Genetic determinants and cellular constraints in noisy gene expression

Abstract

In individual cells, transcription is a random process obeying single-molecule kinetics. Often, it occurs in a bursty, intermittent manner. The frequency and size of these bursts affect the magnitude of temporal fluctuations in messenger RNA and protein content within a cell, creating variation or "noise" in gene expression. It is still unclear to what degree transcriptional kinetics are specific to each gene and determined by its promoter sequence. Alternative scenarios have been proposed, in which the kinetics of transcription are governed by cellular constraints and follow universal rules across the genome. Evidence from genome-wide noise studies and from systematic perturbations of promoter sequences suggest that both scenarios-namely gene-specific versus genome-wide regulation of transcription kinetics-may be present to different degrees in bacteria, yeast, and animal cells.

Figure 1. Gene-specific versus global determinants of transcription kinetics

Two alternative scenarios are presented, representing different ways in which stochastic promoter activity may be governed. In the first scenario (top), the rates of promoter activation and inactivation are controlled exclusively by gene-specific mechanisms. In the second scenario (bottom), gene-specific regulation occurs in the presence of a global constraint on the kinetics. We illustrate the consequences of the two scenarios using simple mathematical “toy models” of promoter kinetics (see Supplementary Materials). For each model, we calculate both the mean expression level and the size of transcription bursts for a large set of promoters and plot these two variables against each other. In the plot, black markers denote 300 randomly-chosen individual promoters, the red curve represents the smoothed behavior of 10⁴ promoters, and the shaded region is a guide-to-the-eye that depicts the full range of possible burst sizes for a given mean expression (see Supplementary Materials).

Figure 2. Evidence for genome-wide constraints on promoter kinetics in bacteria and mammalian cells, but not yeast

Data from three studies in yeast ((14, 23, 24), panel A) show no obvious correlation between the mean expression level of a gene and the transcription burst size. In particular, both low-expression and high-expression genes can exhibit non-bursty behavior, consistent with a scenario of gene-specific regulation. In contrast, two studies in E. coli ((17, 32), panel B) and three in mammalian cells ((16, 34, 38), panel C) show that higher expression is accompanied by increased burstiness, consistent with the presence of a global cellular constraint on promoter kinetics. Excluding live-cell measurements (panels B–iii and C–i), the burst sizes were estimated using the Fano factor of the corresponding distribution (protein measurements, excluding panel B–i), after correcting for the level of extrinsic noise. Black circles designate the individual measurements. Red curves are calculated trend lines. The shaded area highlights the full range of burst sizes covered by each data set. For more details see Supplementary Materials.

Figure 3. Bursting kinetics in yeast are promoter dependent, and not subject to strong constraints

(A) Both Poissonian and bursty kinetics are found in endogenous yeast promoters. Copy-number statistics of mature (left) and nascent (right) mRNA are consistent with Poissonian promoter activity for MDN1 (above), while indicating bursty activity of PDR5 (below) (adapted by permission from Macmillan Publishers Ltd: Nature Structural & Molecular Biology (27) copyright 2008). (B–E) Manipulating promoter architecture leads to a different relation between the mean expression and the burst size, such that two promoters with the same mean expression level can exhibit different burst sizes. The burst size is plotted as a function of the mean amount of expression for various perturbations of promoter architecture, specifically: changing the number of operator sites from one to seven (Panel B (29)); changing the position of the operator site from a location proximal to the first transcribed nucleotide, to a more distant location (Panel C (15)); the presence (red dots) or absence of a TATA box (black dots) (Panel D (24)), including spontaneous mutations that delete it (red dots that overlap with the promoters lacking the TATA box); promoters engineered to yield the same mean level of expression by either adding a nucleosome disfavoring poly dA:dT sequence or by increasing the strength of a transcription factor binding site (+BS) (Panel E (13)). The same transcription factor acting as a repressor (red dots) or as an activator (black dots) of a promoter leads to different burst sizes for the same mean level of expression (Panel F (14)). For more details see Supplementary Materials.