Functional diversity of eukaryotic non-coding RNAs.
PI prof. Andrzej Dziembowski
PROJECT NUMBER: PSPB-183/2010
FINANCIAL AGREEMENT NUMBER: 2/2012, dated on 12.01.2012
PROJECT BUDGET: 3.020.046,00 PLN (1.000.000,00 CHF)
Polish Partner od the Project: University Of Warsaw, Faculty of Biology, PI prof. Joanna Kufel
Swiss Partner of the Project: Department of Cell Biology, Sciences III, University of Geneva, PI prof. Francoise Stutz
SUMMARY OF THE JOINT RESEARCH PROJECT:
The project “Functional diversity of non-coding RNAs” realized by the NOCORE (Non-Coding RNA Enterprise) consortium aims at furthering our understanding of long non-coding RNAs (lncRNA) function yeast and higher eukaryotic cells. Owing to the progress in high-throughput technologies over the past 10 years, myriads of non-coding transcripts, which cannot be regarded merely as a “transcriptional noise”, were discovered. Increasing evidence indicates that these ncRNAs play a central role in the regulation of gene expression both at the transcriptional (chromatin modification) and post-transcriptional (mRNA decay, inhibition of translation) levels. It is also well documented that many of these RNAs are regulated and accumulate under certain conditions, including metabolic changes, aging, starvation or activation of death programmes, to control physiological processes, such as signaling, developmental or adaptation pathways. Interestingly, ncRNAs often accumulate in defective cells, including many cancer lines, and are linked with various diseases, though definite evidence of their direct involvement is still limited to single cases. Despite the diversity and continually growing abundanceof ncRNAs , their cellular functions and set of targets are hugely under-investigated.
The general aim of this proposal is to use global approaches to extend the repertoire of ncRNAs in various physiological and stress conditions or mutant cells deficient in specific RNA degradation pathways. In a second step, the role and mechanisms of action of these ncRNAs will be investigated by searching for potential targets using bioinformatics tools. Over-expression and mutagenesis experiments will be used subsequently to validate these targets and to test specific and overall effects they exercise on cellular processes. In parallel, genetic approaches using appropriate reporter systems will be developed to screen for the trans-acting factors mediating the ncRNA-driven changes in gene expression. Additionally, sensitive tests will be set up to visualize and localize these transcripts in single cells. In the first place these approaches will be carried out in a model laboratory eukaryotic organism, yeast Saccharomyces cerevisiae. To extend the findings determined in yeast and to address the conservation of revealed processes, global identification and functional analyses of ncRNAs will be undertaken in parallel in chicken DT40 cells. This highly recombinogenic cell line, particularly well suited for genetic experiments, will allow us to define whether higher eukaryotes employ analogous non-coding transcripts, functionally related to those acting in yeast.
We will also study the RNA-dependent gene cosuppression in yeast, which is devoid of the standard RNA silencing machinery. We plan to identify components acting in the cosuppression pathway and reveal molecular mechanisms underlying this mode of regulation of gene expression.
The output of the proposed project will greatly contribute to the description of RNA-mediated regulation of such important cellular processes as response and adaptation to metabolic changes, stress and signaling pathways and finally programmed cell death. There is no doubt that, in the long run, these results will broaden our knowledge concerning the function of non-codning RNAs of various origins and structures in development and tumorigenesis in more complex metazoan systems and will advance implementation of ncRNA-based applications in medical sciences.