A Computational Framework for Analyzing Stochasticity in Gene Expression

Stochastic fluctuations in gene expression give rise to distributions of protein levels across cell populations. Despite a mounting number of theoretical models explaining stochasticity in protein expression, we lack a robust, efficient, assumption-free approach for inferring the molecular mechanisms that underlie the shape of protein distributions. Here we propose a method for inferring sets of biochemical rate constants that govern chromatin modification, transcription, translation, and RNA and protein degradation from stochasticity in protein expression. We asked whether the rates of these underlying processes can be estimated accurately from protein expression distributions, in the absence of any limiting assumptions. To do this, we (1) derived analytical solutions for the first four moments of the protein distribution, (2) found that these four moments completely capture the shape of protein distributions, and (3) developed an efficient algorithm for inferring gene expression rate constants from the moments of protein distributions. Using this algorithm we find that most protein distributions are consistent with a large number of different biochemical rate constant sets. Despite this degeneracy, the solution space of rate constants almost always informs on underlying mechanism. For example, we distinguish between regimes where transcriptional bursting occurs from regimes reflecting constitutive transcript production. Our method agrees with the current standard approach, and in the restrictive regime where the standard method operates, also identifies rate constants not previously obtainable. Even without making any assumptions we obtain estimates of individual biochemical rate constants, or meaningful ratios of rate constants, in 91% of tested cases. In some cases our method identified all of the underlying rate constants. The framework developed here will be a powerful tool for deducing the contributions of particular molecular mechanisms to specific patterns of gene expression.Author Summary: Proteins, the molecular machines encoded by our genes, serve essential roles in every living cell. Investigators were therefore surprised to find widely variable levels of a particular protein within populations of genetically identical cells. This variation in protein level, called stochasticity, arises from the chemical nature of the processes that underlie protein production. The “central dogma” of biology dictates that the DNA encoding a particular gene transmits information via RNA to molecular factories called ribosomes in order to create proteins. Each step in transcription and translation introduces some variation, or stochasticity, into the production of the protein. In the current work, we tackled how one might learn more about the machinery responsible for creating proteins by the character of the stochasticity in the central dogma process. We find that many different mechanisms can explain any given stochastic protein signature. Even though there were many explanations for any particular pattern of stochasticity, the set of explanations still inform on how a given gene creates its protein. Our mathematical and computational framework will permit others to better understand how the machinery that expresses genes works. This, in turn, will enable investigators to better predict how a given mutation is likely to affect gene expression.