New proteomic methods to quantify chromatin changes to identify regulators of cellular senescence

• Applicant: Dr. Christian Feller
• Subject Area: General Genetics and Functional Genome Biology ; Cell Biology
• Term: Funded in 2015
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 272585787

The specific composition of chromatin is an important determinant for the cell state. Multiple factors define the composition of chromatin. Among them are post-translational modifications at histones and the association of a wealth of non-histone proteins. While our knowledge of the chromatin composition in some individual cell states is already quite advanced, how the composition of chromatin changes during the gradual transitions between cell states remains mostly unknown. Current proteomic methods present a major obstacle to follow the changes over time, because they are too limited to reliably quantify proteins and their interactions at chromatin as well as the complexity of post-translational modifications at histones and non-histone proteins. During the transition from young to old cells, constitutive stress leads to progressively accumulating damage, which ultimately causes an irreversible growth arrest, known as cellular senescence. Recent studies provided a first glimpse in the reorganization of the composition of chromatin in senescent cells. However, currently we neither know the extent of chromatin alterations during cellular aging in primary human cells nor do we know how they are progressively established and how they contribute to define the onset of senescence and its stable manifestation. This proposal aims to fill the technological and conceptual gap by developing quantitative proteomic methods to reliably monitor the composition of chromatin and its associated proteins between different conditions. While these methods will be broadly applicable, I will apply it to generate a resource that quantitatively describes the changes to the composition of chromatin during the course of cellular aging and in different senescence models. Specifically, I will develop proteomic workflows that allow the precise quantification of i) complex combinatorial histone modifications, ii) differential association of proteins to chromatin or the nucleoplasm and iii) protein-protein interactions at chromatin. A further goal is to test the usability of the resource to identify and validate chromatin factors that modulate the onset or maintenance of cellular senescence. Cellular senescence is implicated in regeneration following tissue damage, organismal aging, tumour progression as well as relapse after chemotherapy, hence, identifying mechanisms that modulate this process will have strong and immediate biomedical relevance.

• DFG Programme: Research Fellowships
• International Connection: Switzerland
• Host: Professor Dr. Rudolf Aebersold