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Transcriptional Circuit Fragility Influences HIV Proviral Fate.

Cell reports | 2019

Transcriptional circuit architectures in several organisms have been evolutionarily selected to dictate precise given responses. Unlike these cellular systems, HIV is regulated through a complex circuit composed of two successive phases (host and viral), which create a positive feedback loop facilitating viral replication. However, it has long remained unclear whether both phases operate identically and to what extent the host phase influences the entire circuit. Here, we report that, although the host phase is regulated by a checkpoint whereby KAP1 mediates transcription activation, the virus evolved a minimalist system bypassing KAP1. Given the complex circuit's architecture, cell-to-cell KAP1 fluctuations impart heterogeneity in the host transcriptional responses, thus affecting the feedback loop. Mathematical modeling of a complete circuit reveals how these oscillations ultimately influence homogeneous reactivation potential of a latent virus. Thus, although HIV drives molecular innovation to fuel robust gene activation, it experiences transcriptional fragility, thereby influencing viral fate and cure efforts.

Pubmed ID: 30943398 RIS Download

Research resources used in this publication

Additional research tools detected in this publication

Associated grants

  • Agency: NIAID NIH HHS, United States
    Id: R21 AI123035
  • Agency: NIGMS NIH HHS, United States
    Id: T32 GM007062
  • Agency: NIAID NIH HHS, United States
    Id: R01 AI114362
  • Agency: NIAID NIH HHS, United States
    Id: U01 AI111598
  • Agency: NIAID NIH HHS, United States
    Id: R33 AI122377
  • Agency: NIAID NIH HHS, United States
    Id: R33 AI116222

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This is a list of tools and resources that we have found mentioned in this publication.


NIH AIDS Reagent Program (tool)

RRID:SCR_023191

NIH HIV Reagent Program has been managed under contract by American Type Culture Collection (ATCC) since 2020. ATCC shall maintain the NIH HIV Reagent Program through identification, acquisition, production, receipt, storage, maintenance, distribution and disposal of biological and chemical research organisms and materials for HIV and other infectious diseases for use in basic and translational research.

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GraphPad Prism (software resource)

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NSR Physiome Project (software resource)

RRID:SCR_007379

Database of physiological, pharmacological, and pathological information on humans and other organisms and integration through computational modeling. Models include everything from diagrammatic schema, suggesting relationships among elements composing a system, to fully quantitative, computational models describing the behavior of physiological systems and an organism''s response to environmental change. Each mathematical model is an internally self-consistent summary of available information, and thereby defines a working hypothesis about how a system operates. Predictions from such models are subject to test, with new results leading to new models.BR /> A Tool developed for the NSR Physiome project is JSim, an open source, free software. JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim''s primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim''s model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats. All JSim models are open source. Goals of the Physiome Project: - To develop and database observations of physiological phenomenon and interpret these in terms of mechanism (a fundamentally reductionist goal). - To integrate experimental information into quantitative descriptions of the functioning of humans and other organisms (modern integrative biology glued together via modeling). - To disseminate experimental data and integrative models for teaching and research. - To foster collaboration amongst investigators worldwide, to speed up the discovery of how biological systems work. - To determine the most effective targets (molecules or systems) for therapy, either pharmaceutic or genomic. - To provide information for the design of tissue-engineered, biocompatible implants.

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J-Lat 8.4 (cell line)

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RRID:SCR_003070

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RRID:SCR_008520

Software for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.

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RRID:CVCL_8280

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U2OS (cell line)

RRID:CVCL_0042

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HEK293T/17 (cell line)

RRID:CVCL_1926

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SUP-T1 (cell line)

RRID:CVCL_1714

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Jurkat E6.1 (cell line)

RRID:CVCL_0367

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J-Lat 10.6 (cell line)

RRID:CVCL_8281

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GraphPad Prism (software resource)

RRID:SCR_002798

Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.

View all literature mentions

ImageJ (software resource)

RRID:SCR_003070

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View all literature mentions

BD FACSDiva Software (software resource)

RRID:SCR_001456

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RRID:SCR_016445

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NSR Physiome Project (software resource)

RRID:SCR_007379

Database of physiological, pharmacological, and pathological information on humans and other organisms and integration through computational modeling. Models include everything from diagrammatic schema, suggesting relationships among elements composing a system, to fully quantitative, computational models describing the behavior of physiological systems and an organism''s response to environmental change. Each mathematical model is an internally self-consistent summary of available information, and thereby defines a working hypothesis about how a system operates. Predictions from such models are subject to test, with new results leading to new models.BR /> A Tool developed for the NSR Physiome project is JSim, an open source, free software. JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim''s primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim''s model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats. All JSim models are open source. Goals of the Physiome Project: - To develop and database observations of physiological phenomenon and interpret these in terms of mechanism (a fundamentally reductionist goal). - To integrate experimental information into quantitative descriptions of the functioning of humans and other organisms (modern integrative biology glued together via modeling). - To disseminate experimental data and integrative models for teaching and research. - To foster collaboration amongst investigators worldwide, to speed up the discovery of how biological systems work. - To determine the most effective targets (molecules or systems) for therapy, either pharmaceutic or genomic. - To provide information for the design of tissue-engineered, biocompatible implants.

View all literature mentions

mouse-IgG-control-human (antibody)

RRID:AB_737182

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HU CD184 PE MAB 100TST 12G5 (antibody)

RRID:AB_396267

This monoclonal targets CD184 (CXCR4)

View all literature mentions

Cdk9 (C-20) (antibody)

RRID:AB_2275986

This polyclonal targets Cdk9 (C-20)

View all literature mentions

NELFE-human (antibody)

RRID:AB_2177858

This polyclonal targets NELFE

View all literature mentions

Anti-β-Actin Antibody (C4) (antibody)

RRID:AB_626632

This monoclonal targets β-Actin

View all literature mentions