An In-Silico Mammalian Whole-Cell Model Reveals the Influence of Spatial Organization on RNA Splicing Efficiency

Abstract

Spatial organization is a characteristic of eukaryotic cells, achieved by utilizing both membrane-bound and non-bound organelles. We model the effects of this organization and of organelle heterogeneity on RNA splicing (the process of making translationally-ready messenger RNA) and on splicing particles (the building blocks of splicing machinery) in mammalian cells. We constructed a spatially-resolved whole HeLa cell model from various experimental data and developed reaction networks to describe the RNA splicing processes. We incorporated these networks into our whole-cell model and performed stochastic simulations for up to 15 minutes of biological time. We find that the number of nuclear pore complexes affects the number of assembled splicing particles; that a slight increase of splicing particle localization in nuclear speckles (non-membrane-bound or- ganelles) leads to disproportionate enhancement in the mRNA splicing and reduction in the transcript noise; and that compartmentalization is critical for a correctly-assembled particle yield. Our model also predicts that the distance between genes and speckles has a considerable effect on effective mRNA production rate, further emphasizing the importance of genome organization around speckles. The HeLa cell model, including organelles and subcompartments, provides an adaptable foundation to study other cellular processes which are strongly modulated by spatio-temporal heterogeneity.\n\nSignificance StatementThe spliceosome is one of the most complex cellular machineries that cuts and splices the RNA code in eukaryotic cells. It dynamically assembles, disassembles, and its components are formed in multiple compartments. The efficiency of splicing process depends on localization of its components in nuclear membrane-less organelles. Therefore, a computational model of spliceosomal function must contain a spatial model of the entire cell. However, building such a model is a challenging task, mainly due to the lack of homogeneous experimental data and a suitable computational framework. Here, we overcome these challenges and present a whole HeLa cell model, with nuclear, subnuclear, and extensive cytoplasmic structures. The three-dimensional model is supplemented by reaction-diffusion processes to shed light on the function of the spliceosome.