Transcriptional Bursting from the HIV-1 Promoter Is a Significant Source of Stochastic Noise in HIV-1 Gene Expression

Abstract

Analysis of noise in gene expression has proven a powerful approach for analyzing gene regulatory architecture. To probe the regulatory mechanisms controlling expression of HIV-1, we analyze noise in gene-expression from HIV-1's long terminal repeat (LTR) promoter at different HIV-1 integration sites across the human genome. Flow cytometry analysis of GFP expression from the HIV-1 LTR shows high variability (noise) at each integration site. Notably, the measured noise levels are inconsistent with constitutive gene expression models. Instead, quantification of expression noise indicates that HIV-1 gene expression occurs through randomly timed bursts of activity from the LTR and that each burst generates an average of 2-10 mRNA transcripts before the promoter returns to an inactive state. These data indicate that transcriptional bursting can generate high variability in HIV-1 early gene products, which may critically influence the viral fate-decision between active replication and proviral latency.

Transcriptional burst frequency and burst size are equally modulated across the human genome

“…3B and SI Appendix, Fig. S4), which is consistent with our previous study (17) showing that the LTR promoter displays relatively higher levels of noise than other eukaryotic promoters in yeast (6,7). This shift in noise magnitude is consistent with the well-known transcriptional elongation stall that characterizes LTR expression (26).…”

“…This stall results in Fig. 2D (18 h). delayed switching to the transcriptional ON state in a two-state transcription model (17) and predicts that noise frequency (not only noise magnitude) (27) is modulated in different genomic or chromatin environments (SI Appendix). In agreement with this prediction, the distribution of points in the LTR noise map indicates significant differences from the UBC and EF1A noise maps.…”

“…The burst size, or number of mRNAs generated per activity pulse, is typically defined as k m ∕k off and, in the limit of k off ≫ k on , the burst frequency is defined as k on (Fig. 4A) (17). To directly test if transcriptional burst frequency changes across genome location, we analyzed the polyclonal three-dimensional noise-space data to fit values for k m , k off , and k on .…”

“…However, a tedious experimental bottleneck of subcloning and expansion of isogenic populations necessarily limits the throughput of these noise-analysis approaches. Here, we circumvent this subcloning requirement to globally apply the analytical (17)(18)(19) have tackled these questions for specific genes, but no clear and broad consensus has yet emerged.…”

Self-regulation in a minimal model of chemical self-replication

“…In general, our results show that negative feedback can yield simpler dynamical behaviors when coupled with a biochemical mechanism, and that positive feedback can have drastic dynamical effects on simple oscillatory behavior. From the previous discussion, it seems that the type of regulation considered in our analysis may be related to so-called gene bursting [64][65][66].…”