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

Projektbeschreibung

Neues über die wichtige Rolle des DEK-Proteins und der Nukleosomen-Kupplungen bei der Tumorregulierung

Das DEK-Protein ist ein Faktor der Chromatinarchitektur, der immer wieder mit Tumorprogression in Verbindung gebracht wurde. Sein Expressionsspiegel fällt bei normalen und Krebszellen unterschiedlich aus, was es zum nützlichen Marker werden lässt. Superauflösende Bildgebung hat kürzlich offenbart, dass Nukleosomen diskrete Gruppen verschiedener Größe und Dichte bilden können, die als Kupplungen bezeichnet werden. Die Verbindung zwischen den DEK-Proteinen und diesen Kupplungen konnte jedoch noch nicht entschlüsselt werden. Das im Rahmen der Marie-Skłodowska-Curie-Maßnahmen finanzierte Projekt qCHROMDEK hat das Ziel, zu einem präzisen quantitativen Verständnis eines möglichen Zusammenhangs zwischen DEK-Expressionsspiegeln und lokalen Chromatinstrukturen zu gelangen. Wissen über die Verknüpfung der DEK-Expression mit der Anzahl der Nukleosomen pro Kupplung könnte das Verständnis der Rolle der Chromatinorganisation auf den verschiedenen Ebenen der Tumorentstehung verbessern.

Ziel

"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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