nucleotides within the target segment and nucleotides in the presumed DNA stem were replaced. The details of target sequence and the replacement nucleotides were represented in text.
