Stream transcription could be detected independently of the viral integration site. HIV-infected primary CD4+ T cells contain significant levels of transcription upstream of the 5'LTR To identify transcription upstream of the 5'LTR in HIV-infected peripheral blood lymphocytes (PBLs), we used the above method. After activation of HIV-infected PBLs with IL-2 and PHA, we rested them and isolated CD4+
Es obtained with the LTR-specific primers represent a sum of transcripts originating from the host promoter and of viral transcripts, which also contain LTR sequence at their 3' ends. Therefore, the measured ratio corresponds to the equation a+b/b, where `a' is the number of host-viral chimeric transcripts and `b' the number of viral transcripts (see Supplemental text 2). First, we determined this
Nificant levels of the host-viral chimeric transcripts. Because they indicate active transcription upstream of the 5'LTR, these findings suggest that viral transcription is subjected to TI in these cells. Transcriptional interference by the actively transcribed host gene reverses viral transcription from the 5' to the 3'LTR Next, we investigated in detail how active transcription of the upstream P
Nificant levels of the host-viral chimeric transcripts. Because they indicate active transcription upstream of the 5'LTR, these findings suggest that viral transcription is subjected to TI in these cells. Transcriptional interference by the actively transcribed host gene reverses viral transcription from the 5' to the 3'LTR Next, we investigated in detail how active transcription of the upstream P
Es 3B and S3). We decided to use this cell line because of a smaller ratio between HIV transcripts and *mRNA in these cells compared to those in J-Lat 9.2 cells (Figure 2D, bars 3 and 4). The ratio between LTRand Rev-containing transcripts increased with the decreased levels of viral expression consistent with the rational equation (see Supplemental text 2), and revealed that the upstream transcri
Ly 20 activation of viral transcription (see Figure 7) already precludes detection of the upstream transcription. This finding is not surprising, as we demonstrated that there is 11-fold or 38-fold more viral mRNA than *mRNA in TNF- treated cells (Figure 2D, bars 3 and 4). Predictably, our control experiments demonstrate that the ratio between the Rev- and Env-containing transcripts was 1 in untr
Tream of the 5'LTR Existence of the host-viral chimeric transcripts that originate from a host promoter and include 5'LTR could be useful for identifying ongoing transcription upstream of the 5'LTR independently of the site of viral integration. Therefore, we next devised an assay, which determines the ratio between transcripts containing LTR sequences and those containing sequences present solely
Ranscription units (Han et al., 2004; Lewinski et al., 2005). In the present work, we extended this knowledge by a detailed analysis of how TI impacts viral transcription in latent cells. Although TI occurs regardless of the orientation of the two promoters, we studied TI phenomenon in two J-Lat cell lines with the same orientation of the host and viral promoters, which allowed us to detect and an