Final Report Summary - CHROMATIN IN SKIN (Deciphering the role of chromatin in epidermal stem cell biology)
The work performed in the duration of the IEF CHROMATIN IN SKIN has shown to be successful. Using a system to inactivate a large set of genes individually we have devised a strategy to infer functional and genetic interactions between chromatin-factors in a primary human adult stem cell system. This has led to profound insight into how stem cells regulate the genes required at different stages of maturation. Furthermore, using contemporary genome-wide localisation approaches an bioinformatics we have provided evidence explaining why this system is very robust and resistant to pertubation.
First we developed methods to initiate primary human epidermal stem cell differentiation using distinct stimuli in culture. Second we optimised transfection protocols to allow silencing of the chromatin-factors of our interest. This, in combination with our quantitative read-out and our newly established conditions for induction of differentiation, enabled us to determine the role of a set of 332 chromatin related factors in epidermal differentiation and self-renewal. The resulting dataset of approximately 5 000 quantitative functional data-points was subjected to bioinformatics analysis based on logic and methodology used in conventional mRNA expression profiling studies.
The rediscovery of two known epigenetic mechanisms implicated in epidermal self-renewal validated our approach. Strikingly, we found that these mechanisms are functionally connected. In addition, we could show that they form a functional network with two newly implicated chromatin complexes.
Using Chromatin immunoprecipitation coupled to massively parallel sequencing (ChIP-seq) we found that this network targets several distinct downstream gene sets, reaffirming the robustness of this network.
First we developed methods to initiate primary human epidermal stem cell differentiation using distinct stimuli in culture. Second we optimised transfection protocols to allow silencing of the chromatin-factors of our interest. This, in combination with our quantitative read-out and our newly established conditions for induction of differentiation, enabled us to determine the role of a set of 332 chromatin related factors in epidermal differentiation and self-renewal. The resulting dataset of approximately 5 000 quantitative functional data-points was subjected to bioinformatics analysis based on logic and methodology used in conventional mRNA expression profiling studies.
The rediscovery of two known epigenetic mechanisms implicated in epidermal self-renewal validated our approach. Strikingly, we found that these mechanisms are functionally connected. In addition, we could show that they form a functional network with two newly implicated chromatin complexes.
Using Chromatin immunoprecipitation coupled to massively parallel sequencing (ChIP-seq) we found that this network targets several distinct downstream gene sets, reaffirming the robustness of this network.