Abstract
Fluctuation ('noise') in gene expression is critical for mammalian cellular processes. Numerous mechanisms contribute to its origins, yet the mechanisms behind large fluctuations that are induced by single transcriptional activators remain elusive. Here, we probed putative mechanisms by studying the dynamic regulation of transcriptional activator binding, histone regulator inhibitors, chromatin accessibility, and levels of mRNAs and proteins in single cells. Using a light-induced expression system, we showed that the transcriptional activator could form an interplay with dual functional co-activator/histone acetyltransferases CBP/p300. This interplay resulted in substantial heterogeneity in H3K27ac, chromatin accessibility, and transcription. Simultaneous attenuation of CBP/p300 and HDAC4/5 reduced heterogeneity in the expression of endogenous genes, suggesting that this mechanism is universal. We further found that the noise was reduced by pulse-wide modulation of transcriptional activator binding possibly as a result of alternating the epigenetic states. Our findings suggest a mechanism for the modulation of noise in synthetic and endogenous gene expression systems.
Highlights
Isogenic cells in a homogenous environment can exhibit significant variations in gene expression
The LightOn system consists of a synthetic transcriptional activator GAVPO and the mRuby3 (Bajar et al, 2016) reporter driven by a synthetic 5xUAS promoter consisting of five GAL4 binding elements and a TATA box
To assess the contribution of variation in GAVPO expression to the mRuby noise, the expression of GAVPO is driven by a noise reduction circuit of pCMV-tetO2-tetR-GFP-T2A-GAVPO (Nevozhay et al, 2013), where GFP provides an indirect measurement of GAVPO expression in individual cells
Summary
Isogenic cells in a homogenous environment can exhibit significant variations in gene expression. Many general mechanisms that contribute to gene expression noise in mammalian cells have been identified, including partition at cell division, transcriptional bursting, epigenetic modifications, and 3D chromosome structure (Huh and Paulsson, 2011; Nicolas et al, 2018; Rodriguez et al, 2019; Singer et al, 2014; Suter et al, 2011). These studies often involved gene expression systems that are regulated by multiple transcriptional activators and complex interactions.
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