Missions

During HIV-1 assembly, two copies of unspliced genomic RNA are selectively packaged into virions from a complex mixture of cellular and spliced viral RNAs. This specificity is driven by cis-acting packaging signals (Ψ) within the 5' untranslated region (5'UTR) of the viral RNA, which are recognized by the Pr55Gag polyprotein. Packaging signals are not only crucial for viral replication but also for the design of lentiviral vectors, widely used in gene therapy, vaccine development, and genome-wide CRISPR screens. They a also a promising therapeutic target, as interfering with genome packaging could inhibit viral propagation while reducing the risk of resistance.

This RNA-focused project aimed at unraveling structural rearrangements within the HIV-1 5′UTR that regulate key steps of the viral life cycle, including Pr55Gag binding, genome packaging, and reverse transcription. Following the laboratory's established expertise, we will conduct an in vitro RNA structural analysis of the HIV-1 5′UTR in both unspliced and spliced transcripts, in the presence or absence of RNA co-factors. These findings will be validated in cellular and viral models, and a proof-of-principle study will assess the potential of targeting 5′UTR RNA structures for therapeutic intervention. The project will be primarily conducted in the Smyth lab, with select biophysical assays supported by high-quality in-house collaborations.

Activities

- Preparation and validation of molecular clones and generation of gene libraries by random mutagenesis. Molecular clones and libraries will be used for both in vitro transcription and transfection into human cell lines.
- Preparation of sequencing libraries for illumina and nanopore sequencing. The successful candidate will convert the RNA into molecules compatible with high-throughput sequencing by adding barcodes and sequencing adapters and purifying the resulting libraries to achieve a quality compatible with different sequencing technologies.
- Bioinformatic analysis of the sequence content of enriched DNA libraries. In collaboration with bioinformaticians, the successful candidate will be responsible for analyzing sequencing data using a existing bioinformatics pipelines.
- In vitro molecular biology. The successful candidate will conduct RNA structural analysis of the HIV-1 genome structural analysis of HIV-1 genome using chemical probing and biophysical experiments in the presence of co-factors, such as ASOs and tRNAlys3.
- Virology. The successful candidate will conduct HIV-1 virology experiments using replication defective HIV-1 viruses using standarized assays, such as RT-qPCR of HIV cDNA.

Skills

- The candidate must hold a recent PhD in molecular biology, biochemistry or molecular virology.
- Demonstrated scientific excellence, supported by significant publications (preprints accepted) in the field.
- Recognized expertise in synthesizing and handling RNA molecules and familiarity with lentiviral vectors, virology or ideally HIV-1 biology.
- Ability to independently analyze high-throughput sequencing data using bioinformatics. Although he/she will be assisted by bioinformaticians, the candidate must have skills in analyzing sequencing data, ideally using Python, but other training in other suitable programming languages are acceptable.

Work Context

Dr. Redmond Smyth's laboratory, located within the Institute of Molecular and Cellular Biology (IBMC), studies the mechanisms of virus replication and assembly using advanced RNA biology techniques. Dr. Smyth's team focuses on characterizing the structures and functions of viral RNAs, with potential applications for the development of new antiviral therapeutic approaches. The IBMC is a renowned research unit under the supervision of the French National Center for Scientific Research (CNRS), located in Strasbourg. The IBMC is distinguished by its cutting-edge scientific environment, dedicated to understanding the fundamental mechanisms of molecular and cellular biology. Its research covers a range of fields, from structural biology and molecular interactions to genetics, immunology, and virology, contributing to crucial advances in biology and medicine.

The laboratory benefits from a large network of national and international collaborations and access to cutting-edge technological platforms, including advanced microscopy, high-throughput sequencing, and mass spectrometry. With multidisciplinary research teams and a dynamic setting, the IBMC offers a stimulating environment conducive to scientific innovation. The IBMC is also affiliated with the University of Strasbourg, giving it direct access to an active academic community and excellent doctoral programs. The candidate will be enrolled in the university's doctoral school.

Constraints and risks

The candidate must have experience working with RNA and eukaryotic cell culture. High precision and good organizational skills will be required for library preparation and handling nanopore technology. He/she will be required to work with infectious HIV-1 virus in LSB3 and handle hazardous substances (Carcinogenic, Mutagenic, and Reprotoxic) under a chemical fume hood. Appropriate personal protective equipment and biosafety training will be provided.