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Related Experiment Video

Updated: Jan 6, 2026

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Stable integrant-specific differences in bimodal HIV-1 expression patterns revealed by high-throughput analysis.

David F Read1,2, Edmond Atindaana2,3, Kalyani Pyaram2

  • 1Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.

Plos Pathogens
|October 5, 2019
PubMed
Summary
This summary is machine-generated.

HIV-1 gene expression varies significantly between individual proviral DNA copies within infected cells. This study reveals that HIV-1 proviruses can switch between active and inactive states, with distinct clones maintaining stable expression levels despite these fluctuations.

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Area of Science:

  • Virology
  • Molecular Biology
  • Genetics

Background:

  • HIV-1 gene expression is a complex process influenced by host factors, viral elements, and proviral DNA integration sites.
  • Understanding the dynamics of HIV-1 gene expression at the clonal level is crucial for comprehending viral persistence and therapeutic strategies.
  • Previous studies have observed variations in HIV-1 expression, but detailed tracking of individual proviral clones over time has been limited.

Purpose of the Study:

  • To investigate the variability and dynamics of HIV-1 gene expression among individual proviral clones within a polyclonal population.
  • To identify host and viral factors, including integration site characteristics, that influence HIV-1 expression states.
  • To elucidate the mechanisms driving HIV-1 population dynamics, such as clonal expansion and epigenetic regulation.

Main Methods:

  • Tracking hundreds of individual proviral clones using unique genomic "zip codes" across multiple rounds of replication.
  • Utilizing a GFP reporter in the nef gene to quantify proviral expression (GFP+ vs. GFP-) within individual clones.
  • Analyzing integration site features (orientation, proximity to repressive histone marks like H3K9me3) and correlating them with expression phenotypes and clonal expansion rates.

Main Results:

  • HIV-1 proviral inactivation during reverse transcription was rare; however, clonal expansion and expression states varied widely.
  • Distinct clone-specific variations in the proportion of actively expressing (GFP+) and non-expressing (GFP-) cells were observed, spanning three orders of magnitude.
  • Proviral expression exhibited phenotypic oscillations (on/off switching), yet clones maintained stable equilibrium mixtures of GFP+ and GFP- cells.
  • Integration in the sense orientation of host genes and proximity to repressive H3K9me3 marks correlated with lower GFP+ proportions.
  • Clones with lower GFP+ frequencies expanded more rapidly, suggesting differential clonal expansion contributes significantly to population dynamics.

Conclusions:

  • HIV-1 gene expression demonstrates significant temporal and quantitative variability among proviral clones, independent of metabolic or cell-type specific factors.
  • Cell-intrinsic regulatory layers, including epigenetic modifications at integration sites and differential clonal expansion, play a critical role in shaping HIV-1 population dynamics.
  • These findings provide insights into the complex regulation of HIV-1 persistence and offer potential targets for therapeutic intervention.