Development of a Method for the detection of protein-nucleic acid interactions in situ

• Applicant: Privatdozent Dr. Björn Koos
• Subject Area: Biochemistry
• Term: from 2011 to 2014
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 215063385

Interactions between proteins and nucleic acids such as DNA and RNA are very important events in a cell. They control transcription, translation, DNA duplication, proliferation as well as cell death and differentiation. Keeping in mind the importance of these interactions for the cell, especially during tumorigenesis it seems surprising that there is no method able to detect these interactions on a single cell basis with high sensitivity. Therefore the high heterogeneity that has been shown for protein-protein interactions as well as mRNA and protein expression in different cells can only be hypothesized for protein-nucleic acid interactions. Methods like chromatin immunoprecipitation (ChIP) only give averaged data over a large cell population. This has the danger of averaging diversity in this cell population as well as leaving out interactions that only happen in a subpopulation of the cells. However, especially for cancer, prognosis often depends on small cell population (e.g. tumor stem cells). Therefore detecting interaction on a single cell level is imperative. However some methods can detect protein-DNA interactions in situ (e.g. Immuno-FISH). The major disadvantage of these methods is the low sensitivity which hampers detection of single events such as transcription factor binding.Therefore technics enabling the visualization of such events are urgently needed. The aim of this project is to develop and establish a method that is able to detect single binding events of Protein and DNA / RNA in a single cell. Modification of in situ PLA, a method already able to detect protein-protein interactions with high sensitivity is going to be the first step to achieve this goal.

• DFG Programme: Research Fellowships
• International Connection: Sweden
• Host: Professor Ola Söderberg, Ph.D.