TuNR: Orthogonal Control of Mean and Variability of Endogenous Genes in a Human Cell Line

Abstract

Stochastic fluctuations at the transcriptional level contribute to isogenic cell-to-cell heterogeneity in mammalian cell populations. However, we still have no clear understanding of the repercussions of this heterogeneity, given the lack of tools to independently control mean expression and variability of a gene. Here, we engineered a synthetic circuit to independently modulate mean expression and heterogeneity of transgenes and endogenous human genes.1

Changes in Biomechanical Properties of A375 Cells Due to the Silencing of TMSB4X Expression Are Not Directly Correlated with Alterations in Their Stemness Features

“…This research field is gaining more and more attention recently and focuses on how fluctuations in transcription result in different phenotypes and cell behavior. Splendid work published by Bonny and colleagues [ 89 ] presents an elegant system to study phenotypic heterogeneity, i.e., Tunable Noise Rheostat (TuNR). Using it on the PC9 cell line of human lung adenocarcinoma, the researchers proved varying degrees of gene expression heterogeneity within this cell line.…”

Independent control of mean and noise by convolution of gene expression distributions

“…Independent control of mean and noise in a single strain requires manipulation of two separate processes impacting protein copy number (36). This result has been demonstrated by combining two small molecule responsive regulators in a cascade (37)(38)(39)(40), altering both the frequency and bias of promoter state switching (41), tuning both transcription and mRNA degradation rates (42) or using a time-varying input to independently control promoter activation frequency and transcription rate (43).…”

“…Additionally, there may be fundamental limitations on the levels of gene expression and noise that can be achieved using these approaches. For example, a two-step cascade primarily allows control of extrinsic noise as it relies on transmission of noise from the upstream regulator to the output (39,40).…”

“…Additionally, there may be fundamental limitations on the levels of gene expression and noise that can be achieved using these approaches. For example, a two-step cascade primarily allows control of extrinsic noise as it relies on transmission of noise from the upstream regulator to the output ( 39 , 40 ). Likewise, modulation of promoter kinetics is expected to primarily modulate intrinsic noise ( 39 ), and is unlikely to be effective at high copy numbers.…”