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

Autoři: David F. Read aff001;  Edmond Atindaana aff002;  Kalyani Pyaram aff002;  Feng Yang aff002;  Sarah Emery aff001;  Anna Cheong aff001;  Katherine R. Nakama aff002;  Cleo Burnett aff002;  Erin T. Larragoite aff004;  Emilie Battivelli aff005;  Eric Verdin aff005;  Vicente Planelles aff004;  Cheong-Hee Chang aff002;  Alice Telesnitsky aff002;  Jeffrey M. Kidd aff001
Působiště autorů: Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America aff001;  Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America aff002;  West African Centre for Cell Biology of Infectious Pathogens (WACCBIP) and Department of Biochemistry, Cell & Molecular Biology, University of Ghana, Legon, Greater Accra Region, Ghana aff003;  Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America aff004;  Department of Medicine, University of California San Francisco, San Francisco, California, United States of America aff005;  Buck Institute for Research on Aging, Novato, California, United States of America aff006
Vyšlo v časopise: Stable integrant-specific differences in bimodal HIV-1 expression patterns revealed by high-throughput analysis. PLoS Pathog 15(10): e32767. doi:10.1371/journal.ppat.1007903
Kategorie: Research Article
doi: 10.1371/journal.ppat.1007903


HIV-1 gene expression is regulated by host and viral factors that interact with viral motifs and is influenced by proviral integration sites. Here, expression variation among integrants was followed for hundreds of individual proviral clones within polyclonal populations throughout successive rounds of virus and cultured cell replication, with limited findings using CD4+ cells from donor blood consistent with observations in immortalized cells. Tracking clonal behavior by proviral “zip codes” indicated that mutational inactivation during reverse transcription was rare, while clonal expansion and proviral expression states varied widely. By sorting for provirus expression using a GFP reporter in the nef open reading frame, distinct clone-specific variation in on/off proportions were observed that spanned three orders of magnitude. Tracking GFP phenotypes over time revealed that as cells divided, their progeny alternated between HIV transcriptional activity and non-activity. Despite these phenotypic oscillations, the overall GFP+ population within each clone was remarkably stable, with clones maintaining clone-specific equilibrium mixtures of GFP+ and GFP- cells. Integration sites were analyzed for correlations between genomic features and the epigenetic phenomena described here. Integrants inserted in the sense orientation of genes were more frequently found to be GFP negative than those in the antisense orientation, and clones with high GFP+ proportions were more distal to repressive H3K9me3 peaks than low GFP+ clones. Clones with low frequencies of GFP positivity appeared to expand more rapidly than clones for which most cells were GFP+, even though the tested proviruses were Vpr-. Thus, much of the increase in the GFP- population in these polyclonal pools over time reflected differential clonal expansion. Together, these results underscore the temporal and quantitative variability in HIV-1 gene expression among proviral clones that are conferred in the absence of metabolic or cell-type dependent variability, and shed light on cell-intrinsic layers of regulation that affect HIV-1 population dynamics.

Klíčová slova:

Cell cycle and cell division – Gene expression – HIV-1 – Polymerase chain reaction – Primary cells – Viral replication – Gene pool


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