The work will be carried in our group "Chromatin and epigenetics" at the Institute for Advanced Biosciences. The group has a long history in chromatin research covering a large scale of approaches to study the chromatin structure and function (from structural high resolution approaches through cellular and molecular biology up to animal models). The group is recently composed of four permanent scientists, and two Ph.D. students.
The student will work on the problematic of the structure of nucleosome invasion mechanism by the Sox pioneer transcription factor family using high resolution cryo-electron microscopy and molecular biology aproach.
The goal of the project is to understand the nucleosome invasion mechanism of the Sox pioneer transcription factor family and shed light on its in vivo function. The project has following objectives: (i) to analyze Sox binding to NCP by structural approaches (ii) to determine the effect of linker histone H1 on Sox binding to the nucleosome; (iii) to investigate the 3D structure of Sox-bound mononucleosomes and nucleosome arrays in which the Sox binding site faces the solution.
This project aims to determine how the Sox binds to a moonucleosomal template, how the binding affects the structure of nucleosome and of the higher order chromatin organization and how these structural alterations in turn may influence the nucleosomal DNA accessibility. The goal of the Ph.D. thesis project will be to determine the structure of nucleosome/Sox complex using high resolution cryo-electron microscopy. In the first stage the chromatin structure at the mononucleosome level will be analyzed, with aim to determine in atomic detail how do the Sox recognize the nucleosome, and how it alters its structure. The second part of the thesis project will focus on a higher level of chromatin organization in order to determine how the Sox association modifies the 3D architecture of a tandem array and thus the overall chromatin compaction.
The structural approach will be complemented by top level molecular biology and biochemistry, including EMSA and •OH footprinting followed by UV laser crosslinking. The student, through the project, will acquire both the state of the arts experimental skills and theoretical knowledge, which will be of great help for his future career in either science or industry.
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