Missions

Background
At IGMM, our group Integrative RNA Networks in Development aims to elucidate the function of transcription factors (TFs) in mRNA processing and their contribution to cell identity. Here, the project funded by the AFM Téléthon (ISOFHORM project) aims to redefine the role of transcription factors in muscle morphogenesis. The project involves mapping the splicing and isoform networks regulated by Ultrabithorax (Ubx), a Drosophila Hox TF, and determining its isoform-specific function throughout the development of Drosophila embryonic muscle.

The engineer will,
-be in charge of a project based on detecting, analysing and validating splicing profiles and isoforms regulated by Ubx during embryonic muscle development. This involves establishing protocols for the purification of nuclear RNA compatible with Illumina (short-read) and nanopore (long-read) sequencing, followed by the analysis of splicing profiles and isoforms using transcriptomics (bioinformatics) and the functional validation of these isoforms (genetics) during muscle development, in an independent manner (60%)
-Provide support for the molecular biology and biochemistry of protein-RNA complexes in vitro (20%)
-Contribute to the establishment and maintenance of Drosophila lines (10%)
-Contribute to protocol monitoring and stock management for the team (10%)

Activités

In vivo experiments in Drosophila
-Maintenance of lines and crosses, embryo collections, fixation, immunolabelling and confocal microscopy
-Setting up a biochemical purification protocol for nuclear RNAs to analyse differential transcriptomes from Drosophila embryonic muscle using Illumina (short-read) and Nanopore (long-read) sequencing
-Target validation using alternative methods (qPCR, smFISH, exogenous expression of isoforms)
In vitro experiments
-Applying cloning techniques, protein and RNA biochemistry (SDS-PAGE, WBlot, RT-qPCR, RNA-IP)
Bioinformatics analyses
-Develop and implement bioinformatics pipelines in collaboration with the platforms and collaborators.
-Analyse splicing and isoform profiles from Illumina (short-read) and Nanopore (long-read) sequencing data.
-Perform computational data analysis, including statistical analysis

Responsibilities
-Choose and adapt technologies based on previously discussed objectives
-Develop and write protocols and structured reports in English
-Process and analyse data, format results for presentation in English
-Share knowledge and skills in their field of study
-Participate in the dissemination and valorisation of results in the form of presentations and publications in English
-Ensure scientific and technological monitoring in their field of activity

Compétences

Skills/knowledge
-Knowledge of transcriptomics, biochemistry and molecular biology
-Basic knowledge of alternative splicing and RNA detection methods
-Ability to communicate orally and in writing in English (C1 level equivalent)
-Appreciated knowledge of Drosophila genetics or transcriptome analysis with bioinformatics

Practical Skills
-Excellent molecular biology skills (cloning, PCR, DNA production, purification, western-blot)
-Excellent skills in one (or more) of the following categories: transcriptomics, biochemical methods related to RNA or Drosophila genetics
-Basic skills in confocal immunofluorescence
-Good computer skills (excel, word, powerpoint)
-Experience in transcriptomic data analysis would be appreciated

Personal skills
-Ability to work independently on the pipelines discussed
-Strong curiosity to learn new techniques and contribute to the team's various projects
-Strong organisational skills
-Rigour in reporting activities, following protocols in English, experimental planning
-Ability to work as part of a team and contribute to the life of the laboratory (joint actions, general tasks)
-General qualities: Communication, Thoroughness, Team spirit, Autonomy, Enthusiasm

General, theoretical or disciplinary knowledge
-Knowledge of or deep interest in co-transcriptional gene regulation
-Knowledge or experience of RNA biology or the Drosophila model
-Knowledge of or motivation to participate in bioinformatics analyses is essential

Contexte de travail

The Montpellier Institute of Molecular Genetics (IGMM) is a joint CNRS and University of Montpellier research unit with a staff of 200 divided into 17 research groups, 9 shared services (5 of which are shared with other units on the CNRS campus) and 9 technological and scientific platforms. The IGMM is a multidisciplinary institute whose work has an international impact, both fundamental and applied, in molecular and cellular biology (www.igmm.cnrs.fr).
The engineer will be assigned to the team led by Julie Carnesecchi, recently opened at the IGMM. The engineer will work on a central laboratory project funded by the AFM (ISOFHORM project) and will be trained and supervised directly by Julie. The teamwork is international (English) and interdisciplinary (molecular biology, structural biology, transcriptomics, imaging), with the opportunity to contribute to the exploration of TF-RNA interactions at various scales (in vitro, in cells, in vivo in embryonic muscle).
The project benefits from the privileged scientific environment of the Biocampus and its technological platforms (proteomics, sequencing, imaging, www.biocampus.cnrs.fr). The initial contract is 6 months and is renewable.

Contraintes et risques

Some weekends and public holidays will be necessary for live sample maintenance and collection (1 to 2 hours max/weekend).