M2 - Development of a pipeline for NGS -omics data integration

Type de poste
Niveau d'étude minimal
Dates
Durée du poste
Contrat renouvelable
Contrat non renouvelable
Date de prise de fonction
Date de fin de validité de l'annonce
Localisation
Nom de la structure d'accueil
Adresse

Campus Scientifique de Luminy
163, Avenue de Luminy
13009 Marseille
France

Contacts
Bianca Habermann, Group Leader 'Computational Biology'
Cedrique Maurange, Group Leader 'Neuronal Stem Cell Plasticity'
Email du/des contacts
bianca.habermann@univ-amu.fr
cedric.maurange@univ-amu.fr
Description

• Description:
During tissue formation, transcriptional programs are deployed in a specific temporal order to ensure that progenitor cells first amplify and then differentiate to generate the functional cells of a mature organ. In principle, epigenetic marks on chromatin are used to limit the repertoire of genes that can possibly be dynamically regulated at a given time, ensuring robustness in transcriptional dynamics. However, the mechanisms that determine when and at which genes these epigenetic marks have to be deposited are unclear.
We have recently identified an important transition in the development of the wing tissue in Drosophila. This transition switches progenitor cells from a default proliferative state to a differentiation-competent state. We have identified two transcription factors, Chinmo and Broad, that define these two phases but their mode of action is unclear.
This project will aim at developing a bioinformatic pipeline to analyze and integrate a set of transcriptomic, ATAC-seq and ChIP-seq data for a detailed investigation of the dynamics of chromatin structure, epigenetic marks and transcriptional activity along this transition.
Our long-term goal is to understand how transcriptional programs, as they are deployed along development, modify the chromatin landscape to ensure that the correct set of genes are dynamically regulated.

• Required Competences:
NGS data analysis ; RNA-seq and epigenetic data analysis ; programming in python, and R ; scripting in bash/shell commands ; communication skills (written/spoken) in English

• References:
Narbonne-Reveau K, Maurange C , (2019) Developmental regulation of regenerative potential in Drosophila by ecdysone through a bistable loop of ZBTB transcription factors. PLoS Biol. 2019 Feb 11;17(2):e3000149. https://doi.org/10.1371/journal.pbio.3000149
Iwafuchi-Doi M. (2019). The mechanistic basis for chromatin regulation by pioneer transcription factors. Wiley Interdiscip Rev Syst Biol Med. 2019 Jan;11(1):e1427. doi: 10.1002/wsbm.1427. Epub 2018 Jun 27. Review.

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