Project

Discipline

viral cycle; reprogramming; miRNA; deep sequencing; RNA-seq; ChIP-seq; dynamic Bayesian netowrks

Lead
Lay summary
The life cycle of HIV-1, the AIDS virus, in the cell is generally completed in 24 hours. During this period of time, the virus invades the cell, and uses its machinery to complete the necessary steps for a productive infection. The cell is profoundly disturbed by this action. On its turn, the cell can mount antiviral responses that aim at limiting the progression of the viral life cycle, and inform other cells of the presence of a pathogen. This proposal aims at the in-depth characterization of the reprogramming of the cell upon HIV infection. The analysis will cover, through repeated measurements, the life cycle of the virus. During this period, the virus undergoes entry and uncoating, reverse transcription, nuclear import, integration, transcription, export of viral transcripts, translation, and viral assembly and release. Each step can be assessed precisely and in a quantitative fashion. The host cellular environment is greatly perturbed following viral invasion, with numerous parameters that can be measured and matched temporarily to the progression of the viral cycle. The present proposal will address the timing of key steps of the viral cycle in the context of cellular responses, as assessed by the analysis of expression reprogramming and the mounting of antiviral defense, including cellular miRNA responses. To achieve this goal, we will integrate the molecular profiling time series into a single interaction model. Probabilistic graphical models, including dynamic Bayesian networks and factorial hidden Markov models, will be applied to capture the temporal dynamics among the molecular events during the HIV life cycle. This project represents a step towards understanding the viral life cycle and the modification of the cellular environment by the infection. This represents a unique opportunity to integrate host and viral aspects in a temporal frame in an effort towards modeling of the HIV life cycle. The analyses will provide a scaffold and reference to in vivo large scale genome and cellular screens.

Direct link to Lay Summary

Last update: 21.02.2013

SAGE data

Author	Mohammadi, Pejman
Publication date	13.12.2012
Persistent Identifier (PID)	http://peachi.labtelenti.org/
Repository	PEACHI website
Abstract

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Active participation

Communication	Title	Media	Place	Year

Title	Year

Number	Title	Start	Funding scheme

This proposal aims at the in-depth characterization of expression reprogramming of the cell upon HIV infection. The analysis will cover, through repeated measurements, the classical 24-hour life cycle of the virus. During this period, the virus undergoes entry and uncoating, reverse transcription, nuclear import, integration, transcription, Rev-mediated export of viral transcripts, translation, and viral assembly and release. Each step can be assessed precisely and in a quantitative fashion. The host cellular environment is greatly perturbed following viral invasion, with numerous parameters that can be measured and matched temporarily with the progression of the viral cycle. Members of the research team and collaborators have in the past assessed, separately, many of the steps of the viral cycle, as well as changes in the cellular response, in vitro and in vivo. This has also required the development and implementation of all the necessary tools and techniques needed to follow the various viral and host parameters. The current proposal aims at increasing both the depth of the analysis, and the frequency of measurements required for high temporal resolution of viral and cellular corresponding measurements. For this, we propose to assess every two hours over 24 hours, in an in vitro cellular infection model, the following parameters:VIRUSHOSTReverse transcription (early and late RT products)Reprogramming by viral proteins (ChIP-Seq)Integration (2-LTR circles, proviral DNA)Gene expression profiling (RNA-seq)Transcription and splicing (unspliced, multiply spliced, 5' transcripts, main intronic transcripts)microRNA expression (RNA-seq)Translation (GFP expression, cell-associated p24)Release (extracellular p24)The present proposal will address the timing of key steps of the viral cycle in the context of cellular responses, as assessed by the analysis of expression reprogramming and the mounting of antiviral defense, including cellular miRNA responses. To achieve this goal, we will integrate the molecular profiling time series into a single interaction model. Probabilistic graphical models, including dynamic Bayesian networks and factorial hidden Markov models, will be applied to capture the temporal dynamics among the molecular events during the HIV life cycle. This project represents an additional step towards understanding the viral life cycle and the modification of the cellular environment by the infection. Beyond the interest of conducting the individual analyses discussed above, there is an opportunity to increasingly integrate host and viral aspects in a temporal frame in an effort towards modeling of the HIV life cycle. The analyses will provide a scaffold and reference to in vivo large scale genome and cellular screens.