An in-silico human cell model reveals the influence of spatial organization on RNA splicing
Zhaleh Ghaemi , Joseph R. Peterson, Martin Gruebele, Zaida Luthey-Schulten
Published: March 25, 2020 https://doi.org/10.1371/journal.pcbi.1007717
Abstract
Spatial organization is a characteristic of all cells, achieved in eukaryotic cells by utilizing both membrane-bound and membrane-less organelles. One of the key processes in eukaryotes is RNA splicing, which readies mRNA for translation. This complex and highly dynamical chemical process involves assembly and disassembly of many molecules in multiple cellular compartments and their transport among compartments. Our goal is to model the effect of spatial organization of membrane-less organelles (specifically nuclear speckles) and of organelle heterogeneity on splicing particle biogenesis in mammalian cells. Based on multiple sources of complementary experimental data, we constructed a spatial model of a HeLa cell to capture intracellular crowding effects. We then developed chemical reaction networks to describe the formation of RNA splicing machinery complexes and splicing processes within nuclear speckles (specific type of non-membrane-bound organelles). We incorporated these networks into our spatially-resolved human cell model and performed stochastic simulations for up to 15 minutes of biological time, the longest thus far for a eukaryotic cell. We find that an increase (decrease) in the number of nuclear pore complexes increases (decreases) the number of assembled splicing particles; and that compartmentalization is critical for the yield of correctly-assembled particles. We also show that a slight increase of splicing particle localization into nuclear speckles leads to a disproportionate enhancement of mRNA splicing and a reduction in the noise of generated mRNA. Our model also predicts that the distance between genes and speckles has a considerable effect on the mRNA production rate, with genes located closer to speckles producing mRNA at higher levels, emphasizing the importance of genome organization around speckles. The HeLa cell model, including organelles and sub-compartments, provides a flexible foundation to study other cellular processes that are strongly modulated by spatiotemporal heterogeneity.
Author summary
The spliceosome is one of the most complex cellular machineries. It cuts and splices the RNA code in eukaryotic cells by dynamically assembling and disassembling. The components of spliceosome are formed in both the nucleus and the cytoplasm within the cell and primarily localized 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 spatially-resolved 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.
Citation: Ghaemi Z, Peterson JR, Gruebele M, Luthey-Schulten Z (2020) An in-silico human cell model reveals the influence of spatial organization on RNA splicing. PLoS Comput Biol 16(3): e1007717.
Editor: Attila Csikász-Nagy, King’s College London, UNITED KINGDOM
Received: August 14, 2019; Accepted: February 6, 2020; Published: March 25, 2020
Copyright: © 2020 Ghaemi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the manuscript and its Supporting Information files. Additionally, the code we developed can be downloaded from Github through: https://eukaryoticcellbuilder.github.io/HeLa_Builder/.
Funding: This work was supported by the NSF grants MCB-1244570 on the Evolution of Translation:From Molecules to Cells to Z.G. and Z.L-S. and NSF Center for the Physics of Living Cells grant PHY-1430124 to M.G. and Z.L-S.,the NSF Graduate Fellowship [grant DGE-1144245] to J.R.P., and the NIH P41-GM104601 to Z.L-S. Z.L-S held the Murchison-Mallory Chair and M.G. held the James R. Eiszner Chair while this work was carried out. Supercomputer time was provided by XStream-XSEDE [grant TG-MCA03S027]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
FREE PDF GRATIS: PLoS Computational Biology
