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

Descrizione del progetto

La ricerca scopre il ruolo determinante della proteina DEK e dei clutch di nucleosomi nella regolazione del tumore

La proteina DEK è un fattore architettonico della cromatina che è stato costantemente associato alla progressione del tumore. Il suo livello di espressione differisce tra cellule normali e cancerose, il che lo rende utile come marcatore. L’imaging a super risoluzione ha recentemente rivelato che i nucleosomi possono formare gruppi discreti di varie dimensioni e densità chiamati «clutch». Tuttavia, la connessione tra le proteine DEK e tali clutch non è stata ancora decifrata. Finanziato dal programma Marie Skłodowska-Curie, il progetto qCHROMDEK intende comprendere in maniera precisa e quantitativa una possibile connessione tra i livelli di espressione di DEK e le strutture locali della cromatina. Collegare l’espressione di DEK con il numero di nucleosomi per clutch potrebbe migliorare la comprensione del ruolo di organizzazione della cromatina in diversi livelli di tumorigenesi.

Obiettivo

"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.
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