Figure 4

Factors influencing reactivation potentials of latent HIV-1 promoters in TNF-α and SAHA-responsive single mCherry positive (M_TSC+) cell clones. (a) Reactivation potentials of latent HIV-1 promoters in TNF-α and SAHA-responsive single mCherry positive (M_TSC+) cell clones with different LTatC[M] integration sites were reactivated with TNF-α and SAHA 54–106 days post sorting. The means of at least two independent measurements (n = 2–22) are indicated by the heights of the bars and standard error means are indicated by the error bars. Two-tailed Mann-Whitney U test with 95% confidence level was used to test for statistical significance; *P < 0.05; **P < 0.01. Subscripts 1 and 2 indicate two independent transduction and sorting experiments from which the cell clones were derived. DP: double positive. (b) Gene expression patterns in SUP-T1 cells during the first 24 hours upon infection with an HIV-1-based vector. Median log₂ fold changes in expression of genes into which LTatC[M] was found integrated in different M_TSC+ cell clones are shown. The majority of the HIV-1 integration process are defined as complete at 18 hours post infection. + and − indicate significant (P < 0.01) upregulation and downregulation in gene expression, respectively, whereas 0 indicates no significant changes in gene expression compared to data at time point 0 hour. Data were obtained from the Patterns of Expression and Analysis of Clusters of HIV/Host interactions (PEACHi) database²⁷. Subscripts 1 and 2 indicate two independent transduction and sorting experiments from which the cell clones were derived. (c) Predicted RNA secondary structure of HIV-1 transactivation response element. The RNA secondary structures of HIV-1 transactivation response (TAR) element found in cell clone M_TSC₁+12 (top) and in the original vector LTatC[M] (bottom) were predicted using CLC Main Workbench 7. Red circle indicates the mutation in the TAR element of M_TSC₁+12.