Ns dormant. In contrast, we demonstrated that TI could be counteracted by specific inhibition of the upstream transcription or by cooperative activation of transcription initiation and elongation from the 5'LTR by the viral and host TFs. In the latter scenario, we envision that RNAPII initiating from the viral promoter competes successfully with the RNAPII that is elongating through the 5'LTR. Bec
Lation than the 5'LTR, suggesting that the latter LTR is much stronger subjected to TI. Even if there is transcription from host gene `reading through' both LTRs in some latent cells, this does not diminish the impact of TI on the 5'LTR.NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptCell Host Microbe. Author manuscript; available in PMC 2014 November 03.Lenasi et al.Page
Tiful in genes and they are recognized by the spliceosome when there is no stronger splice site downstream of them, such aberrant splicing probably takes place in many cases of integration of the viral genome. On one hand, these transcripts reflected active transcription upstream of the provirus in both J-Lat cell lines. On the other hand, LTR sequence in the transcripts enabled us to use them as
Ost Microbe. Author manuscript; available in PMC 2014 November 03.Lenasi et al.PageWestern blotting 107 J-Lat or J-Lat shER cells were lysed in 0.8 ml of lysis buffer A (10 mM Tris-HCl [pH 7.4], 150 mM NaCl, 2 mM EDTA, 1 NP-40, 0.1 protease inhibitor) for 40 min at 4 . Proteins in the lysates were separated on SDS-PAGE electrophoresis. Western blotting was performed according to the standard pro
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
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
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