Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA

Authors:
Federica Ciocchetta;Jane Hillston;Martin Kos;David Tollervey
Affiliations:
Laboratory for Foundations of Computer Science, The University of Edinburgh, Edinburgh EH8 9AB, Scotland, UK;Laboratory for Foundations of Computer Science, The University of Edinburgh, Edinburgh EH8 9AB, Scotland, UK and Centre for Systems Biology at Edinburgh (CSBE),11The Centre for Systems Biology at ...;The Wellcome Trust Center for Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK;The Wellcome Trust Center for Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK and Centre for Systems Biology at Edinburgh (CSBE),11The Centre for Systems Biology at Edin ...
Venue:
Theoretical Computer Science
Year:
2008

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Abstract

In this paper we present a quantified model of the synthesis of pre-rRNAs in yeast. The chemical kinetics simulation software Dizzy has been used as both the modelling and simulation framework of our study. The simulations have been used to investigate the mechanism of co-transcriptional cleavage which can occur during the synthesis of pre-rRNAs. Throughout the paper we emphasise the strong role of experimental data both in shaping the model and in guiding the analysis which is carried out. Parameter estimation procedures have been used to fit the model to the data and we discuss the validation of the model against the available experimental data. Simulation based on Gillespie's algorithm is considered to be the reference method for our analysis and a comparison with other simulators is reported. Finally, we define an extended model, that relaxes one of the assumptions of the initial model.