Abstract
Gene expression occurs either as an episodic process, characterized by pulsatile “bursts” or as a constitutive, Poisson-like accumulation of gene products. It is not clear which mode of gene expression (constitutive versus bursty) predominates across a genome or how transcriptional dynamics are influenced by genomic position and promoter sequence. Here, we use time-lapse fluorescence microscopy, building off of theoretical studies that exploit the time-resolved structure of stochastic fluctuations in gene expression, to develop a three-dimensional method for mapping underlying gene-regulatory mechanisms. Over 8,000 individual human genomic loci were analyzed, and at virtually all loci, episodic bursting—as opposed to constitutive expression—was found to be the predominant mode of expression. Quantitative analysis of the expression dynamics at these 8,000 loci indicates that both frequency and size of transcriptional bursts vary equally across the human genome independent of promoter sequence. Strikingly, weaker expression loci modulate burst frequency to increase activity, while stronger expression loci modulate burst size to increase activity. Transcriptional activators, such as TNF, generate similar patterns of change in burst frequency and burst size. In summary, transcriptional bursting dominates across the human genome, both burst frequency and burst size vary by chromosomal location, and transcriptional activators alter burst frequency and burst size, depending on the expression level of the locus.