qCHROMDEK · Quantitative insight into chromatin nanoscale structure: sub-nuclear organisation of oncoprotein DEK

DEK protein is a chromatin architectural factor which has been consistently associated with tumour progression. Its expression level differs between normal and cancer cells, raising the possibility of using DEK as a tumour marker. On the other hand, super-resolution imaging revealed recently that nucleosomes can form discrete groups called ""clutches"" of various dimensions and densities. However, the quantitative analysis of the connection between proteins playing chromatin architectural role and nucleosome clutches has not been yet deciphered.Within this project, I hypothesize that there is a correlation between the organisation of DEK oncoprotein and the local chromatin structure related to the proliferation level of cells.The overall aim of the proposed work is to provide a more precise, quantitative understanding of possible connection between DEK expression level and local chromatin structures and by that to gain the additional information about DEK role in cancer. This project will take advantage of cutting-edge biophysical tool such as DNA origami, single-molecule localisation microscopy and cellular biology. Experimental design is based on the construction and application of a bi-dimentional DNA origami to calibrate and mimic subnuclear structures. The quantitative approach will rely on STochastic Optical Reconstruction Microscopy (STORM). This study will be done using normal cells with different level of proliferation and cancer cells with different level of malignancy.Finding the relation between DEK expression, connected to the proliferation level of normal and cancer cells, and the number of nucleosomes per clutch could improve the comprehension of chromatin organisation role in different levels of tumorigenesis. Quantitative insight to the number of nucleosomes per clutch in relation to the level of cell proliferation could be in the future an input for a precise recognition of cancer in the early stage of tumorigenesis.""