One of the functions of the cell nucleus is to help regulate gene expression by controlling molecular traffic across the nuclear envelope. We investigated, by way of the master equation and stochastic simulation, what effects, if any, does segregation of biochemical processes into the nuclear and cytoplasmic compartments have on the protein copy number fluctuations in the nucleus. To answer this question we generated one hundred unique parameter sets for three types of systems : one without a nucleus , and two with a nucleus : one in which the nuclear import was mediated by a single type of importin, and another where two types of importins were required. The sets were selected randomly subject to a realistic range of values for the reaction rates and the condition that the average protein numbers of all three systems closely followed a reference curve. Since noise (or lack thereof) plays an important role in developmental gene regulatory networks, which are largely governed by threshold dynamics, we wanted to examine the activation times – times at which a protein concentration reaches a specific threshold. Results of stochastic simulations (using the Gibson-Bruck algorithm) showed that the system with a nucleus outcompeted the nucleus-free system by more than 3:1 on average. The significance of these results, the fact and necessity of spatiotemporal precision in developmental stages of Eukaryotes, and the absence of such precision in Prokaryotes, suggest that it was in part for the purpose of noise reduction that the nucleus has evolved.

stochastic noise, gene expression, cell nucleus, development