27, boulevard Lei Roure
Proposed project for a Master 2 traineeship in bioinformatics at the center for Cancer Research of Marseille
Our laboratory is interesting in deciphering epigenetic events involved in hematopoietic differentiation, aging and leukemia onset. PLZF (promyelocytic leukemia zinc finger) is a transcription factor acting as a global regulator of hematopoietic commitment (Vincent Fabert et al, Blood 2016). PLZF displays an epigenetic specificity by recruiting chromatin-modifying factors (Koubi et al, NAR 2018) but little is known about its role in remodeling chromatin of cells committed towards a given specific hematopoietic lineage. In murine myeloid progenitors, using genome-wide approaches (ChIP-seq and RNA-seq) we decipher a new role for PLZF in restraining active genes and enhancers by targeting acetylated lysine 27 of Histone H3 (H3K27ac) (Poplineau et al, NAR 2019). Functional analyses reveal that active enhancers bound by PLZF are involved in biological processes are associated with hematopoietic aging. Comparing the epigenome of young and old myeloid progenitors, we reveal that H3K27ac variation at active enhancers is a hallmark of hematopoietic aging.
The proposed project will be a direct follow up of this previous study. We have already generated ChIP-seq datasets on old mutant mice and aim to analyze the impact of PLZF loss upon aging and upon serial bone marrow transplantations.
The Master2 candidate will be in charge of the ChIP-seq data analyses and will develop new analysis pipelines. We are looking for a motivated, hard-working and creative candidate with interests in analyzing NGS datasets.
- Good general knowledge in bioinformatics
- Programming skills: bash, python, R, perl or similar
- Experience in the analysis of NGS datasets is not mandatory but would be appreciated