Detailed project information

Epigenetic gene regulation is crucial to orchestrate gene expression patterns that determine cellular identity. Epigenetic regulatory mechanisms, such as histone modifications, have been directly linked with transcriptional regulation and domain-wide changes in chromatin structure. Our current understanding of this complex process is predominantly qualitative. The mechanistic interaction of individual epigenetic factors that determine the transcription rate of single genes, is largely unknown. Such processes are often simply portrayed as all-or-none, i.e. gene silencing or activation. I propose to quantitatively study the contribution of epigenetic mechanisms in regulating the rate of transcription using a combined approach of mathematical modelling and quantative experiments. Aim of my research is to unravel the complex mechanisms of in vivo epigenetic gene control.

A novel in vivo cell system is used, engineered by the applicant, allowing systematic and quantitative measurements of the change in transcription rate as function of the epigenetic status of the domain. Real-time transcription rate of the engineered cell system is measured in single cells. Transcripts containing MS2 viral-RNA are detected by constitutively expressed fluorescently tagged MS2 protein. The initial and steady-state rate of transcription of the engineered domain is studied as function of (i) integration of the domain in a high or low expressing region in the genome, (ii) targeting and accumulation of epigenetic regulatory proteins and (iii) local chromatin compaction. Kinetic models are used to analyze the quantitative kinetic data. The models are used to quantify and explain the reduction or increase of transcription rate, as function of the epigenetic status of the domain. Stochastic kinetic models are used to explain cell-cell variability (?noise?).

The combined experimental-modelling approach enables us to obtain insight into the mechanistic behaviour of the system. This interdisciplinary approach represents a yet unexplored path in the field of epigenetic gene control.