Phosphoinositides (PIPs) are recognized as regulators of many nuclear processes including chromatin remodeling, splicing, transcription, and DNA repair. These processes are spatially organized in different nuclear compartments. Various nuclear compartments are formed by entropy-driven mechanism - phase separation. The surface of such membrane-less structures spatiotemporally coordinates complex nuclear processes. The integration of PIPs into the surface of nuclear structures might therefore provide an additional step in their functional diversification by controlling the localization of different components, in a similar way as PIPs do in membranous cytoplasmic environment. This project focuses on deciphering the molecular mechanisms of various PIPs in establishing a dynamic nuclear architecture. In this project PhD candidate will characterize the PIPs-containing nuclear structures by combination of lipidomics, proteomics (quantitative MS), molecular biology (e.g. CRISPR/Cas9), biochemical and advanced microscopy (e.g. confocal, SIM, STED, FRAP) methods. We will concentrate on Nuclear Lipids Islets (NLIs), which we discovered as important nuclear structures involved in modulation of gene transcription. In collaboration with other two laboratories, we will develop an experimental system using nanodiamonds mimicking the properties of NLIs and using phosphoinositides of various properties, we will study their involvement in DNA transcription using an in vitro system.
