Horizon 2020 ITN funded doctoral position - DNA
The genome of higher eukaryotes is organized in a hierarchy of structures, from chromatin loops, to topologically associating domains (TADs), to genome compartments (GCs), to chromosome territories (CTs) that are spatially co-organized in the 3D space of the cell nucleus. At each level, chromatin architecture is regulated and iMPIMGnges on genome functions, such as gene expression, DNA replication and repair. Recent studies, including work in the participant's labs, have identified players that define loops, TADs and GCs, but their mechanisms of action are not understood. In particular, we have described that the boundaries of TADs can involve transcribed genes, but we showed that the act of transcription per se is not sufficient in order to drive the formation of a TAD (Bonev et al., Cell, 2017). Furthermore, we know that CTCF can form TAD boundaries, but little is known of its mechanism of action. In particular, Drosophila also has a CTCF protein that binds the same sequence motifs, but does not suffice to specify TAD boundaries in that species. Finally, gene silencing components of the Polycomb group were shown to induce the formation of extremely long-range interactions (ELRI) over tens of Mb of linear distance in ES cells, but many of these are disrupted in neurons and it is not known whether this is important for differentiation. Here, we will dissect these aspects of genome regulation, which we expect to have profound implication to understand differentiation in normal cells and diseases (cancer), where nuclear architecture is a major alteration frequently observed but not understood.
This European doctoral thesis, carried out on an ITC program called ChromDesign, focuses on the role of the regulation of chromosome structure on gene expression and cell differentiation. The objectives of the PhD student's project will be to understand the role of
- DNA binding
- insulin proteins
- Polycomb components in the establishment of chromatin architecture during neuronal differentiation
The student will be based at IGH, Montpellier. IGH is a flagship institute for life science research and is located in the vibrant city of Montpellier, in the southern French riviera. It offers state of the art equipments and facilities in a top-notch international environment.
At IGH, the student will be mentored by Giacomo Cavalli, by a postdoctoral fellow in the lab, Ivana Jerkovic, and by a permanent researcher, Frédéric Bantignies.
This thesis will be carried out in the framework of the ChromDesign ITN program of the european union, under the H2O20 program. In this program, there will be secondments to be carried out at CRG, Barcelona, under supervision of L. Di Croce and M. Martí-Renom and in the laboratory of Tony Kouzarides, Milner Therapeutics Institute, University of Cambridge, UK. This will allow the student to expand her/his expertise by establishing academic and private sector links.
The PhD student will target DNA binding proteins to a genomic region where they are normally not bound, or prevent them from binding when they should. We will then study the effect of disruption of DNA binding on the 3D architecture of chromosomal domains, separating the effects of DNA binding from those of transcriptional induction.
In addition, the PhD student will dissect the function of mouse CTCF versus that of the homologous Drosophila protein. We will try to replace mouse CTCF with its fly counterpart and study cell viability and genome function. Conversely, we will express the mouse protein in the fly. We will also dissect them further by performing partial exchanges of the only DNA binding domain or part of its intrinsically disordered domain. Hi-C and microscopy will identify the protein portions involved in species-specific functions for this gene. Finally, the student will analyze the specific function of a group of PcG proteins, including the PHC1, PHC2 and PHC3 components of the PRC1 complex. The expression of these genes varies during neuronal differentiation, in parallel with the strong loss of extremely long-range chromatin interactions (ELRI). We will identify which of these proteins can fulfill this function and study its mechanisms of action and the consequences of ELRIs in neuronal differentiation.
In short, the expected skills imply:
- cell culture
- molecular and cellular biology
- high-end fluorescence microscopy
- genomics and epigenomics
- bioinformatics applied to genomics and imaging
- English language (level 2 at least)
It is imperative for this hiring that, in addition to the application via the Portail d'emploi, the candidates applies via the ChromDesign website, which is found at http://www.chromdesign.eu/call-for-applicants/
Without this second application, the candidates will not be considered eligible